diff --git a/README.md b/README.md index 7db33c8b..0d3ce95f 100644 --- a/README.md +++ b/README.md @@ -11,6 +11,7 @@ Installation ------------ ARIBA has the following dependencies, which need to be installed: + * [cd-hit] [cdhit] version >= 4.6 * [samtools and bcftools] [samtools] version >= 1.2 * [SSPACE-basic scaffolder] [sspace] * [GapFiller] [gapfiller] @@ -39,6 +40,7 @@ Usage Please read the [ARIBA wiki page] [ARIBA wiki] for usage instructions. + [cdhit]: http://weizhongli-lab.org/cd-hit/ [ARIBA wiki]: https://github.com/sanger-pathogens/ariba/wiki [gapfiller]: http://www.baseclear.com/genomics/bioinformatics/basetools/gapfiller [mummer]: http://mummer.sourceforge.net/ diff --git a/ariba/__init__.py b/ariba/__init__.py index 2c86f770..fdffcc0f 100644 --- a/ariba/__init__.py +++ b/ariba/__init__.py @@ -1,9 +1,11 @@ __all__ = [ 'bam_parse', + 'cdhit', 'cluster', 'clusters', 'common', 'external_progs', + 'faidx', 'flag', 'histogram', 'link', diff --git a/ariba/cdhit.py b/ariba/cdhit.py new file mode 100644 index 00000000..d1ea02a7 --- /dev/null +++ b/ariba/cdhit.py @@ -0,0 +1,121 @@ +import tempfile +import shutil +import os +import pyfastaq +from ariba import common + +class Error (Exception): pass + + + +class Runner: + def __init__( + self, + infile, + outfile, + seq_identity_threshold=0.9, + threads=1, + length_diff_cutoff=0.9, + verbose=False, + ): + + if not os.path.exists(infile): + raise Error('File not found: "' + infile + '". Cannot continue') + + self.infile = os.path.abspath(infile) + self.outfile = os.path.abspath(outfile) + self.seq_identity_threshold = seq_identity_threshold + self.threads = threads + self.length_diff_cutoff = length_diff_cutoff + self.verbose = verbose + + + def run(self): + tmpdir = tempfile.mkdtemp(prefix='tmp.run_cd-hit.', dir=os.getcwd()) + cdhit_fasta = os.path.join(tmpdir, 'cdhit') + cluster_info_outfile = cdhit_fasta + '.bak.clstr' + infile_renamed = os.path.join(tmpdir, 'input.renamed.fa') + + # cd-hit truncates all names to 19 bases in its report of which + # sequences belong to which clusters. So need to temporarily + # rename all sequences to have short enough names. Grrr. + new_to_old_name = self._enumerate_fasta(self.infile, infile_renamed) + + cmd = ' '.join([ + 'cd-hit', + '-i', infile_renamed, + '-o', cdhit_fasta, + '-c', str(self.seq_identity_threshold), + '-T', str(self.threads), + '-s', str(self.length_diff_cutoff), + '-bak 1', + ]) + + common.syscall(cmd, verbose=self.verbose) + + cluster_representatives = self._get_ids(cdhit_fasta) + clusters, cluster_rep_to_cluster = self._parse_cluster_info_file(cluster_info_outfile, new_to_old_name, cluster_representatives) + self._rename_fasta(cdhit_fasta, self.outfile, cluster_rep_to_cluster) + shutil.rmtree(tmpdir) + return clusters + + + def _enumerate_fasta(self, infile, outfile): + rename_file = outfile + '.tmp.rename_info' + assert not os.path.exists(rename_file) + pyfastaq.tasks.enumerate_names(infile, outfile, rename_file=rename_file) + + with open(rename_file) as f: + lines = [x.rstrip().split('\t') for x in f.readlines() if x != '#old\tnew\n'] + new_to_old_name = {x[1]: x[0] for x in lines} + if len(lines) != len(new_to_old_name): + raise Error('Sequence names in input file not unique! Cannot continue') + + os.unlink(rename_file) + return new_to_old_name + + + def _rename_fasta(self, infile, outfile, names_dict): + seq_reader = pyfastaq.sequences.file_reader(infile) + f = pyfastaq.utils.open_file_write(outfile) + for seq in seq_reader: + seq.id = names_dict[seq.id] + print(seq, file=f) + + pyfastaq.utils.close(f) + + + def _parse_cluster_info_file(self, infile, names_dict, cluster_representatives): + f = pyfastaq.utils.open_file_read(infile) + clusters = {} + cluster_representative_to_cluster_number = {} + for line in f: + data = line.rstrip().split() + cluster = data[0] + seqname = data[2] + if not (seqname.startswith('>') and seqname.endswith('...')): + raise Error('Unexpected format of sequence name in line:\n' + line) + seqname = seqname[1:-3] + + if seqname in cluster_representatives: + cluster_representative_to_cluster_number[seqname] = cluster + + seqname = names_dict[seqname] + + if cluster not in clusters: + clusters[cluster] = set() + + if seqname in clusters[cluster]: + raise Error('Duplicate name "' + seqname + '" found in cluster ' + str(cluster)) + + clusters[cluster].add(seqname) + + pyfastaq.utils.close(f) + + return clusters, cluster_representative_to_cluster_number + + + def _get_ids(self, infile): + seq_reader = pyfastaq.sequences.file_reader(infile) + return set([seq.id for seq in seq_reader]) + diff --git a/ariba/cluster.py b/ariba/cluster.py index e47e6288..6f2689be 100644 --- a/ariba/cluster.py +++ b/ariba/cluster.py @@ -5,7 +5,7 @@ import operator import pyfastaq import pymummer -from ariba import common, mapping, bam_parse, flag +from ariba import common, mapping, bam_parse, flag, faidx class Error (Exception): pass @@ -13,6 +13,7 @@ class Error (Exception): pass class Cluster: def __init__(self, root_dir, + name, assembly_kmer=0, assembler='velvet', max_insert=1000, @@ -39,22 +40,24 @@ def __init__(self, sspace_exe='SSPACE_Basic_v2.0.pl', velvet_exe='velvet', # prefix of velvet{g,h} spades_other=None, + clean=1, ): self.root_dir = os.path.abspath(root_dir) if not os.path.exists(self.root_dir): raise Error('Directory ' + self.root_dir + ' not found. Cannot continue') + self.name = name self.reads1 = os.path.join(self.root_dir, 'reads_1.fq') self.reads2 = os.path.join(self.root_dir, 'reads_2.fq') self.gene_fa = os.path.join(self.root_dir, 'gene.fa') + self.genes_fa = os.path.join(self.root_dir, 'genes.fa') self.gene_bam = os.path.join(self.root_dir, 'gene.reads_mapped.bam') - for fname in [self.reads1, self.reads2, self.gene_fa]: + for fname in [self.reads1, self.reads2, self.genes_fa]: if not os.path.exists(fname): raise Error('File ' + fname + ' not found. Cannot continue') - self.gene = self._get_gene() self.max_insert = max_insert self.min_scaff_depth = min_scaff_depth @@ -104,6 +107,7 @@ def __init__(self, self.unique_threshold = unique_threshold self.status_flag = flag.Flag() self.flag_file = os.path.join(self.root_dir, 'flag') + self.clean = clean self.assembly_dir = os.path.join(self.root_dir, 'Assembly') try: @@ -123,7 +127,64 @@ def __init__(self, self.variants = {} - def _get_gene(self): + def _get_total_alignment_score(self, gene_name): + tmp_bam = os.path.join(self.root_dir, 'tmp.get_total_alignment_score.bam') + assert not os.path.exists(tmp_bam) + tmp_fa = os.path.join(self.root_dir, 'tmp.get_total_alignment_score.ref.fa') + assert not os.path.exists(tmp_fa) + faidx.write_fa_subset([gene_name], self.genes_fa, tmp_fa, samtools_exe=self.samtools_exe, verbose=self.verbose) + mapping.run_smalt( + self.reads1, + self.reads2, + tmp_fa, + tmp_bam[:-4], + threads=self.threads, + samtools=self.samtools_exe, + smalt=self.smalt_exe, + verbose=self.verbose, + ) + + score = mapping.get_total_alignment_score(tmp_bam) + os.unlink(tmp_bam) + os.unlink(tmp_fa) + os.unlink(tmp_fa + '.fai') + return score + + + def _get_best_gene_by_alignment_score(self): + cluster_size = pyfastaq.tasks.count_sequences(self.genes_fa) + if cluster_size == 1: + seqs = {} + pyfastaq.tasks.file_to_dict(self.genes_fa, seqs) + assert len(seqs) == 1 + gene_name = list(seqs.values())[0].id + if self.verbose: + print('No need to choose gene for this cluster because only has one gene:', gene_name) + return gene_name + + if self.verbose: + print('\nChoosing best gene from cluster of', cluster_size, 'genes...') + file_reader = pyfastaq.sequences.file_reader(self.genes_fa) + best_score = 0 + best_gene_name = None + for seq in file_reader: + score = self._get_total_alignment_score(seq.id) + if self.verbose: + print('Total alignment score for gene', seq.id, 'is', score) + if score > best_score: + best_score = score + best_gene_name = seq.id + + if self.verbose: + print('Best gene is', best_gene_name, 'with total alignment score of', best_score) + print() + + return best_gene_name + + + def _choose_best_gene(self): + gene_name = self._get_best_gene_by_alignment_score() + faidx.write_fa_subset([gene_name], self.genes_fa, self.gene_fa, samtools_exe=self.samtools_exe, verbose=self.verbose) seqs = {} pyfastaq.tasks.file_to_dict(self.gene_fa, seqs) assert len(seqs) == 1 @@ -342,6 +403,7 @@ def _fix_contig_orientation(self): else: to_revcomp.add(hit.qry_name) + os.unlink(tmp_coords) in_both = to_revcomp.intersection(not_revcomp) for name in in_both: print('WARNING: hits to both strands of gene for scaffold. Interpretation of any variants cannot be trusted', name, file=sys.stderr) @@ -649,7 +711,7 @@ def _make_report_lines(self): self.report_lines = [] if len(self.variants) == 0: - self.report_lines.append([self.gene.id, self.status_flag.to_number(), len(self.gene)] + ['.'] * 11) + self.report_lines.append([self.gene.id, self.status_flag.to_number(), self.name, len(self.gene)] + ['.'] * 11) for contig in self.variants: for variants in self.variants[contig]: @@ -660,6 +722,7 @@ def _make_report_lines(self): self.report_lines.append([ self.gene.id, self.status_flag.to_number(), + self.name, len(self.gene), pymummer.variant.var_types[v.var_type], effect, @@ -675,7 +738,52 @@ def _make_report_lines(self): ]) + def _clean(self): + if self.verbose: + print('Cleaning', self.root_dir) + + if self.clean > 0: + if self.verbose: + print(' rm -r', self.assembly_dir) + shutil.rmtree(self.assembly_dir) + + to_clean = [ + [ + 'assembly.reads_mapped.unsorted.bam', + ], + [ + 'assembly.fa.fai', + 'assembly.reads_mapped.bam.scaff', + 'assembly.reads_mapped.bam.soft_clipped', + 'assembly.reads_mapped.bam.unmapped_mates', + 'assembly_vs_gene.coords', + 'assembly_vs_gene.coords.snps', + 'genes.fa', + 'genes.fa.fai', + 'reads_1.fq', + 'reads_2.fq', + ], + [ + 'assembly.fa.fai', + 'assembly.reads_mapped.bam', + 'assembly.reads_mapped.bam.vcf', + 'assembly_vs_gene.coords', + 'assembly_vs_gene.coords.snps', + ] + ] + + for i in range(self.clean + 1): + for fname in to_clean[i]: + fullname = os.path.join(self.root_dir, fname) + if os.path.exists(fullname): + if self.verbose: + print(' rm', fname) + os.unlink(fullname) + + def run(self): + self.gene = self._choose_best_gene() + if self.assembler == 'velvet': self._assemble_with_velvet() elif self.assembler == 'spades': @@ -720,3 +828,4 @@ def run(self): self._get_vcf_variant_counts() self._make_report_lines() + self._clean() diff --git a/ariba/clusters.py b/ariba/clusters.py index 4f27a3c4..d3ce2335 100644 --- a/ariba/clusters.py +++ b/ariba/clusters.py @@ -4,7 +4,7 @@ import openpyxl import pysam import pyfastaq -from ariba import cluster, common, mapping, histogram +from ariba import cdhit, cluster, common, mapping, histogram, faidx class Error (Exception): pass @@ -37,17 +37,25 @@ def __init__(self, spades_exe='spades.py', sspace_exe='SSPACE_Basic_v2.0.pl', velvet_exe='velvet', # prefix of velvet{g,h} + cdhit_seq_identity_threshold=0.9, + cdhit_length_diff_cutoff=0.9, + clean=1, ): self.db_fasta = os.path.abspath(db_fasta) self.reads_1 = os.path.abspath(reads_1) self.reads_2 = os.path.abspath(reads_2) self.outdir = os.path.abspath(outdir) + self.clusters_outdir = os.path.join(self.outdir, 'Clusters') + self.clusters_info_file = os.path.join(self.outdir, 'clusters.tsv') + self.clean = clean self.assembler = assembler assert self.assembler in ['velvet', 'spades'] self.assembly_kmer = assembly_kmer self.spades_other = spades_other + self.db_fasta_clustered = os.path.join(self.outdir, 'genes.clustered.fa') + self.cluster_ids = {} self.bam_prefix = os.path.join(self.outdir, 'map_all_reads') self.bam = self.bam_prefix + '.bam' self.report_file_tsv = os.path.join(self.outdir, 'report.tsv') @@ -95,17 +103,41 @@ def __init__(self, self.velvet = velvet_exe - try: - os.mkdir(self.outdir) - except: - raise Error('Error mkdir ' + self.outdir) + self.cdhit_seq_identity_threshold = cdhit_seq_identity_threshold + self.cdhit_length_diff_cutoff = cdhit_length_diff_cutoff + for d in [self.outdir, self.clusters_outdir]: + try: + os.mkdir(d) + except: + raise Error('Error mkdir ' + d) - def _map_reads(self): + def _run_cdhit(self): + r = cdhit.Runner( + self.db_fasta, + self.db_fasta_clustered, + seq_identity_threshold=self.cdhit_seq_identity_threshold, + threads=self.threads, + length_diff_cutoff=self.cdhit_length_diff_cutoff, + verbose=self.verbose, + ) + self.cluster_ids = r.run() + + + def _write_clusters_info_file(self): + f = pyfastaq.utils.open_file_write(self.clusters_info_file) + print('#Cluster\tGene', file=f) + for c in sorted([int(x) for x in self.cluster_ids]): + for seqname in sorted(list(self.cluster_ids[str(c)])): + print(c, seqname, sep='\t', file=f) + pyfastaq.utils.close(f) + + + def _map_reads_to_clustered_genes(self): mapping.run_smalt( self.reads_1, self.reads_2, - self.db_fasta, + self.db_fasta_clustered, self.bam_prefix, index_k=self.smalt_k, index_s=self.smalt_s, @@ -183,7 +215,7 @@ def _bam_to_clusters_reads(self): assert ref not in filehandles_1 assert ref not in filehandles_2 - new_dir = os.path.join(self.outdir, ref) + new_dir = os.path.join(self.clusters_outdir, ref) try: os.mkdir(new_dir) except: @@ -192,6 +224,8 @@ def _bam_to_clusters_reads(self): self.cluster_to_dir[ref] = new_dir filehandles_1[ref] = pyfastaq.utils.open_file_write(os.path.join(new_dir, 'reads_1.fq')) filehandles_2[ref] = pyfastaq.utils.open_file_write(os.path.join(new_dir, 'reads_2.fq')) + if self.verbose: + print('New cluster with reads that hit:', ref, flush=True) print(read1, file=filehandles_1[ref]) print(read2, file=filehandles_2[ref]) @@ -202,6 +236,8 @@ def _bam_to_clusters_reads(self): pyfastaq.utils.close(filehandles_1[ref]) pyfastaq.utils.close(filehandles_2[ref]) + if self.verbose: + print('Total clusters to perform local assemblies:', len(self.cluster_to_dir), flush=True) def _set_insert_size_data(self): assert len(self.insert_hist) > 0 @@ -215,19 +251,6 @@ def _set_insert_size_data(self): print() - def _write_gene_fa(self, gene_name, outfile): - if not os.path.exists(self.db_fasta + '.fai'): - common.syscall(self.samtools_exe + ' faidx ' + self.db_fasta, verbose=self.verbose) - - common.syscall(' '.join([ - self.samtools_exe + ' faidx', - self.db_fasta, - gene_name, - '>', outfile - ])) - - - def _init_and_run_clusters(self): if len(self.cluster_to_dir) == 0: raise Error('Did not get any reads mapped to genes. Cannot continue') @@ -237,11 +260,20 @@ def _init_and_run_clusters(self): for gene in sorted(self.cluster_to_dir): counter += 1 if self.verbose: - print('\nAssembling cluster', counter, 'of', str(len(self.cluster_to_dir)) + ':', gene) + print('\nAssembling cluster', counter, 'of', str(len(self.cluster_to_dir))) new_dir = self.cluster_to_dir[gene] - self._write_gene_fa(gene, os.path.join(new_dir, 'gene.fa')) + + faidx.write_fa_subset( + self.cluster_ids[gene], + self.db_fasta, + os.path.join(new_dir, 'genes.fa'), + samtools_exe=self.samtools_exe, + verbose=self.verbose + ) + self.clusters[gene] = cluster.Cluster( new_dir, + gene, assembly_kmer=self.assembly_kmer, assembler=self.assembler, max_insert=self.insert_proper_pair_max, @@ -262,7 +294,8 @@ def _init_and_run_clusters(self): spades_exe=self.spades_exe, sspace_exe=self.sspace_exe, velvet_exe=self.velvet, - spades_other=self.spades_other + spades_other=self.spades_other, + clean=self.clean, ) self.clusters[gene].run() @@ -272,6 +305,7 @@ def _write_reports(self): columns = [ '#gene', 'flag', + 'cluster', 'gene_len', 'var_type', 'var_effect', @@ -303,23 +337,61 @@ def _write_reports(self): workbook.save(self.report_file_xls) + def _clean(self): + to_clean = [ + [ + ], + [ + self.bam + ], + [ + self.db_fasta_clustered, + self.db_fasta_clustered + '.fai', + self.clusters_info_file, + ] + ] + + for i in range(self.clean + 1): + for fname in to_clean[i]: + if os.path.exists(fname): + if self.verbose: + print(' rm', fname) + os.unlink(fname) + + if self.clean >= 2: + if self.verbose: + print(' rm -r', self.clusters_outdir) + shutil.rmtree(self.clusters_outdir) def run(self): + cwd = os.getcwd() + os.chdir(self.outdir) + if self.verbose: - print('{:_^79}'.format(' Mapping reads to reference genes ')) - self._map_reads() + print('{:_^79}'.format(' Running cd-hit '), flush=True) + self._run_cdhit() + self._write_clusters_info_file() + if self.verbose: + print('Finished cd-hit\n') + print('{:_^79}'.format(' Mapping reads to clustered genes '), flush=True) + self._map_reads_to_clustered_genes() if self.verbose: print('Finished mapping\n') - print('{:_^79}'.format(' Generating clusters ')) + print('{:_^79}'.format(' Generating clusters '), flush=True) self._bam_to_clusters_reads() self._set_insert_size_data() if self.verbose: - print('{:_^79}'.format(' Assembling each cluster ')) + print('{:_^79}'.format(' Assembling each cluster '), flush=True) self._init_and_run_clusters() if self.verbose: print('Finished assembling clusters\n') - print('{:_^79}'.format(' Writing report files ')) + print('{:_^79}'.format(' Writing report files '), flush=True) self._write_reports() if self.verbose: - print('Finished writing report files. All done!') + print('Finished writing report files. Cleaning files', flush=True) + self._clean() + if self.verbose: + print('\nAll done!\n') + + os.chdir(cwd) diff --git a/ariba/common.py b/ariba/common.py index a5004a40..c521f95f 100644 --- a/ariba/common.py +++ b/ariba/common.py @@ -13,7 +13,7 @@ def syscall(cmd, allow_fail=False, verbose=False): print('The following command failed with exit code', error.returncode, file=sys.stderr) print(cmd, file=sys.stderr) print('\nThe output was:\n', file=sys.stderr) - print(errors, file=sys.stderr) + print(errors, file=sys.stderr, flush=True) if allow_fail: return False, errors diff --git a/ariba/external_progs.py b/ariba/external_progs.py index 7bb37f50..275fcba2 100644 --- a/ariba/external_progs.py +++ b/ariba/external_progs.py @@ -15,6 +15,7 @@ def is_in_path(prog): prog_to_default = { 'bcftools': 'bcftools', + 'cdhit': 'cd-hit', 'gapfiller': 'GapFiller.pl', 'nucmer' : 'nucmer', 'samtools': 'samtools', @@ -35,6 +36,7 @@ def is_in_path(prog): prog_to_version_cmd = { 'bcftools': ('', re.compile('^Version: ([0-9\.]+)')), + 'cdhit': ('', re.compile('CD-HIT version ([0-9\.]+) \(')), 'gapfiller': ('', re.compile('^Usage: .*pl \[GapFiller_(.*)\]')), 'nucmer': ('--version', re.compile('^NUCmer \(NUCleotide MUMmer\) version ([0-9\.]+)')), 'samtools': ('', re.compile('^Version: ([0-9\.]+)')), @@ -48,6 +50,7 @@ def is_in_path(prog): min_versions = { 'bcftools': '1.2', + 'cd-hit': '4.6', 'nucmer': '3.1', 'samtools': '1.2', 'smalt': '0.7.4', @@ -104,6 +107,7 @@ def check_versions(opts, verbose=False): to_check = [ 'bcftools', + 'cdhit', 'nucmer', 'smalt', 'samtools', diff --git a/ariba/faidx.py b/ariba/faidx.py new file mode 100644 index 00000000..a9939abe --- /dev/null +++ b/ariba/faidx.py @@ -0,0 +1,19 @@ +import os +from ariba import common + + +def write_fa_subset(seq_names, infile, outfile, samtools_exe='samtools', verbose=False): + if not os.path.exists(infile + '.fai'): + common.syscall(samtools_exe + ' faidx ' + infile, verbose=verbose) + + if os.path.exists(outfile): + os.path.unlink(outfile) + + for name in seq_names: + common.syscall(' '.join([ + samtools_exe + ' faidx', + infile, + name, + '>>', outfile + ])) + diff --git a/ariba/mapping.py b/ariba/mapping.py index 348c4b61..5131c332 100644 --- a/ariba/mapping.py +++ b/ariba/mapping.py @@ -1,4 +1,5 @@ import os +import pysam from ariba import common class Error (Exception): pass @@ -74,3 +75,16 @@ def run_smalt( common.syscall(index_cmd, verbose=verbose) for fname in clean_files: os.unlink(fname) + + +def get_total_alignment_score(bam): + '''Returns total of AS: tags in the input BAM''' + sam_reader = pysam.Samfile(bam, "rb") + total = 0 + for sam in sam_reader.fetch(until_eof=True): + try: + total += sam.opt('AS') + except: + pass + return total + diff --git a/ariba/tasks/run.py b/ariba/tasks/run.py index 1a18c558..627c9209 100644 --- a/ariba/tasks/run.py +++ b/ariba/tasks/run.py @@ -12,6 +12,10 @@ def run(): parser.add_argument('reads_2', help='Name of rev reads fastq file') parser.add_argument('outdir', help='Output directory (must not already exist)') + cdhit_group = parser.add_argument_group('cd-hit options') + cdhit_group.add_argument('--cdhit_seq_identity_threshold', type=float, help='Sequence identity threshold (cd-hit option -c) [%(default)s]', default=0.9, metavar='FLOAT') + cdhit_group.add_argument('--cdhit_length_diff_cutoff', type=float, help='length difference cutoff (cd-hit option -s) [%(default)s]', default=0.9, metavar='FLOAT') + smalt_group = parser.add_argument_group('smalt options') smalt_group.add_argument('--smalt_k', type=int, help='kmer to use when indexing with smalt (smalt index -k) [%(default)s]', default=13, metavar='INT') smalt_group.add_argument('--smalt_s', type=int, help='Step length to use when indexing with smalt (see smalt index -s) [%(default)s]', default=2, metavar='INT') @@ -34,10 +38,12 @@ def run(): other_group.add_argument('--threads', type=int, help='Number of threads for smalt and spades [%(default)s]', default=1, metavar='INT') other_group.add_argument('--assembled_threshold', type=float, help='If proportion of gene assembled (regardless of into how many contigs) is at least this value then the flag gene_assembled is set [%(default)s]', default=0.95, metavar='FLOAT (between 0 and 1)') other_group.add_argument('--unique_threshold', type=float, help='If proportion of bases in gene assembled more than once is <= this value, then the flag unique_contig is set [%(default)s]', default=0.03, metavar='FLOAT (between 0 and 1)') + other_group.add_argument('--clean', type=int, choices=[0,1,2], help='Specify how much cleaning to do. 0=none, 1=some, 2=only keep the report [%(default)s]', default=1, metavar='INT') other_group.add_argument('--verbose', action='store_true', help='Be verbose') executables_group = parser.add_argument_group('executables locations') executables_group.add_argument('--bcftools', help='bcftools executable [bcftools]', metavar='PATH') + executables_group.add_argument('--cdhit', help=argparse.SUPPRESS) executables_group.add_argument('--gapfiller', help='GapFiller executable [GapFiller.pl]', metavar='PATH') executables_group.add_argument('--nucmer', help=argparse.SUPPRESS, default='nucmer') executables_group.add_argument('--samtools', help='samtools executable [samtools]', metavar='PATH') @@ -80,6 +86,9 @@ def run(): spades_exe=options.spades, sspace_exe=options.sspace, velvet_exe=options.velvet, + cdhit_seq_identity_threshold=options.cdhit_seq_identity_threshold, + cdhit_length_diff_cutoff=options.cdhit_length_diff_cutoff, + clean=options.clean, ) c.run() diff --git a/ariba/tests/cdhit_test.py b/ariba/tests/cdhit_test.py new file mode 100644 index 00000000..7cc4fe16 --- /dev/null +++ b/ariba/tests/cdhit_test.py @@ -0,0 +1,80 @@ +import unittest +import os +import filecmp +from ariba import cdhit + +modules_dir = os.path.dirname(os.path.abspath(cdhit.__file__)) +data_dir = os.path.join(modules_dir, 'tests', 'data') + +class TestCdhit(unittest.TestCase): + def test_init_fail_infile_missing(self): + '''test init_fail_infile_missing''' + with self.assertRaises(cdhit.Error): + r = cdhit.Runner('oopsnotafile', 'out') + + + def test_enumerate_fasta(self): + '''test _enumerate_fasta''' + infile = os.path.join(data_dir, 'cdhit_test_enumerate_fasta.in.fa') + expected_outfile = os.path.join(data_dir, 'cdhit_test_enumerate_fasta.out.fa') + tmpfile = 'tmp.test_enumerate_fasta.out.fa' + expected_dict = {'1': 'a', '2': 'b', '3': 'c'} + r = cdhit.Runner(infile, 'out') + got_dict = r._enumerate_fasta(infile, tmpfile) + self.assertTrue(filecmp.cmp(expected_outfile, tmpfile, shallow=False)) + self.assertEqual(expected_dict, got_dict) + os.unlink(tmpfile) + + + def test_get_ids(self): + '''test _get_ids''' + infile = os.path.join(data_dir, 'cdhit_test_get_ids.fa') + expected = {'id1', 'id2', 'id3'} + r = cdhit.Runner(infile, 'out') + got = r._get_ids(infile) + self.assertEqual(expected, got) + + + def test_parse_cluster_info_file(self): + '''test _parse_cluster_info_file''' + infile = os.path.join(data_dir, 'cdhit_test_parse_cluster_info_file.in.fa') + r = cdhit.Runner(infile, 'out') + names_dict = {str(i): 'seq' + str(i) for i in range(1,5)} + cluster_representatives = {'1', '4'} + cluster_file = os.path.join(data_dir, 'cdhit_test_parse_cluster_info_file.out.fa.bak.clstr') + got_clusters, got_reps = r._parse_cluster_info_file(cluster_file, names_dict, cluster_representatives) + expected_clusters = { + '0': {'seq1', 'seq2', 'seq3'}, + '1': {'seq4'} + } + expected_reps = {'1': '0', '4': '1'} + self.assertEqual(expected_clusters, got_clusters) + self.assertEqual(expected_reps, got_reps) + + + def test_rename_fasta(self): + '''test _rename_fasta''' + infile = os.path.join(data_dir, 'cdhit_test_rename_fasta.in.fa') + tmpfile = 'tmp.rename_fasta.out.fa' + expected = os.path.join(data_dir, 'cdhit_test_rename_fasta.out.fa') + names_dict = {'a': 'seq1', 'b': 'seq2', 'c': 'seq3'} + r = cdhit.Runner(infile, 'out') + r._rename_fasta(infile, tmpfile, names_dict) + self.assertTrue(filecmp.cmp(expected, tmpfile, shallow=False)) + os.unlink(tmpfile) + + + def test_run(self): + '''test run''' + infile = os.path.join(data_dir, 'cdhit_test_run.in.fa') + expected_outfile = os.path.join(data_dir, 'cdhit_test_run.out.fa') + tmpfile = 'tmp.cdhit_test_run.out.fa' + r = cdhit.Runner(infile, tmpfile) + clusters = r.run() + expected_clusters = { + '0': {'seq1', 'seq2', 'seq3'}, + '1': {'seq4'}, + } + self.assertEqual(clusters, expected_clusters) + self.assertTrue(filecmp.cmp(tmpfile, expected_outfile, shallow=False)) + os.unlink(tmpfile) diff --git a/ariba/tests/cluster_test.py b/ariba/tests/cluster_test.py index af46113e..915edd5a 100644 --- a/ariba/tests/cluster_test.py +++ b/ariba/tests/cluster_test.py @@ -17,7 +17,7 @@ def clean_cluster_dir(d, exclude=None): return '''Cleans up all files made except original ones in a cluster directory''' - keep = set(['gene.fa', 'reads_1.fq', 'reads_2.fq']) + keep = set(['genes.fa', 'reads_1.fq', 'reads_2.fq']) if exclude is not None: for f in exclude: keep.add(f) @@ -31,12 +31,20 @@ def clean_cluster_dir(d, exclude=None): os.unlink(full_path) +def load_gene(filename): + file_reader = pyfastaq.sequences.file_reader(filename) + seq = None + for seq in file_reader: + pass + return seq + + class TestCluster(unittest.TestCase): def test_init_fail_files_missing(self): '''test init_fail_files_missing''' dirs = [ 'cluster_test_directorynotexist' - 'cluster_test_init_no_gene_fa', + 'cluster_test_init_no_genes_fa', 'cluster_test_init_no_reads_1', 'cluster_test_init_no_reads_2', ] @@ -44,18 +52,47 @@ def test_init_fail_files_missing(self): for d in dirs: clean_cluster_dir(d) with self.assertRaises(cluster.Error): - c = cluster.Cluster(d) + c = cluster.Cluster(d, 'name') clean_cluster_dir(d) - def test_get_gene(self): - '''test _get_gene''' - cluster_dir = os.path.join(data_dir, 'cluster_test_get_gene') + def test_get_total_alignment_score(self): + '''test _get_total_alignment_score''' + cluster_dir = os.path.join(data_dir, 'cluster_test_get_total_alignment_score') + clean_cluster_dir(cluster_dir) + c = cluster.Cluster(cluster_dir, 'name') + got_score = c._get_total_alignment_score('1') + expected_score = 1500 + self.assertEqual(got_score, expected_score) + clean_cluster_dir(cluster_dir) + + + def test_get_best_gene_by_alignment_score(self): + '''test _get_best_gene_by_alignment_score''' + cluster_dir = os.path.join(data_dir, 'cluster_test_get_best_gene_by_alignment_score') clean_cluster_dir(cluster_dir) - c = cluster.Cluster(cluster_dir) - expected = pyfastaq.sequences.Fasta('name_of_gene', 'CATGCGAAAGAAAAC') - got = c._get_gene() - self.assertEqual(expected, got) + c = cluster.Cluster(cluster_dir, 'name') + got_name = c._get_best_gene_by_alignment_score() + self.assertEqual(got_name, '1') + clean_cluster_dir(cluster_dir) + + + def test_choose_best_gene(self): + '''test _choose_best_gene''' + cluster_dir = os.path.join(data_dir, 'cluster_test_choose_best_gene') + clean_cluster_dir(cluster_dir) + c = cluster.Cluster(cluster_dir, 'name') + expected_gene = pyfastaq.sequences.Fasta('1', ''.join([ + 'AGCGCCTAGCTTTGGCACTTCAGGAGCGCCCGGAAATAATGGCGGGCGATGAAGGTTCTG', + 'TAGGTACGCAAGATCCCTCTTAATCACAGTGGTGTAATCTGCGGGTCAGACCCTGTTAAC', + 'CCGTGGCTTTCACACTCCCTCCTATGGGTAATCAATCCAGAAAGGGGCCGAAATGCAAAA', + 'GTCTTAAGGACTCTGCGAGGCAAAGTACGGGCGAACTAAACCCCCGTGACAGGTCAGACG', + 'TTGTTTCGGCAATCTGTCGCGCTCCCACACCTATAAGCGTACACCGTCTCTTCTGCCAGC', + ])) + expected_gene_fa = os.path.join(data_dir, 'cluster_test_choose_best_gene.gene.fa') + got = c._choose_best_gene() + self.assertEqual(got, expected_gene) + self.assertTrue(filecmp.cmp(expected_gene_fa, c.gene_fa, shallow=False)) clean_cluster_dir(cluster_dir) @@ -63,29 +100,20 @@ def test_set_assembly_kmer(self): '''test _set_assembly_kmer''' cluster_dir = os.path.join(data_dir, 'cluster_test_set_assembly_kmer') clean_cluster_dir(cluster_dir) - c = cluster.Cluster(cluster_dir, assembly_kmer=42) + c = cluster.Cluster(cluster_dir, 'name', assembly_kmer=42) self.assertEqual(c.assembly_kmer, 42) clean_cluster_dir(cluster_dir) - c = cluster.Cluster(os.path.join(data_dir, 'cluster_test_set_assembly_kmer')) + c = cluster.Cluster(os.path.join(data_dir, 'cluster_test_set_assembly_kmer'), 'name') self.assertEqual(c.assembly_kmer, 5) clean_cluster_dir(cluster_dir) - #def test_assemble_with_velvet(self): - # '''test _assemble_with_velvet''' - # cluster_dir = os.path.join(data_dir, 'cluster_test_assemble_with_velvet') - # clean_cluster_dir(cluster_dir, exclude=set(['gene.reads_mapped.unsorted.bam'])) - # c = cluster.Cluster(cluster_dir) - # c._assemble_with_velvet() - # self.assertEqual(c.status_flag.to_number(), 0) - # clean_cluster_dir(cluster_dir, exclude=set(['gene.reads_mapped.unsorted.bam'])) - - def test_assemble_with_spades(self): '''test _assemble_with_spades''' cluster_dir = os.path.join(data_dir, 'cluster_test_assemble_with_spades') clean_cluster_dir(cluster_dir) - c = cluster.Cluster(cluster_dir) + c = cluster.Cluster(cluster_dir, 'name') + shutil.copyfile(os.path.join(data_dir, 'cluster_test_assemble_with_spades.gene.fa'), c.gene_fa) c._assemble_with_spades(unittest=True) self.assertEqual(c.status_flag.to_number(), 0) clean_cluster_dir(cluster_dir) @@ -95,7 +123,8 @@ def test_assemble_with_spades_fail(self): '''test _assemble_with_spades handles spades fail''' cluster_dir = os.path.join(data_dir, 'cluster_test_assemble_with_spades') clean_cluster_dir(cluster_dir) - c = cluster.Cluster(cluster_dir) + c = cluster.Cluster(cluster_dir, 'name') + shutil.copyfile(os.path.join(data_dir, 'cluster_test_assemble_with_spades.gene.fa'), c.gene_fa) c._assemble_with_spades() self.assertEqual(c.status_flag.to_number(), 64) clean_cluster_dir(cluster_dir) @@ -105,11 +134,12 @@ def test_scaffold_with_sspace(self): '''test _scaffold_with_sspace''' cluster_dir = os.path.join(data_dir, 'cluster_test_scaffold_with_sspace') clean_cluster_dir(cluster_dir) - c = cluster.Cluster(cluster_dir) + c = cluster.Cluster(cluster_dir, 'name') shutil.copyfile( os.path.join(data_dir, 'cluster_test_scaffold_with_sspace.contigs.fa'), c.assembly_contigs ) + #shutil.copyfile(os.path.join(data_dir, 'cluster_test_scaffold_with_sspace.gene.fa'), c.gene_fa) c._scaffold_with_sspace() self.assertTrue(os.path.exists(c.scaffolder_scaffolds)) clean_cluster_dir(cluster_dir) @@ -119,11 +149,12 @@ def test_gap_fill_with_gapfiller_no_gaps(self): '''test _gap_fill_with_gapfiller no gaps''' cluster_dir = os.path.join(data_dir, 'cluster_test_gapfill_with_gapfiller') clean_cluster_dir(cluster_dir) - c = cluster.Cluster(cluster_dir) + c = cluster.Cluster(cluster_dir, 'name') shutil.copyfile( os.path.join(data_dir, 'cluster_test_gapfill_with_gapfiller.scaffolds_no_gaps.fa'), c.scaffolder_scaffolds ) + c.gene = pyfastaq.sequences.Fasta('name_of_gene', 'AAACCCGGGTTT') c._gap_fill_with_gapfiller() self.assertTrue(os.path.exists(c.gapfilled_scaffolds)) clean_cluster_dir(cluster_dir) @@ -133,11 +164,12 @@ def test_gap_fill_with_gapfiller_with_gaps(self): '''test _gap_fill_with_gapfiller with gaps''' cluster_dir = os.path.join(data_dir, 'cluster_test_gapfill_with_gapfiller') clean_cluster_dir(cluster_dir) - c = cluster.Cluster(cluster_dir) + c = cluster.Cluster(cluster_dir, 'name') shutil.copyfile( os.path.join(data_dir, 'cluster_test_gapfill_with_gapfiller.scaffolds_with_gaps.fa'), c.scaffolder_scaffolds ) + c.gene = pyfastaq.sequences.Fasta('name_of_gene', 'AAACCCGGGTTT') c._gap_fill_with_gapfiller() self.assertTrue(os.path.exists(c.gapfilled_scaffolds)) clean_cluster_dir(cluster_dir) @@ -147,7 +179,8 @@ def test_rename_scaffolds(self): '''test _rename_scaffolds''' cluster_dir = os.path.join(data_dir, 'cluster_test_rename_scaffolds') clean_cluster_dir(cluster_dir) - c = cluster.Cluster(cluster_dir) + c = cluster.Cluster(cluster_dir, 'name') + c.gene = pyfastaq.sequences.Fasta('name_of_gene', 'AAACCCGGGTTT') infile = os.path.join(data_dir, 'cluster_test_rename_scaffolds.in.fa') outfile = os.path.join(data_dir, 'cluster_test_rename_scaffolds.out.fa') tmpfile = 'tmp.fa' @@ -161,10 +194,11 @@ def test_fix_contig_orientation(self): '''test _fix_contig_orientation''' cluster_dir = os.path.join(data_dir, 'cluster_test_fix_contig_orientation') clean_cluster_dir(cluster_dir) - c = cluster.Cluster(cluster_dir) + c = cluster.Cluster(cluster_dir, 'name') scaffs_in = os.path.join(data_dir, 'cluster_test_fix_contig_orientation.in.fa') scaffs_out = os.path.join(data_dir, 'cluster_test_fix_contig_orientation.out.fa') shutil.copyfile(scaffs_in, c.gapfilled_scaffolds) + shutil.copyfile(os.path.join(data_dir, 'cluster_test_fix_contig_orientation.gene.fa'), c.gene_fa) c._fix_contig_orientation() self.assertTrue(filecmp.cmp(scaffs_out, c.final_assembly_fa, shallow=False)) clean_cluster_dir(cluster_dir) @@ -174,7 +208,7 @@ def test_load_final_contigs(self): '''test _load_final_contigs''' cluster_dir = os.path.join(data_dir, 'cluster_test_load_final_contigs') clean_cluster_dir(cluster_dir) - c = cluster.Cluster(cluster_dir) + c = cluster.Cluster(cluster_dir, 'name') contigs_file = os.path.join(data_dir, 'cluster_test_load_final_contigs.contigs.fa') shutil.copyfile(contigs_file, c.final_assembly_fa) c._load_final_contigs() @@ -192,8 +226,9 @@ def test_parse_assembly_vs_gene_coords(self): cluster_dir = os.path.join(data_dir, 'cluster_test_parse_assembly_vs_gene_coords') coords_file = os.path.join(data_dir, 'cluster_test_parse_assembly_vs_gene_coords.coords') clean_cluster_dir(cluster_dir) - c = cluster.Cluster(cluster_dir) + c = cluster.Cluster(cluster_dir, 'name') shutil.copyfile(coords_file, c.assembly_vs_gene_coords) + c.gene = pyfastaq.sequences.Fasta('gene', 'AAACCCGGGTTT') c._parse_assembly_vs_gene_coords() line1 = ['1', '1000', '1', '1000', '1000', '1000', '100.00', '1000', '1000', '1', '1', 'gene', 'contig1'] line2 = ['1', '240', '1', '240', '240', '240', '100.00', '1000', '580', '1', '1', 'gene', 'contig2'] @@ -210,7 +245,7 @@ def test_parse_assembly_bam(self): '''test _parse_assembly_bam''' cluster_dir = os.path.join(data_dir, 'cluster_test_parse_assembly_bam') clean_cluster_dir(cluster_dir) - c = cluster.Cluster(cluster_dir) + c = cluster.Cluster(cluster_dir, 'name') bam = os.path.join(data_dir, 'cluster_test_parse_assembly_bam.bam') assembly_fa = os.path.join(data_dir, 'cluster_test_parse_assembly_bam.assembly.fa') shutil.copyfile(bam, c.final_assembly_bam) @@ -226,7 +261,7 @@ def test_nucmer_hits_to_scaff_coords(self): '''test _nucmer_hits_to_scaff_coords''' cluster_dir = os.path.join(data_dir, 'cluster_test_generic') clean_cluster_dir(cluster_dir) - c = cluster.Cluster(cluster_dir) + c = cluster.Cluster(cluster_dir, 'name') hits = [ ['1', '10', '1', '10', '10', '10', '100.00', '1000', '1000', '1', '1', 'gene', 'scaff1'], ['9', '42', '9', '42', '34', '34', '100.00', '1000', '1000', '1', '1', 'gene', 'scaff1'], @@ -261,7 +296,7 @@ def test_nucmer_hits_to_ref_coords(self): '''test _nucmer_hits_to_ref_coords''' cluster_dir = os.path.join(data_dir, 'cluster_test_generic') clean_cluster_dir(cluster_dir) - c = cluster.Cluster(cluster_dir) + c = cluster.Cluster(cluster_dir, 'name') hits = [ ['1', '42', '1', '42', '42', '42', '100.00', '1000', '1000', '1', '1', 'gene', 'contig1'], ['100', '142', '200', '242', '42', '42', '99.42', '1000', '1000', '1', '1', 'gene', 'contig1'] @@ -282,7 +317,7 @@ def test_whole_gene_covered_by_nucmer_hits(self): '''test _whole_gene_covered_by_nucmer_hits''' cluster_dir = os.path.join(data_dir, 'cluster_test_generic') clean_cluster_dir(cluster_dir) - c = cluster.Cluster(cluster_dir) + c = cluster.Cluster(cluster_dir, 'name') c.gene = pyfastaq.sequences.Fasta('gene', 'ACGTGTGCAT') hit1 = ['1', '10', '1', '10', '10', '10', '100.00', '10', '10', '1', '1', 'gene', 'contig1'] hit2 = ['1', '5', '1', '5', '5', '5', '100.00', '10', '10', '1', '1', 'gene', 'contig2'] @@ -304,7 +339,7 @@ def test_gene_coverage_unique(self): '''test _gene_coverage_unique''' cluster_dir = os.path.join(data_dir, 'cluster_test_generic') clean_cluster_dir(cluster_dir) - c = cluster.Cluster(cluster_dir) + c = cluster.Cluster(cluster_dir, 'name') c.gene = pyfastaq.sequences.Fasta('gene', 'ACGTGTGCAT') hit1 = ['1', '10', '1', '10', '10', '10', '100.00', '10', '10', '1', '1', 'gene', 'contig1'] hit2 = ['1', '5', '1', '5', '5', '5', '100.00', '10', '10', '1', '1', 'gene', 'contig2'] @@ -318,7 +353,7 @@ def test_gene_covered_by_complete_contig_with_orf(self): '''test _gene_covered_by_complete_contig_with_orf''' cluster_dir = os.path.join(data_dir, 'cluster_test_generic') clean_cluster_dir(cluster_dir) - c = cluster.Cluster(cluster_dir) + c = cluster.Cluster(cluster_dir, 'name') gene = pyfastaq.sequences.Fasta('gene', 'GATCGCGAAGCGATGACCCATGAAGCGACCGAACGCTGA') gene_no_orf = pyfastaq.sequences.Fasta('gene', 'GATTGAGAAGCGATGACCCATGAAGCGACCGAACGCTGA') c.gene = gene @@ -350,7 +385,7 @@ def test_gene_covered_by_at_least_one_full_length_contig(self): '''test _gene_covered_by_at_least_one_full_length_contig''' cluster_dir = os.path.join(data_dir, 'cluster_test_generic') clean_cluster_dir(cluster_dir) - c = cluster.Cluster(cluster_dir) + c = cluster.Cluster(cluster_dir, 'name') c.gene = pyfastaq.sequences.Fasta('gene', 'GATCGCGAAGCGATGACCCATGAAGCGACCGAACGCTGA') hit1 = ['1', '39', '1', '39', '39', '39', '100.00', '39', '39', '1', '1', 'gene', 'contig1'] hit2 = ['1', '20', '1', '20', '20', '20', '100.00', '39', '39', '1', '1', 'gene', 'contig1'] @@ -370,7 +405,7 @@ def test_get_mummer_variants(self): '''test _get_mummer_variants''' cluster_dir = os.path.join(data_dir, 'cluster_test_generic') clean_cluster_dir(cluster_dir) - c = cluster.Cluster(cluster_dir) + c = cluster.Cluster(cluster_dir, 'name') snp_file = os.path.join(data_dir, 'cluster_test_get_mummer_variants.none.snps') shutil.copyfile(snp_file, c.assembly_vs_gene_coords + '.snps') c._get_mummer_variants() @@ -397,7 +432,7 @@ def test_filter_mummer_variants(self): '''test filter_mummer_variants''' cluster_dir = os.path.join(data_dir, 'cluster_test_generic') clean_cluster_dir(cluster_dir) - c = cluster.Cluster(cluster_dir) + c = cluster.Cluster(cluster_dir, 'name') c.gene = pyfastaq.sequences.Fasta('gene', 'GATCGCGAAGCGATGACCCATGAAGCGACCGAACGCTGA') v1 = pymummer.variant.Variant(pymummer.snp.Snp('4\tC\tT\t4\tx\tx\t39\t39\tx\tx\tgene\tcontig')) v2 = pymummer.variant.Variant(pymummer.snp.Snp('6\tC\tA\t6\tx\tx\t39\t39\tx\tx\tgene\tcontig')) @@ -413,7 +448,7 @@ def test_get_codon_start(self): '''test _get_codon_start''' cluster_dir = os.path.join(data_dir, 'cluster_test_generic') clean_cluster_dir(cluster_dir) - c = cluster.Cluster(cluster_dir) + c = cluster.Cluster(cluster_dir, 'name') tests = [ (0, 5, 3), (0, 0, 0), @@ -435,7 +470,7 @@ def test_get_variant_effect(self): '''test _get_variant_effect''' cluster_dir = os.path.join(data_dir, 'cluster_test_generic') clean_cluster_dir(cluster_dir) - c = cluster.Cluster(cluster_dir) + c = cluster.Cluster(cluster_dir, 'name') c.gene = pyfastaq.sequences.Fasta('gene', 'GATCGCGAAGCGATGACCCATGAAGCGACCGAACGCTGA') v1 = pymummer.variant.Variant(pymummer.snp.Snp('6\tC\tT\t6\tx\tx\t39\t39\tx\tx\tgene\tcontig')) v1 = pymummer.variant.Variant(pymummer.snp.Snp('6\tC\tT\t6\tx\tx\t39\t39\tx\tx\tgene\tcontig')) @@ -481,7 +516,7 @@ def test_make_assembly_vcf(self): '''test _make_assembly_vcf''' cluster_dir = os.path.join(data_dir, 'cluster_test_generic') clean_cluster_dir(cluster_dir) - c = cluster.Cluster(cluster_dir) + c = cluster.Cluster(cluster_dir, 'name') c.final_assembly_fa = os.path.join(data_dir, 'cluster_test_make_assembly_vcf.assembly.fa') c.final_assembly_bam = os.path.join(data_dir, 'cluster_test_make_assembly_vcf.assembly.bam') expected_vcf = os.path.join(data_dir, 'cluster_test_make_assembly_vcf.assembly.vcf') @@ -501,7 +536,7 @@ def test_get_vcf_variant_counts(self): '''test _get_vcf_variant_counts''' cluster_dir = os.path.join(data_dir, 'cluster_test_generic') clean_cluster_dir(cluster_dir) - c = cluster.Cluster(cluster_dir) + c = cluster.Cluster(cluster_dir, 'name') hit = ['1', '42', '1', '42', '42', '42', '100.00', '1000', '1000', '1', '1', 'gene', 'scaff1'] c.nucmer_hits = { 'scaff1': [pymummer.alignment.Alignment('\t'.join(hit))] @@ -518,7 +553,7 @@ def test_make_report_lines(self): '''test _make_report_lines''' cluster_dir = os.path.join(data_dir, 'cluster_test_generic') clean_cluster_dir(cluster_dir) - c = cluster.Cluster(cluster_dir) + c = cluster.Cluster(cluster_dir, 'cluster_name') c.gene = pyfastaq.sequences.Fasta('gene', 'GATCGCGAAGCGATGACCCATGAAGCGACCGAACGCTGA') v1 = pymummer.variant.Variant(pymummer.snp.Snp('6\tC\tT\t6\tx\tx\t39\t39\tx\tx\tgene\tcontig')) c.variants = {'contig': [[v1]]} @@ -527,6 +562,7 @@ def test_make_report_lines(self): expected = [[ 'gene', 42, + 'cluster_name', 39, 'SNP', 'SYN', diff --git a/ariba/tests/clusters_test.py b/ariba/tests/clusters_test.py index d5ed8aeb..4cf47fca 100644 --- a/ariba/tests/clusters_test.py +++ b/ariba/tests/clusters_test.py @@ -79,10 +79,10 @@ def test_bam_to_clusters_reads(self): ] got = [ - os.path.join(clusters_dir, 'ref1/reads_1.fq'), - os.path.join(clusters_dir, 'ref1/reads_2.fq'), - os.path.join(clusters_dir, 'ref2/reads_1.fq'), - os.path.join(clusters_dir, 'ref2/reads_2.fq'), + os.path.join(clusters_dir, 'Clusters/ref1/reads_1.fq'), + os.path.join(clusters_dir, 'Clusters/ref1/reads_2.fq'), + os.path.join(clusters_dir, 'Clusters/ref2/reads_1.fq'), + os.path.join(clusters_dir, 'Clusters/ref2/reads_2.fq'), ] @@ -116,16 +116,6 @@ def test_set_insert_size_data(self): self.assertEqual(self.clusters.insert_sspace_sd, 0.91) - def test_write_gene_fa(self): - '''Test _write_gene_fa''' - self.clusters.db_fasta = os.path.join(data_dir, 'clusters_test_write_gene_fa.db.fa') - expected = os.path.join(data_dir, 'clusters_test_write_gene_fa.out.fa') - tmp_file = 'tmp.test_write_gene_fa.fa' - self.clusters._write_gene_fa('gene2', tmp_file) - self.assertTrue(filecmp.cmp(expected, tmp_file, shallow=False)) - os.unlink(tmp_file) - - def test_write_reports(self): class FakeCluster: def __init__(self, lines): diff --git a/ariba/tests/data/cdhit_test_enumerate_fasta.in.fa b/ariba/tests/data/cdhit_test_enumerate_fasta.in.fa new file mode 100644 index 00000000..85ca4cb1 --- /dev/null +++ b/ariba/tests/data/cdhit_test_enumerate_fasta.in.fa @@ -0,0 +1,6 @@ +>a +A +>b +G +>c +T diff --git a/ariba/tests/data/cdhit_test_enumerate_fasta.out.fa b/ariba/tests/data/cdhit_test_enumerate_fasta.out.fa new file mode 100644 index 00000000..4b36e898 --- /dev/null +++ b/ariba/tests/data/cdhit_test_enumerate_fasta.out.fa @@ -0,0 +1,6 @@ +>1 +A +>2 +G +>3 +T diff --git a/ariba/tests/data/cdhit_test_get_ids.fa b/ariba/tests/data/cdhit_test_get_ids.fa new file mode 100644 index 00000000..f2012398 --- /dev/null +++ b/ariba/tests/data/cdhit_test_get_ids.fa @@ -0,0 +1,6 @@ +>id1 +A +>id2 +G +>id3 +T diff --git a/ariba/tests/data/cdhit_test_parse_cluster_info_file.in.fa b/ariba/tests/data/cdhit_test_parse_cluster_info_file.in.fa new file mode 100644 index 00000000..bf8b12c8 --- /dev/null +++ b/ariba/tests/data/cdhit_test_parse_cluster_info_file.in.fa @@ -0,0 +1,40 @@ +>seq1 +TGGGGAATATAGTGGGTACTGTGTGTTGAGCGATTCCCGAGCCCTATGCAGGCTTGTGAA +GGAGGTCGTGGGATGCTCGTGTCTTCACGAACTTAAAGCCCCTCTTTGGCTTAGGGCCGG +AGATCGCGTCATAAGTGTAATCTAGCGTTGCAGGTATGGGTAAGGCCATACACTTAGCTC +TGATGTGATGTGTCAGGTCTGGAGTTTACATATGTCCTGCCACGGTCCTATTTGTTAGAG +AGGCCTTCAGGCGGCCCCTGCCCGTCGATTCGGCAAACTGCCGAAAACGGAGAGACAGCC +ACGGTGAATAGAATCTTGGCATACGGTTAATCAGTGCTCTGCTAGTCCTGCTTTCTCTAA +GCTTATAGAATTCCTGATATATTAAGTAACTTTTCCATTCCATAGACGCGACGAACTGGA +TACACTCACGTAGGCTCGATCATGAAAGTGAAAGGCGCTCCAAGTTGCGAATTGAAACAA +AACTCTATCGTAGGGTCGCA +>seq2 +TGGGGAATATAGTGGGTACTGTGTGTTGAGCGATTCCCGAGCCCTATGCAGGCTTGTGAA +GGAGTTCGTGGGATGCTCGTGTCTTCACGAACTTAAAGCCCCTCTTTGGCTTAGGGCCGG +AGATCGCGTCATAAGTGTAATCTAGCGTTGCAGGTATGGGTAAGGCCATACACTTAGCTC +TGATGTGATGTGTCAGGTCTGGAGTTTACATATGTCCTGCCACGGTCCTATTTGTTAGAG +AGGCCTTCAGGCGGCCCCTGCCCGTCGATTCGGCAAACTGCCGAAAACGGAGAGACAGCC +ACGGTGAATGGAATCTTGGCATACGGTTAATCAGTGCTCTGCTAGTCCTGCTTTCTCTAA +GCTTATAGAATTCCTGATATATTAAGTAACTTTTCCATTCCATAGACGCGACGAACTGGA +TACACTCACGTATGCTCGATCATGAAAGTGAAAGGCGCTCCAAGTTGCGAATTGAAACAA +AACTCTATGTAGGGTCGCA +>seq3 +TGGGGAATATAGTGGGTACTGTGTGTTGAGCGATTCCCGAGTTCTATGCAGGCTTGTGAA +GGAGTTCGTGGGATGCTCGTGTCTTCACGAACTTAAAGCCCCTCTTTGGCTTAGGGCCGG +AGATCGCGTCATAAGTGTAATCTAGCGTTGCAGGTATGGGTAGGCCATACACTTAGCTCA +TGATGTGATGTGTCAGGTCTGGAGTTTACATATGTCCTGCCACGGTCCTATTTGTTAGAG +AGGCCTTCAGGCGGCCCCTGCCCGTCGATTCGGCAAACTGCCGAAAACGGAGAGATAGCC +ACGGTGAATGGAATCTTGGCATACGGTTAATCAGTGCTCTGCTAGTCCTGCTTTCTCTAA +GCTTATAGAATTCCTGATATATTAAGTAACTTTTCCATTCCATAGACGCGACGAACTGGA +TACACTCACGTATGCTCGATCATGAAAGTGAAAGGCGCTCCAAGATGCGAATTGAAACAA +AACTCTATGTAGGGTCGCA +>seq4 +CAAGGGCGGATTCGAACGGGTAACAGGGATCTGATTGGCTCCGGCCAGCTGGTGGATATC +TGCATCCGTTGACCCACCAACTTTAGCAGTATAGACCCTAAACTGGCATGGTGCCCTTTT +TATATCCCGATGCATCTGGAGAAACCGTCAGGACCTCTTAAGCCCCGTGGAGAGCCAAAC +TTCCAACCACGTCAAGGCAACCTTGGTTTAGCACAGGGCTCCCAGTGGGTGTAAGGGATG +AACACTACCCGGCCCACCGTCGATTTAGCCCTAAATGGTCTATTGCTCACGGGTAGCACA +CAAGTAATAAAAACGTATTCAGCTCGAGTCAGCGTCCAGCCATTTTACTTTGCGTCATCG +AGGGGTAGTGCCTCCGAGAATCAAGGTTTGATTATACTAAACGGAGGGGCCTACCACTCA +GCCAGTCTTTGCATCGTCCATTCCCGCCGTTTATGGGTCACTATTCATTCGGAATTTGGA +TGCGGTCAACAAGTCCAGGT diff --git a/ariba/tests/data/cdhit_test_parse_cluster_info_file.in.renamed.fa b/ariba/tests/data/cdhit_test_parse_cluster_info_file.in.renamed.fa new file mode 100644 index 00000000..9f7eca5d --- /dev/null +++ b/ariba/tests/data/cdhit_test_parse_cluster_info_file.in.renamed.fa @@ -0,0 +1,40 @@ +>1 +TGGGGAATATAGTGGGTACTGTGTGTTGAGCGATTCCCGAGCCCTATGCAGGCTTGTGAA +GGAGGTCGTGGGATGCTCGTGTCTTCACGAACTTAAAGCCCCTCTTTGGCTTAGGGCCGG +AGATCGCGTCATAAGTGTAATCTAGCGTTGCAGGTATGGGTAAGGCCATACACTTAGCTC +TGATGTGATGTGTCAGGTCTGGAGTTTACATATGTCCTGCCACGGTCCTATTTGTTAGAG +AGGCCTTCAGGCGGCCCCTGCCCGTCGATTCGGCAAACTGCCGAAAACGGAGAGACAGCC +ACGGTGAATAGAATCTTGGCATACGGTTAATCAGTGCTCTGCTAGTCCTGCTTTCTCTAA +GCTTATAGAATTCCTGATATATTAAGTAACTTTTCCATTCCATAGACGCGACGAACTGGA +TACACTCACGTAGGCTCGATCATGAAAGTGAAAGGCGCTCCAAGTTGCGAATTGAAACAA +AACTCTATCGTAGGGTCGCA +>2 +TGGGGAATATAGTGGGTACTGTGTGTTGAGCGATTCCCGAGCCCTATGCAGGCTTGTGAA +GGAGTTCGTGGGATGCTCGTGTCTTCACGAACTTAAAGCCCCTCTTTGGCTTAGGGCCGG +AGATCGCGTCATAAGTGTAATCTAGCGTTGCAGGTATGGGTAAGGCCATACACTTAGCTC +TGATGTGATGTGTCAGGTCTGGAGTTTACATATGTCCTGCCACGGTCCTATTTGTTAGAG +AGGCCTTCAGGCGGCCCCTGCCCGTCGATTCGGCAAACTGCCGAAAACGGAGAGACAGCC +ACGGTGAATGGAATCTTGGCATACGGTTAATCAGTGCTCTGCTAGTCCTGCTTTCTCTAA +GCTTATAGAATTCCTGATATATTAAGTAACTTTTCCATTCCATAGACGCGACGAACTGGA +TACACTCACGTATGCTCGATCATGAAAGTGAAAGGCGCTCCAAGTTGCGAATTGAAACAA +AACTCTATGTAGGGTCGCA +>3 +TGGGGAATATAGTGGGTACTGTGTGTTGAGCGATTCCCGAGTTCTATGCAGGCTTGTGAA +GGAGTTCGTGGGATGCTCGTGTCTTCACGAACTTAAAGCCCCTCTTTGGCTTAGGGCCGG +AGATCGCGTCATAAGTGTAATCTAGCGTTGCAGGTATGGGTAGGCCATACACTTAGCTCA +TGATGTGATGTGTCAGGTCTGGAGTTTACATATGTCCTGCCACGGTCCTATTTGTTAGAG +AGGCCTTCAGGCGGCCCCTGCCCGTCGATTCGGCAAACTGCCGAAAACGGAGAGATAGCC +ACGGTGAATGGAATCTTGGCATACGGTTAATCAGTGCTCTGCTAGTCCTGCTTTCTCTAA +GCTTATAGAATTCCTGATATATTAAGTAACTTTTCCATTCCATAGACGCGACGAACTGGA +TACACTCACGTATGCTCGATCATGAAAGTGAAAGGCGCTCCAAGATGCGAATTGAAACAA +AACTCTATGTAGGGTCGCA +>4 +CAAGGGCGGATTCGAACGGGTAACAGGGATCTGATTGGCTCCGGCCAGCTGGTGGATATC +TGCATCCGTTGACCCACCAACTTTAGCAGTATAGACCCTAAACTGGCATGGTGCCCTTTT +TATATCCCGATGCATCTGGAGAAACCGTCAGGACCTCTTAAGCCCCGTGGAGAGCCAAAC +TTCCAACCACGTCAAGGCAACCTTGGTTTAGCACAGGGCTCCCAGTGGGTGTAAGGGATG +AACACTACCCGGCCCACCGTCGATTTAGCCCTAAATGGTCTATTGCTCACGGGTAGCACA +CAAGTAATAAAAACGTATTCAGCTCGAGTCAGCGTCCAGCCATTTTACTTTGCGTCATCG +AGGGGTAGTGCCTCCGAGAATCAAGGTTTGATTATACTAAACGGAGGGGCCTACCACTCA +GCCAGTCTTTGCATCGTCCATTCCCGCCGTTTATGGGTCACTATTCATTCGGAATTTGGA +TGCGGTCAACAAGTCCAGGT diff --git a/ariba/tests/data/cdhit_test_parse_cluster_info_file.out.fa b/ariba/tests/data/cdhit_test_parse_cluster_info_file.out.fa new file mode 100644 index 00000000..dba7562b --- /dev/null +++ b/ariba/tests/data/cdhit_test_parse_cluster_info_file.out.fa @@ -0,0 +1,20 @@ +>1 +TGGGGAATATAGTGGGTACTGTGTGTTGAGCGATTCCCGAGCCCTATGCAGGCTTGTGAA +GGAGGTCGTGGGATGCTCGTGTCTTCACGAACTTAAAGCCCCTCTTTGGCTTAGGGCCGG +AGATCGCGTCATAAGTGTAATCTAGCGTTGCAGGTATGGGTAAGGCCATACACTTAGCTC +TGATGTGATGTGTCAGGTCTGGAGTTTACATATGTCCTGCCACGGTCCTATTTGTTAGAG +AGGCCTTCAGGCGGCCCCTGCCCGTCGATTCGGCAAACTGCCGAAAACGGAGAGACAGCC +ACGGTGAATAGAATCTTGGCATACGGTTAATCAGTGCTCTGCTAGTCCTGCTTTCTCTAA +GCTTATAGAATTCCTGATATATTAAGTAACTTTTCCATTCCATAGACGCGACGAACTGGA +TACACTCACGTAGGCTCGATCATGAAAGTGAAAGGCGCTCCAAGTTGCGAATTGAAACAA +AACTCTATCGTAGGGTCGCA +>4 +CAAGGGCGGATTCGAACGGGTAACAGGGATCTGATTGGCTCCGGCCAGCTGGTGGATATC +TGCATCCGTTGACCCACCAACTTTAGCAGTATAGACCCTAAACTGGCATGGTGCCCTTTT +TATATCCCGATGCATCTGGAGAAACCGTCAGGACCTCTTAAGCCCCGTGGAGAGCCAAAC +TTCCAACCACGTCAAGGCAACCTTGGTTTAGCACAGGGCTCCCAGTGGGTGTAAGGGATG +AACACTACCCGGCCCACCGTCGATTTAGCCCTAAATGGTCTATTGCTCACGGGTAGCACA +CAAGTAATAAAAACGTATTCAGCTCGAGTCAGCGTCCAGCCATTTTACTTTGCGTCATCG +AGGGGTAGTGCCTCCGAGAATCAAGGTTTGATTATACTAAACGGAGGGGCCTACCACTCA +GCCAGTCTTTGCATCGTCCATTCCCGCCGTTTATGGGTCACTATTCATTCGGAATTTGGA +TGCGGTCAACAAGTCCAGGT diff --git a/ariba/tests/data/cdhit_test_parse_cluster_info_file.out.fa.bak.clstr b/ariba/tests/data/cdhit_test_parse_cluster_info_file.out.fa.bak.clstr new file mode 100644 index 00000000..17451594 --- /dev/null +++ b/ariba/tests/data/cdhit_test_parse_cluster_info_file.out.fa.bak.clstr @@ -0,0 +1,4 @@ +0 500aa, >1... * +0 499aa, >2... at 99.40% +0 499aa, >3... at 98.40% +1 500aa, >4... * diff --git a/ariba/tests/data/cdhit_test_rename_fasta.in.fa b/ariba/tests/data/cdhit_test_rename_fasta.in.fa new file mode 100644 index 00000000..11d5e25a --- /dev/null +++ b/ariba/tests/data/cdhit_test_rename_fasta.in.fa @@ -0,0 +1,6 @@ +>a +A +>b +C +>c +G diff --git a/ariba/tests/data/cdhit_test_rename_fasta.out.fa b/ariba/tests/data/cdhit_test_rename_fasta.out.fa new file mode 100644 index 00000000..7ab37993 --- /dev/null +++ b/ariba/tests/data/cdhit_test_rename_fasta.out.fa @@ -0,0 +1,6 @@ +>seq1 +A +>seq2 +C +>seq3 +G diff --git a/ariba/tests/data/cdhit_test_run.in.fa b/ariba/tests/data/cdhit_test_run.in.fa new file mode 100644 index 00000000..bf8b12c8 --- /dev/null +++ b/ariba/tests/data/cdhit_test_run.in.fa @@ -0,0 +1,40 @@ +>seq1 +TGGGGAATATAGTGGGTACTGTGTGTTGAGCGATTCCCGAGCCCTATGCAGGCTTGTGAA +GGAGGTCGTGGGATGCTCGTGTCTTCACGAACTTAAAGCCCCTCTTTGGCTTAGGGCCGG +AGATCGCGTCATAAGTGTAATCTAGCGTTGCAGGTATGGGTAAGGCCATACACTTAGCTC +TGATGTGATGTGTCAGGTCTGGAGTTTACATATGTCCTGCCACGGTCCTATTTGTTAGAG +AGGCCTTCAGGCGGCCCCTGCCCGTCGATTCGGCAAACTGCCGAAAACGGAGAGACAGCC +ACGGTGAATAGAATCTTGGCATACGGTTAATCAGTGCTCTGCTAGTCCTGCTTTCTCTAA +GCTTATAGAATTCCTGATATATTAAGTAACTTTTCCATTCCATAGACGCGACGAACTGGA +TACACTCACGTAGGCTCGATCATGAAAGTGAAAGGCGCTCCAAGTTGCGAATTGAAACAA +AACTCTATCGTAGGGTCGCA +>seq2 +TGGGGAATATAGTGGGTACTGTGTGTTGAGCGATTCCCGAGCCCTATGCAGGCTTGTGAA +GGAGTTCGTGGGATGCTCGTGTCTTCACGAACTTAAAGCCCCTCTTTGGCTTAGGGCCGG +AGATCGCGTCATAAGTGTAATCTAGCGTTGCAGGTATGGGTAAGGCCATACACTTAGCTC +TGATGTGATGTGTCAGGTCTGGAGTTTACATATGTCCTGCCACGGTCCTATTTGTTAGAG +AGGCCTTCAGGCGGCCCCTGCCCGTCGATTCGGCAAACTGCCGAAAACGGAGAGACAGCC +ACGGTGAATGGAATCTTGGCATACGGTTAATCAGTGCTCTGCTAGTCCTGCTTTCTCTAA +GCTTATAGAATTCCTGATATATTAAGTAACTTTTCCATTCCATAGACGCGACGAACTGGA +TACACTCACGTATGCTCGATCATGAAAGTGAAAGGCGCTCCAAGTTGCGAATTGAAACAA +AACTCTATGTAGGGTCGCA +>seq3 +TGGGGAATATAGTGGGTACTGTGTGTTGAGCGATTCCCGAGTTCTATGCAGGCTTGTGAA +GGAGTTCGTGGGATGCTCGTGTCTTCACGAACTTAAAGCCCCTCTTTGGCTTAGGGCCGG +AGATCGCGTCATAAGTGTAATCTAGCGTTGCAGGTATGGGTAGGCCATACACTTAGCTCA +TGATGTGATGTGTCAGGTCTGGAGTTTACATATGTCCTGCCACGGTCCTATTTGTTAGAG +AGGCCTTCAGGCGGCCCCTGCCCGTCGATTCGGCAAACTGCCGAAAACGGAGAGATAGCC +ACGGTGAATGGAATCTTGGCATACGGTTAATCAGTGCTCTGCTAGTCCTGCTTTCTCTAA +GCTTATAGAATTCCTGATATATTAAGTAACTTTTCCATTCCATAGACGCGACGAACTGGA +TACACTCACGTATGCTCGATCATGAAAGTGAAAGGCGCTCCAAGATGCGAATTGAAACAA +AACTCTATGTAGGGTCGCA +>seq4 +CAAGGGCGGATTCGAACGGGTAACAGGGATCTGATTGGCTCCGGCCAGCTGGTGGATATC +TGCATCCGTTGACCCACCAACTTTAGCAGTATAGACCCTAAACTGGCATGGTGCCCTTTT +TATATCCCGATGCATCTGGAGAAACCGTCAGGACCTCTTAAGCCCCGTGGAGAGCCAAAC +TTCCAACCACGTCAAGGCAACCTTGGTTTAGCACAGGGCTCCCAGTGGGTGTAAGGGATG +AACACTACCCGGCCCACCGTCGATTTAGCCCTAAATGGTCTATTGCTCACGGGTAGCACA +CAAGTAATAAAAACGTATTCAGCTCGAGTCAGCGTCCAGCCATTTTACTTTGCGTCATCG +AGGGGTAGTGCCTCCGAGAATCAAGGTTTGATTATACTAAACGGAGGGGCCTACCACTCA +GCCAGTCTTTGCATCGTCCATTCCCGCCGTTTATGGGTCACTATTCATTCGGAATTTGGA +TGCGGTCAACAAGTCCAGGT diff --git a/ariba/tests/data/cdhit_test_run.out.fa b/ariba/tests/data/cdhit_test_run.out.fa new file mode 100644 index 00000000..12a02b2b --- /dev/null +++ b/ariba/tests/data/cdhit_test_run.out.fa @@ -0,0 +1,20 @@ +>0 +TGGGGAATATAGTGGGTACTGTGTGTTGAGCGATTCCCGAGCCCTATGCAGGCTTGTGAA +GGAGGTCGTGGGATGCTCGTGTCTTCACGAACTTAAAGCCCCTCTTTGGCTTAGGGCCGG +AGATCGCGTCATAAGTGTAATCTAGCGTTGCAGGTATGGGTAAGGCCATACACTTAGCTC +TGATGTGATGTGTCAGGTCTGGAGTTTACATATGTCCTGCCACGGTCCTATTTGTTAGAG +AGGCCTTCAGGCGGCCCCTGCCCGTCGATTCGGCAAACTGCCGAAAACGGAGAGACAGCC +ACGGTGAATAGAATCTTGGCATACGGTTAATCAGTGCTCTGCTAGTCCTGCTTTCTCTAA +GCTTATAGAATTCCTGATATATTAAGTAACTTTTCCATTCCATAGACGCGACGAACTGGA +TACACTCACGTAGGCTCGATCATGAAAGTGAAAGGCGCTCCAAGTTGCGAATTGAAACAA +AACTCTATCGTAGGGTCGCA +>1 +CAAGGGCGGATTCGAACGGGTAACAGGGATCTGATTGGCTCCGGCCAGCTGGTGGATATC +TGCATCCGTTGACCCACCAACTTTAGCAGTATAGACCCTAAACTGGCATGGTGCCCTTTT +TATATCCCGATGCATCTGGAGAAACCGTCAGGACCTCTTAAGCCCCGTGGAGAGCCAAAC +TTCCAACCACGTCAAGGCAACCTTGGTTTAGCACAGGGCTCCCAGTGGGTGTAAGGGATG +AACACTACCCGGCCCACCGTCGATTTAGCCCTAAATGGTCTATTGCTCACGGGTAGCACA +CAAGTAATAAAAACGTATTCAGCTCGAGTCAGCGTCCAGCCATTTTACTTTGCGTCATCG +AGGGGTAGTGCCTCCGAGAATCAAGGTTTGATTATACTAAACGGAGGGGCCTACCACTCA +GCCAGTCTTTGCATCGTCCATTCCCGCCGTTTATGGGTCACTATTCATTCGGAATTTGGA +TGCGGTCAACAAGTCCAGGT diff --git a/ariba/tests/data/cluster_test_assemble_with_spades/gene.fa b/ariba/tests/data/cluster_test_assemble_with_spades.gene.fa similarity index 100% rename from ariba/tests/data/cluster_test_assemble_with_spades/gene.fa rename to ariba/tests/data/cluster_test_assemble_with_spades.gene.fa diff --git a/ariba/tests/data/cluster_test_gapfill_with_gapfiller/gene.fa b/ariba/tests/data/cluster_test_assemble_with_spades/genes.fa similarity index 100% rename from ariba/tests/data/cluster_test_gapfill_with_gapfiller/gene.fa rename to ariba/tests/data/cluster_test_assemble_with_spades/genes.fa diff --git a/ariba/tests/data/cluster_test_assemble_with_velvet/gene.fa b/ariba/tests/data/cluster_test_assemble_with_velvet/gene.fa deleted file mode 100644 index f067cdc9..00000000 --- a/ariba/tests/data/cluster_test_assemble_with_velvet/gene.fa +++ /dev/null @@ -1,9 +0,0 @@ ->02__aac_6prime__1_AY553333 -ATGCAGTACTCCATTCGCTCGGTTCGTGTTTCGGATACATCTGATTGGTTACGCCTTCGC -AATCTCCTGTGGGAAGGGGATGACCACGAAACCGAGATCGCCCAGTTTTTCGCCGGAGCC -CTGGCCGAGCCCAACGAAGTGCTGGTAGCCCATGATGATGCGGGGGCCGTTGTTGGGCAT -GTCGAGTTATCCATCCGCGAGGATGTCGCAGGGCTGGAAGGCATCAGAGCGGGCTATATC -GAAGGCCTGTACATCGAGGAGGCCCATCGCTCGTCCAGCGTCGCGACGCAGTTACTACGG -CACTCCGAGCAATGGGCCCAAAGTCAGGGATGCCGGGCGTTTGCATCGGATCGAGAGGAT -CGCCTGATCATCCATAAGCGGTTTTCTGTGAGTCCGCTTTCTAACCCTTCATTCCAGCGG -ACCGCCTTCGGCGGCCGCTGA diff --git a/ariba/tests/data/cluster_test_assemble_with_velvet/gene.reads_mapped.unsorted.bam b/ariba/tests/data/cluster_test_assemble_with_velvet/gene.reads_mapped.unsorted.bam deleted file mode 100644 index 3b2031f2..00000000 Binary files a/ariba/tests/data/cluster_test_assemble_with_velvet/gene.reads_mapped.unsorted.bam and /dev/null differ diff --git a/ariba/tests/data/cluster_test_assemble_with_velvet/reads_1.fq b/ariba/tests/data/cluster_test_assemble_with_velvet/reads_1.fq deleted file mode 100644 index 28ac2321..00000000 --- a/ariba/tests/data/cluster_test_assemble_with_velvet/reads_1.fq +++ /dev/null @@ -1,772 +0,0 @@ -@test_2__02__aac_6prime__1_AY553333:3:932:1260/1 -GTAGTTCCTGAACCTAAATCTCCAAATGTTTGCCGTGGGGAGATTGGGCTGATTGTTTAGCTTCAACTTATGCAGTACTCCATTCGCTCGGTTCGTGTTT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:9:1187:1470/1 -TTATCCATCCGCGAGGATGTCGCAGGGCTGGAAGGCATCAGAGCGGGCTATATCGAAGGCCTGTACATCGAGGAGGCCCATCGCTCGTCCAGCGTCGCGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:11:1034:1339/1 -GATACATCTGATTGGTTACGCCTTCGCAATCTCCTGTGGGAAGGGGATGACCACGAAACCGAGATCGCCCAGTTTTTCGCCGGAGCCCTGGCCGAGCCCA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:12:813:1107/1 -CAAGCGACGTAGGGTCTGCCTTATCGTCACGGATTCCGGCTACGCTGCACGGTTTCTGAGCTACGTCCATTGGTATATCACCAGGATGGCAAACGGCGGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:18:809:1111/1 -CCGACAAGCGACGTAGGGTCTGCCTTATCGTCACGGATTCCGGCTACGCTGCACGGTTTCTGAGCTACGTCCATTGGTATATCACCAGGATGGCAAACGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:21:1340:1603/1 -TTTGCATCGGATCGAGAGGATCGCCTGATCATCCATAAGCGGTTTTCTGTGAGTCCGCTTTCTAACCCTTCATTCCAGCGGACCGCCTTCGGCGGCCGCT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:22:889:1173/1 -ATCACCAGGATGGCAAACGGCGGGTTAGGGTAGCGTACAGGTCGTAGTTCCTGAACCTAAATCTCCAAATGTTTGCCGTGGGGAGATTGGGCTGATTGTT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:26:1286:1595/1 -ACGCAGTTACTACGGCACTCCGAGCAATGGGCCCAAAGTCAGGGATGCCGGGCGTTTGCATCGGATCGAGAGGATCGCCTGATCATCCATAAGCGGTTTT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:34:921:1212/1 -GCGTACAGGTCGTAGTTCCTGAACCTAAATCTCCAAATGTTTGCCGTGGGGAGATTGGGCTGATTGTTTAGCTTCAACTTATGCAGTACTCCATTCGCTC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:39:1078:1369/1 -GGATGACCACGAAACCGAGATCGCCCAGTTTTTCGCCGGAGCCCTGGCCGAGCCCAACGAAGTGCTGGTAGCCCATGATGATGCGGGGGCCGTTGTTGGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:40:723:1004/1 -TGTCCTAATGGATATCGCAAAAAGTGGAACGGTGGGCGGGCTAAGCTGATAAGCGCTGTGCTCAGTCTTGCTTACTAGAAGGAACCCCGACAAGCGACGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:41:753:1013/1 -GGTGGGCGGGCTAAGCTGATAAGCGCTGTGCTCAGTCTTGCTTACTAGAAGGAACCCCGACAAGCGACGTAGGGTCTGCCTTATCGTCACGGATTCCGGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:45:976:1267/1 -TGGGCTGATTGTTTAGCTTCAACTTATGCAGTACTCCATTCGCTCGGTTCGTGTTTCGGATACATCTGATTGGTTACGCCTTCGCAATCTCCTGTGGGAA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:46:859:1166/1 -GCACGGTTTCTGAGCTACGTCCATTGGTATATCACCAGGATGGCAAACGGCGGGTTAGGGTAGCGTACAGGTCGTAGTTCCTGAACCTAAATCTCCAAAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:52:1024:1314/1 -TCGTGTTTCGGATACATCTGATTGGTTACGCCTTCGCAATCTCCTGTGGGAAGGGGATGACCACGAAACCGAGATCGCCCAGTTTTTCGCCGGAGCCCTG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:57:1294:1584/1 -ACTACGGCACTCCGAGCAATGGGCCCAAAGTCAGGGATGCCGGGCGTTTGCATCGGATCGAGAGGATCGCCTGATCATCCATAAGCGGTTTTCTGTGAGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:60:883:1191/1 -TGGTATATCACCAGGATGGCAAACGGCGGGTTAGGGTAGCGTACAGGTCGTAGTTCCTGAACCTAAATCTCCAAATGTTTGCCGTGGGGAGATTGGGCTG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:61:1296:1576/1 -TACGGCACTCCGAGCAATGGGCCCAAAGTCAGGGATGCCGGGCGTTTGCATCGGATCGAGAGGATCGCCTGATCATCCATAAGCGGTTTTCTGTGAGTCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:63:904:1200/1 -AACGGCGGGTTAGGGTAGCGTACAGGTCGTAGTTCCTGAACCTAAATCTCCAAATGTTTGCCGTGGGGAGATTGGGCTGATTGTTTAGCTTCAACTTATG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:67:999:1285/1 -TTATGCAGTACTCCATTCGCTCGGTTCGTGTTTCGGATACATCTGATTGGTTACGCCTTCGCAATCTCCTGTGGGAAGGGGATGACCACGAAACCGAGAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:69:1081:1387/1 -TGACCACGAAACCGAGATCGCCCAGTTTTTCGCCGGAGCCCTGGCCGAGCCCAACGAAGTGCTGGTAGCCCATGATGATGCGGGGGCCGTTGTTGGGCAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:81:1336:1630/1 -GGCGTTTGCATCGGATCGAGAGGATCGCCTGATCATCCATAAGCGGTTTTCTGTGAGTCCGCTTTCTAACCCTTCATTCCAGCGGACCGCCTTCGGCGGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:82:1029:1311/1 -TTTCGGATACATCTGATTGGTTACGCCTTCGCAATCTCCTGTGGGAAGGGGATGACCACGAAACCGAGATCGCCCAGTTTTTCGCCGGAGCCCTGGCCGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:86:1220:1507/1 -GGCATCAGAGCGGGCTATATCGAAGGCCTGTACATCGAGGAGGCCCATCGCTCGTCCAGCGTCGCGACGCAGTTACTACGGCACTCCGAGCAATGGGCCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:89:1202:1509/1 -GATGTCGCAGGGCTGGAAGGCATCAGAGCGGGCTATATCGAAGGCCTGTACATCGAGGAGGCCCATCGCTCGTCCAGCGTCGCGACGCAGTTACTACGGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:92:877:1170/1 -GTCCATTGGTATATCACCAGGATGGCAAACGGCGGGTTAGGGTAGCGTACAGGTCGTAGTTCCTGAACCTAAATCTCCAAATGTTTGCCGTGGGGAGATT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:95:678:1005/1 -GTCTCAACGTGGGACTGTCTTCTAACCGTGTCTACGGCCGCGCGCTGTCCTAATGGATATCGCAAAAAGTGGAACGGTGGGCGGGCTAAGCTGATAAGCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:96:887:1206/1 -ATATCACCAGGATGGCAAACGGCGGGTTAGGGTAGCGTACAGGTCGTAGTTCCTGAACCTAAATCTCCAAATGTTTGCCGTGGGGAGATTGGGCTGATTG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:97:698:998/1 -TCTAACCGTGTCTACGGCCGCGCGCTGTCCTAATGGATATCGCAAAAAGTGGAACGGTGGGCGGGCTAAGCTGATAAGCGCTGTGCTCAGTCTTGCTTAC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:98:1304:1593/1 -TCCGAGCAATGGGCCCAAAGTCAGGGATGCCGGGCGTTTGCATCGGATCGAGAGGATCGCCTGATCATCCATAAGCGGTTTTCTGTGAGTCCGCTTTCTA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:101:960:1249/1 -TTTGCCGTGGGGAGATTGGGCTGATTGTTTAGCTTCAACTTATGCAGTACTCCATTCGCTCGGTTCGTGTTTCGGATACATCTGATTGGTTACGCCTTCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:104:860:1179/1 -CACGGTTTCTGAGCTACGTCCATTGGTATATCACCAGGATGGCAAACGGCGGGTTAGGGTAGCGTACAGGTCGTAGTTCCTGAACCTAAATCTCCAAATG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:106:990:1295/1 -AGCTTCAACTTATGCAGTACTCCATTCGCTCGGTTCGTGTTTCGGATACATCTGATTGGTTACGCCTTCGCAATCTCCTGTGGGAAGGGGATGACCACGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:110:910:1245/1 -GGGTTAGGGTAGCGTACAGGTCGTAGTTCCTGAACCTAAATCTCCAAATGTTTGCCGTGGGGAGATTGGGCTGATTGTTTAGCTTCAACTTATGCAGTAC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:111:914:1201/1 -TAGGGTAGCGTACAGGTCGTAGTTCCTGAACCTAAATCTCCAAATGTTTGCCGTGGGGAGATTGGGCTGATTGTTTAGCTTCAACTTATGCAGTACTCCA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:114:820:1136/1 -CGTAGGGTCTGCCTTATCGTCACGGATTCCGGCTACGCTGCACGGTTTCTGAGCTACGTCCATTGGTATATCACCAGGATGGCAAACGGCGGGTTAGGGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:116:711:1053/1 -ACGGCCGCGCGCTGTCCTAATGGATATCGCAAAAAGTGGAACGGTGGGCGGGCTAAGCTGATAAGCGCTGTGCTCAGTCTTGCTTACTAGAAGGAACCCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:118:753:1075/1 -GGTGGGCGGGCTAAGCTGATAAGCGCTGTGCTCAGTCTTGCTTACTAGAAGGAACCCCGACAAGCGACGTAGGGTCTGCCTTATCGTCACGGATTCCGGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:119:1249:1552/1 -GTACATCGAGGAGGCCCATCGCTCGTCCAGCGTCGCGACGCAGTTACTACGGCACTCCGAGCAATGGGCCCAAAGTCAGGGATGCCGGGCGTTTGCATCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:124:1178:1459/1 -CATGTCGAGTTATCCATCCGCGAGGATGTCGCAGGGCTGGAAGGCATCAGAGCGGGCTATATCGAAGGCCTGTACATCGAGGAGGCCCATCGCTCGTCCA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:125:1304:1614/1 -TCCGAGCAATGGGCCCAAAGTCAGGGATGCCGGGCGTTTGCATCGGATCGAGAGGATCGCCTGATCATCCATAAGCGGTTTTCTGTGAGTCCGCTTTCTA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:126:1011:1349/1 -CCATTCGCTCGGTTCGTGTTTCGGATACATCTGATTGGTTACGCCTTCGCAATCTCCTGTGGGAAGGGGATGACCACGAAACCGAGATCGCCCAGTTTTT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:128:1031:1347/1 -TCGGATACATCTGATTGGTTACGCCTTCGCAATCTCCTGTGGGAAGGGGATGACCACGAAACCGAGATCGCCCAGTTTTTCGCCGGAGCCCTGGCCGAGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:134:788:1094/1 -TCTTGCTTACTAGAAGGAACCCCGACAAGCGACGTAGGGTCTGCCTTATCGTCACGGATTCCGGCTACGCTGCACGGTTTCTGAGCTACGTCCATTGGTA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:135:1146:1445/1 -TAGCCCATGATGATGCGGGGGCCGTTGTTGGGCATGTCGAGTTATCCATCCGCGAGGATGTCGCAGGGCTGGAAGGCATCAGAGCGGGCTATATCGAAGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:139:750:1022/1 -AACGGTGGGCGGGCTAAGCTGATAAGCGCTGTGCTCAGTCTTGCTTACTAGAAGGAACCCCGACAAGCGACGTAGGGTCTGCCTTATCGTCACGGATTCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:140:989:1305/1 -TAGCTTCAACTTATGCAGTACTCCATTCGCTCGGTTCGTGTTTCGGATACATCTGATTGGTTACGCCTTCGCAATCTCCTGTGGGAAGGGGATGACCACG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:143:1194:1463/1 -TCCGCGAGGATGTCGCAGGGCTGGAAGGCATCAGAGCGGGCTATATCGAAGGCCTGTACATCGAGGAGGCCCATCGCTCGTCCAGCGTCGCGACGCAGTT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:146:1036:1342/1 -TACATCTGATTGGTTACGCCTTCGCAATCTCCTGTGGGAAGGGGATGACCACGAAACCGAGATCGCCCAGTTTTTCGCCGGAGCCCTGGCCGAGCCCAAC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:147:1013:1292/1 -ATTCGCTCGGTTCGTGTTTCGGATACATCTGATTGGTTACGCCTTCGCAATCTCCTGTGGGAAGGGGATGACCACGAAACCGAGATCGCCCAGTTTTTCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:149:1042:1340/1 -TGATTGGTTACGCCTTCGCAATCTCCTGTGGGAAGGGGATGACCACGAAACCGAGATCGCCCAGTTTTTCGCCGGAGCCCTGGCCGAGCCCAACGAAGTG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:152:1003:1295/1 -GCAGTACTCCATTCGCTCGGTTCGTGTTTCGGATACATCTGATTGGTTACGCCTTCGCAATCTCCTGTGGGAAGGGGATGACCACGAAACCGAGATCGCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:158:937:1237/1 -TCCTGAACCTAAATCTCCAAATGTTTGCCGTGGGGAGATTGGGCTGATTGTTTAGCTTCAACTTATGCAGTACTCCATTCGCTCGGTTCGTGTTTCGGAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:160:903:1174/1 -AAACGGCGGGTTAGGGTAGCGTACAGGTCGTAGTTCCTGAACCTAAATCTCCAAATGTTTGCCGTGGGGAGATTGGGCTGATTGTTTAGCTTCAACTTAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:164:1150:1445/1 -CCATGATGATGCGGGGGCCGTTGTTGGGCATGTCGAGTTATCCATCCGCGAGGATGTCGCAGGGCTGGAAGGCATCAGAGCGGGCTATATCGAAGGCCTG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:166:1229:1535/1 -GCGGGCTATATCGAAGGCCTGTACATCGAGGAGGCCCATCGCTCGTCCAGCGTCGCGACGCAGTTACTACGGCACTCCGAGCAATGGGCCCAAAGTCAGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:172:1026:1354/1 -GTGTTTCGGATACATCTGATTGGTTACGCCTTCGCAATCTCCTGTGGGAAGGGGATGACCACGAAACCGAGATCGCCCAGTTTTTCGCCGGAGCCCTGGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:173:1210:1516/1 -AGGGCTGGAAGGCATCAGAGCGGGCTATATCGAAGGCCTGTACATCGAGGAGGCCCATCGCTCGTCCAGCGTCGCGACGCAGTTACTACGGCACTCCGAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:174:706:1004/1 -TGTCTACGGCCGCGCGCTGTCCTAATGGATATCGCAAAAAGTGGAACGGTGGGCGGGCTAAGCTGATAAGCGCTGTGCTCAGTCTTGCTTACTAGAAGGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:176:1114:1396/1 -CGGAGCCCTGGCCGAGCCCAACGAAGTGCTGGTAGCCCATGATGATGCGGGGGCCGTTGTTGGGCATGTCGAGTTATCCATCCGCGAGGATGTCGCAGGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:182:822:1094/1 -TAGGGTCTGCCTTATCGTCACGGATTCCGGCTACGCTGCACGGTTTCTGAGCTACGTCCATTGGTATATCACCAGGATGGCAAACGGCGGGTTAGGGTAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:186:813:1128/1 -CAAGCGACGTAGGGTCTGCCTTATCGTCACGGATTCCGGCTACGCTGCACGGTTTCTGAGCTACGTCCATTGGTATATCACCAGGATGGCAAACGGCGGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:187:1048:1359/1 -GTTACGCCTTCGCAATCTCCTGTGGGAAGGGGATGACCACGAAACCGAGATCGCCCAGTTTTTCGCCGGAGCCCTGGCCGAGCCCAACGAAGTGCTGGTA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:189:891:1195/1 -CACCAGGATGGCAAACGGCGGGTTAGGGTAGCGTACAGGTCGTAGTTCCTGAACCTAAATCTCCAAATGTTTGCCGTGGGGAGATTGGGCTGATTGTTTA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:193:796:1112/1 -ACTAGAAGGAACCCCGACAAGCGACGTAGGGTCTGCCTTATCGTCACGGATTCCGGCTACGCTGCACGGTTTCTGAGCTACGTCCATTGGTATATCACCA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:196:1088:1394/1 -GAAACCGAGATCGCCCAGTTTTTCGCCGGAGCCCTGGCCGAGCCCAACGAAGTGCTGGTAGCCCATGATGATGCGGGGGCCGTTGTTGGGCATGTCGAGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:200:1270:1573/1 -CTCGTCCAGCGTCGCGACGCAGTTACTACGGCACTCCGAGCAATGGGCCCAAAGTCAGGGATGCCGGGCGTTTGCATCGGATCGAGAGGATCGCCTGATC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:203:802:1108/1 -AGGAACCCCGACAAGCGACGTAGGGTCTGCCTTATCGTCACGGATTCCGGCTACGCTGCACGGTTTCTGAGCTACGTCCATTGGTATATCACCAGGATGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:207:1322:1624/1 -AGTCAGGGATGCCGGGCGTTTGCATCGGATCGAGAGGATCGCCTGATCATCCATAAGCGGTTTTCTGTGAGTCCGCTTTCTAACCCTTCATTCCAGCGGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:209:1269:1584/1 -GCTCGTCCAGCGTCGCGACGCAGTTACTACGGCACTCCGAGCAATGGGCCCAAAGTCAGGGATGCCGGGCGTTTGCATCGGATCGAGAGGATCGCCTGAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:210:798:1129/1 -TAGAAGGAACCCCGACAAGCGACGTAGGGTCTGCCTTATCGTCACGGATTCCGGCTACGCTGCACGGTTTCTGAGCTACGTCCATTGGTATATCACCAGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:212:998:1292/1 -CTTATGCAGTACTCCATTCGCTCGGTTCGTGTTTCGGATACATCTGATTGGTTACGCCTTCGCAATCTCCTGTGGGAAGGGGATGACCACGAAACCGAGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:213:896:1212/1 -GGATGGCAAACGGCGGGTTAGGGTAGCGTACAGGTCGTAGTTCCTGAACCTAAATCTCCAAATGTTTGCCGTGGGGAGATTGGGCTGATTGTTTAGCTTC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:214:1235:1523/1 -TATATCGAAGGCCTGTACATCGAGGAGGCCCATCGCTCGTCCAGCGTCGCGACGCAGTTACTACGGCACTCCGAGCAATGGGCCCAAAGTCAGGGATGCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:218:879:1145/1 -CCATTGGTATATCACCAGGATGGCAAACGGCGGGTTAGGGTAGCGTACAGGTCGTAGTTCCTGAACCTAAATCTCCAAATGTTTGCCGTGGGGAGATTGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:219:752:1070/1 -CGGTGGGCGGGCTAAGCTGATAAGCGCTGTGCTCAGTCTTGCTTACTAGAAGGAACCCCGACAAGCGACGTAGGGTCTGCCTTATCGTCACGGATTCCGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:221:1194:1529/1 -TCCGCGAGGATGTCGCAGGGCTGGAAGGCATCAGAGCGGGCTATATCGAAGGCCTGTACATCGAGGAGGCCCATCGCTCGTCCAGCGTCGCGACGCAGTT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:223:838:1151/1 -GTCACGGATTCCGGCTACGCTGCACGGTTTCTGAGCTACGTCCATTGGTATATCACCAGGATGGCAAACGGCGGGTTAGGGTAGCGTACAGGTCGTAGTT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:225:1188:1495/1 -TATCCATCCGCGAGGATGTCGCAGGGCTGGAAGGCATCAGAGCGGGCTATATCGAAGGCCTGTACATCGAGGAGGCCCATCGCTCGTCCAGCGTCGCGAC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:229:808:1086/1 -CCCGACAAGCGACGTAGGGTCTGCCTTATCGTCACGGATTCCGGCTACGCTGCACGGTTTCTGAGCTACGTCCATTGGTATATCACCAGGATGGCAAACG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:231:1239:1521/1 -TCGAAGGCCTGTACATCGAGGAGGCCCATCGCTCGTCCAGCGTCGCGACGCAGTTACTACGGCACTCCGAGCAATGGGCCCAAAGTCAGGGATGCCGGGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:236:1104:1410/1 -AGTTTTTCGCCGGAGCCCTGGCCGAGCCCAACGAAGTGCTGGTAGCCCATGATGATGCGGGGGCCGTTGTTGGGCATGTCGAGTTATCCATCCGCGAGGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:237:818:1098/1 -GACGTAGGGTCTGCCTTATCGTCACGGATTCCGGCTACGCTGCACGGTTTCTGAGCTACGTCCATTGGTATATCACCAGGATGGCAAACGGCGGGTTAGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:241:1297:1582/1 -ACGGCACTCCGAGCAATGGGCCCAAAGTCAGGGATGCCGGGCGTTTGCATCGGATCGAGAGGATCGCCTGATCATCCATAAGCGGTTTTCTGTGAGTCCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:246:726:1048/1 -CCTAATGGATATCGCAAAAAGTGGAACGGTGGGCGGGCTAAGCTGATAAGCGCTGTGCTCAGTCTTGCTTACTAGAAGGAACCCCGACAAGCGACGTAGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:247:863:1164/1 -GGTTTCTGAGCTACGTCCATTGGTATATCACCAGGATGGCAAACGGCGGGTTAGGGTAGCGTACAGGTCGTAGTTCCTGAACCTAAATCTCCAAATGTTT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:250:1208:1522/1 -GCAGGGCTGGAAGGCATCAGAGCGGGCTATATCGAAGGCCTGTACATCGAGGAGGCCCATCGCTCGTCCAGCGTCGCGACGCAGTTACTACGGCACTCCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:251:1123:1421/1 -GGCCGAGCCCAACGAAGTGCTGGTAGCCCATGATGATGCGGGGGCCGTTGTTGGGCATGTCGAGTTATCCATCCGCGAGGATGTCGCAGGGCTGGAAGGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:252:1305:1584/1 -CCGAGCAATGGGCCCAAAGTCAGGGATGCCGGGCGTTTGCATCGGATCGAGAGGATCGCCTGATCATCCATAAGCGGTTTTCTGTGAGTCCGCTTTCTAA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:253:711:1007/1 -ACGGCCGCGCGCTGTCCTAATGGATATCGCAAAAAGTGGAACGGTGGGCGGGCTAAGCTGATAAGCGCTGTGCTCAGTCTTGCTTACTAGAAGGAACCCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:254:1229:1536/1 -GCGGGCTATATCGAAGGCCTGTACATCGAGGAGGCCCATCGCTCGTCCAGCGTCGCGACGCAGTTACTACGGCACTCCGAGCAATGGGCCCAAAGTCAGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:255:817:1158/1 -CGACGTAGGGTCTGCCTTATCGTCACGGATTCCGGCTACGCTGCACGGTTTCTGAGCTACGTCCATTGGTATATCACCAGGATGGCAAACGGCGGGTTAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:258:989:1263/1 -TAGCTTCAACTTATGCAGTACTCCATTCGCTCGGTTCGTGTTTCGGATACATCTGATTGGTTACGCCTTCGCAATCTCCTGTGGGAAGGGGATGACCACG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:259:796:1115/1 -ACTAGAAGGAACCCCGACAAGCGACGTAGGGTCTGCCTTATCGTCACGGATTCCGGCTACGCTGCACGGTTTCTGAGCTACGTCCATTGGTATATCACCA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:263:1225:1525/1 -CAGAGCGGGCTATATCGAAGGCCTGTACATCGAGGAGGCCCATCGCTCGTCCAGCGTCGCGACGCAGTTACTACGGCACTCCGAGCAATGGGCCCAAAGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:272:1297:1568/1 -ACGGCACTCCGAGCAATGGGCCCAAAGTCAGGGATGCCGGGCGTTTGCATCGGATCGAGAGGATCGCCTGATCATCCATAAGCGGTTTTCTGTGAGTCCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:279:1192:1472/1 -CATCCGCGAGGATGTCGCAGGGCTGGAAGGCATCAGAGCGGGCTATATCGAAGGCCTGTACATCGAGGAGGCCCATCGCTCGTCCAGCGTCGCGACGCAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:282:806:1102/1 -ACCCCGACAAGCGACGTAGGGTCTGCCTTATCGTCACGGATTCCGGCTACGCTGCACGGTTTCTGAGCTACGTCCATTGGTATATCACCAGGATGGCAAA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:283:893:1209/1 -CCAGGATGGCAAACGGCGGGTTAGGGTAGCGTACAGGTCGTAGTTCCTGAACCTAAATCTCCAAATGTTTGCCGTGGGGAGATTGGGCTGATTGTTTAGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:285:740:1046/1 -CAAAAAGTGGAACGGTGGGCGGGCTAAGCTGATAAGCGCTGTGCTCAGTCTTGCTTACTAGAAGGAACCCCGACAAGCGACGTAGGGTCTGCCTTATCGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:290:1181:1498/1 -GTCGAGTTATCCATCCGCGAGGATGTCGCAGGGCTGGAAGGCATCAGAGCGGGCTATATCGAAGGCCTGTACATCGAGGAGGCCCATCGCTCGTCCAGCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:292:867:1178/1 -TCTGAGCTACGTCCATTGGTATATCACCAGGATGGCAAACGGCGGGTTAGGGTAGCGTACAGGTCGTAGTTCCTGAACCTAAATCTCCAAATGTTTGCCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:294:1200:1519/1 -AGGATGTCGCAGGGCTGGAAGGCATCAGAGCGGGCTATATCGAAGGCCTGTACATCGAGGAGGCCCATCGCTCGTCCAGCGTCGCGACGCAGTTACTACG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:307:1190:1498/1 -TCCATCCGCGAGGATGTCGCAGGGCTGGAAGGCATCAGAGCGGGCTATATCGAAGGCCTGTACATCGAGGAGGCCCATCGCTCGTCCAGCGTCGCGACGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:310:1041:1359/1 -CTGATTGGTTACGCCTTCGCAATCTCCTGTGGGAAGGGGATGACCACGAAACCGAGATCGCCCAGTTTTTCGCCGGAGCCCTGGCCGAGCCCAACGAAGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:312:1104:1399/1 -AGTTTTTCGCCGGAGCCCTGGCCGAGCCCAACGAAGTGCTGGTAGCCCATGATGATGCGGGGGCCGTTGTTGGGCATGTCGAGTTATCCATCCGCGAGGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:325:728:1039/1 -TAATGGATATCGCAAAAAGTGGAACGGTGGGCGGGCTAAGCTGATAAGCGCTGTGCTCAGTCTTGCTTACTAGAAGGAACCCCGACAAGCGACGTAGGGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:328:792:1067/1 -GCTTACTAGAAGGAACCCCGACAAGCGACGTAGGGTCTGCCTTATCGTCACGGATTCCGGCTACGCTGCACGGTTTCTGAGCTACGTCCATTGGTATATC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:329:1138:1431/1 -AGTGCTGGTAGCCCATGATGATGCGGGGGCCGTTGTTGGGCATGTCGAGTTATCCATCCGCGAGGATGTCGCAGGGCTGGAAGGCATCAGAGCGGGCTAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:333:1153:1462/1 -TGATGATGCGGGGGCCGTTGTTGGGCATGTCGAGTTATCCATCCGCGAGGATGTCGCAGGGCTGGAAGGCATCAGAGCGGGCTATATCGAAGGCCTGTAC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:336:1317:1605/1 -CCCAAAGTCAGGGATGCCGGGCGTTTGCATCGGATCGAGAGGATCGCCTGATCATCCATAAGCGGTTTTCTGTGAGTCCGCTTTCTAACCCTTCATTCCA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:337:894:1172/1 -CAGGATGGCAAACGGCGGGTTAGGGTAGCGTACAGGTCGTAGTTCCTGAACCTAAATCTCCAAATGTTTGCCGTGGGGAGATTGGGCTGATTGTTTAGCT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:342:1180:1488/1 -TGTCGAGTTATCCATCCGCGAGGATGTCGCAGGGCTGGAAGGCATCAGAGCGGGCTATATCGAAGGCCTGTACATCGAGGAGGCCCATCGCTCGTCCAGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:348:1329:1637/1 -GATGCCGGGCGTTTGCATCGGATCGAGAGGATCGCCTGATCATCCATAAGCGGTTTTCTGTGAGTCCGCTTTCTAACCCTTCATTCCAGCGGACCGCCTT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:355:698:1022/1 -TCTAACCGTGTCTACGGCCGCGCGCTGTCCTAATGGATATCGCAAAAAGTGGAACGGTGGGCGGGCTAAGCTGATAAGCGCTGTGCTCAGTCTTGCTTAC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:356:1032:1341/1 -CGGATACATCTGATTGGTTACGCCTTCGCAATCTCCTGTGGGAAGGGGATGACCACGAAACCGAGATCGCCCAGTTTTTCGCCGGAGCCCTGGCCGAGCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:357:1051:1345/1 -ACGCCTTCGCAATCTCCTGTGGGAAGGGGATGACCACGAAACCGAGATCGCCCAGTTTTTCGCCGGAGCCCTGGCCGAGCCCAACGAAGTGCTGGTAGCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:358:862:1183/1 -CGGTTTCTGAGCTACGTCCATTGGTATATCACCAGGATGGCAAACGGCGGGTTAGGGTAGCGTACAGGTCGTAGTTCCTGAACCTAAATCTCCAAATGTT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:360:1242:1552/1 -AAGGCCTGTACATCGAGGAGGCCCATCGCTCGTCCAGCGTCGCGACGCAGTTACTACGGCACTCCGAGCAATGGGCCCAAAGTCAGGGATGCCGGGCGTT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:361:869:1189/1 -TGAGCTACGTCCATTGGTATATCACCAGGATGGCAAACGGCGGGTTAGGGTAGCGTACAGGTCGTAGTTCCTGAACCTAAATCTCCAAATGTTTGCCGTG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:362:1321:1634/1 -AAGTCAGGGATGCCGGGCGTTTGCATCGGATCGAGAGGATCGCCTGATCATCCATAAGCGGTTTTCTGTGAGTCCGCTTTCTAACCCTTCATTCCAGCGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:363:936:1248/1 -TTCCTGAACCTAAATCTCCAAATGTTTGCCGTGGGGAGATTGGGCTGATTGTTTAGCTTCAACTTATGCAGTACTCCATTCGCTCGGTTCGTGTTTCGGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:364:1150:1465/1 -CCATGATGATGCGGGGGCCGTTGTTGGGCATGTCGAGTTATCCATCCGCGAGGATGTCGCAGGGCTGGAAGGCATCAGAGCGGGCTATATCGAAGGCCTG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:373:1177:1458/1 -GCATGTCGAGTTATCCATCCGCGAGGATGTCGCAGGGCTGGAAGGCATCAGAGCGGGCTATATCGAAGGCCTGTACATCGAGGAGGCCCATCGCTCGTCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:376:853:1184/1 -TACGCTGCACGGTTTCTGAGCTACGTCCATTGGTATATCACCAGGATGGCAAACGGCGGGTTAGGGTAGCGTACAGGTCGTAGTTCCTGAACCTAAATCT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:383:1127:1415/1 -GAGCCCAACGAAGTGCTGGTAGCCCATGATGATGCGGGGGCCGTTGTTGGGCATGTCGAGTTATCCATCCGCGAGGATGTCGCAGGGCTGGAAGGCATCA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:390:1350:1638/1 -ATCGAGAGGATCGCCTGATCATCCATAAGCGGTTTTCTGTGAGTCCGCTTTCTAACCCTTCATTCCAGCGGACCGCCTTCGGCGGCCGCTGAGATATAGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:398:1074:1387/1 -AAGGGGATGACCACGAAACCGAGATCGCCCAGTTTTTCGCCGGAGCCCTGGCCGAGCCCAACGAAGTGCTGGTAGCCCATGATGATGCGGGGGCCGTTGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:399:853:1153/1 -TACGCTGCACGGTTTCTGAGCTACGTCCATTGGTATATCACCAGGATGGCAAACGGCGGGTTAGGGTAGCGTACAGGTCGTAGTTCCTGAACCTAAATCT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:400:1202:1493/1 -GATGTCGCAGGGCTGGAAGGCATCAGAGCGGGCTATATCGAAGGCCTGTACATCGAGGAGGCCCATCGCTCGTCCAGCGTCGCGACGCAGTTACTACGGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:404:1056:1331/1 -TTCGCAATCTCCTGTGGGAAGGGGATGACCACGAAACCGAGATCGCCCAGTTTTTCGCCGGAGCCCTGGCCGAGCCCAACGAAGTGCTGGTAGCCCATGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:407:821:1100/1 -GTAGGGTCTGCCTTATCGTCACGGATTCCGGCTACGCTGCACGGTTTCTGAGCTACGTCCATTGGTATATCACCAGGATGGCAAACGGCGGGTTAGGGTA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:414:1329:1613/1 -GATGCCGGGCGTTTGCATCGGATCGAGAGGATCGCCTGATCATCCATAAGCGGTTTTCTGTGAGTCCGCTTTCTAACCCTTCATTCCAGCGGACCGCCTT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:420:977:1281/1 -GGGCTGATTGTTTAGCTTCAACTTATGCAGTACTCCATTCGCTCGGTTCGTGTTTCGGATACATCTGATTGGTTACGCCTTCGCAATCTCCTGTGGGAAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:426:818:1076/1 -GACGTAGGGTCTGCCTTATCGTCACGGATTCCGGCTACGCTGCACGGTTTCTGAGCTACGTCCATTGGTATATCACCAGGATGGCAAACGGCGGGTTAGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:427:956:1269/1 -AATGTTTGCCGTGGGGAGATTGGGCTGATTGTTTAGCTTCAACTTATGCAGTACTCCATTCGCTCGGTTCGTGTTTCGGATACATCTGATTGGTTACGCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:436:940:1228/1 -TGAACCTAAATCTCCAAATGTTTGCCGTGGGGAGATTGGGCTGATTGTTTAGCTTCAACTTATGCAGTACTCCATTCGCTCGGTTCGTGTTTCGGATACA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:437:1129:1432/1 -GCCCAACGAAGTGCTGGTAGCCCATGATGATGCGGGGGCCGTTGTTGGGCATGTCGAGTTATCCATCCGCGAGGATGTCGCAGGGCTGGAAGGCATCAGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:439:941:1262/1 -GAACCTAAATCTCCAAATGTTTGCCGTGGGGAGATTGGGCTGATTGTTTAGCTTCAACTTATGCAGTACTCCATTCGCTCGGTTCGTGTTTCGGATACAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:440:769:1085/1 -TGATAAGCGCTGTGCTCAGTCTTGCTTACTAGAAGGAACCCCGACAAGCGACGTAGGGTCTGCCTTATCGTCACGGATTCCGGCTACGCTGCACGGTTTC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:444:692:1038/1 -CTGTCTTCTAACCGTGTCTACGGCCGCGCGCTGTCCTAATGGATATCGCAAAAAGTGGAACGGTGGGCGGGCTAAGCTGATAAGCGCTGTGCTCAGTCTT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:446:923:1207/1 -GTACAGGTCGTAGTTCCTGAACCTAAATCTCCAAATGTTTGCCGTGGGGAGATTGGGCTGATTGTTTAGCTTCAACTTATGCAGTACTCCATTCGCTCGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:447:879:1188/1 -CCATTGGTATATCACCAGGATGGCAAACGGCGGGTTAGGGTAGCGTACAGGTCGTAGTTCCTGAACCTAAATCTCCAAATGTTTGCCGTGGGGAGATTGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:450:1323:1611/1 -GTCAGGGATGCCGGGCGTTTGCATCGGATCGAGAGGATCGCCTGATCATCCATAAGCGGTTTTCTGTGAGTCCGCTTTCTAACCCTTCATTCCAGCGGAC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:452:1340:1636/1 -TTTGCATCGGATCGAGAGGATCGCCTGATCATCCATAAGCGGTTTTCTGTGAGTCCGCTTTCTAACCCTTCATTCCAGCGGACCGCCTTCGGCGGCCGCT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:459:782:1089/1 -GCTCAGTCTTGCTTACTAGAAGGAACCCCGACAAGCGACGTAGGGTCTGCCTTATCGTCACGGATTCCGGCTACGCTGCACGGTTTCTGAGCTACGTCCA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:462:1137:1404/1 -AAGTGCTGGTAGCCCATGATGATGCGGGGGCCGTTGTTGGGCATGTCGAGTTATCCATCCGCGAGGATGTCGCAGGGCTGGAAGGCATCAGAGCGGGCTA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:463:1306:1584/1 -CGAGCAATGGGCCCAAAGTCAGGGATGCCGGGCGTTTGCATCGGATCGAGAGGATCGCCTGATCATCCATAAGCGGTTTTCTGTGAGTCCGCTTTCTAAC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:468:894:1162/1 -CAGGATGGCAAACGGCGGGTTAGGGTAGCGTACAGGTCGTAGTTCCTGAACCTAAATCTCCAAATGTTTGCCGTGGGGAGATTGGGCTGATTGTTTAGCT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:470:844:1125/1 -GATTCCGGCTACGCTGCACGGTTTCTGAGCTACGTCCATTGGTATATCACCAGGATGGCAAACGGCGGGTTAGGGTAGCGTACAGGTCGTAGTTCCTGAA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:473:930:1213/1 -TCGTAGTTCCTGAACCTAAATCTCCAAATGTTTGCCGTGGGGAGATTGGGCTGATTGTTTAGCTTCAACTTATGCAGTACTCCATTCGCTCGGTTCGTGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:478:813:1078/1 -CAAGCGACGTAGGGTCTGCCTTATCGTCACGGATTCCGGCTACGCTGCACGGTTTCTGAGCTACGTCCATTGGTATATCACCAGGATGGCAAACGGCGGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:479:886:1205/1 -TATATCACCAGGATGGCAAACGGCGGGTTAGGGTAGCGTACAGGTCGTAGTTCCTGAACCTAAATCTCCAAATGTTTGCCGTGGGGAGATTGGGCTGATT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:482:819:1130/1 -ACGTAGGGTCTGCCTTATCGTCACGGATTCCGGCTACGCTGCACGGTTTCTGAGCTACGTCCATTGGTATATCACCAGGATGGCAAACGGCGGGTTAGGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:486:844:1161/1 -GATTCCGGCTACGCTGCACGGTTTCTGAGCTACGTCCATTGGTATATCACCAGGATGGCAAACGGCGGGTTAGGGTAGCGTACAGGTCGTAGTTCCTGAA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:487:1005:1316/1 -AGTACTCCATTCGCTCGGTTCGTGTTTCGGATACATCTGATTGGTTACGCCTTCGCAATCTCCTGTGGGAAGGGGATGACCACGAAACCGAGATCGCCCA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:489:1179:1492/1 -ATGTCGAGTTATCCATCCGCGAGGATGTCGCAGGGCTGGAAGGCATCAGAGCGGGCTATATCGAAGGCCTGTACATCGAGGAGGCCCATCGCTCGTCCAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:490:1101:1398/1 -CCCAGTTTTTCGCCGGAGCCCTGGCCGAGCCCAACGAAGTGCTGGTAGCCCATGATGATGCGGGGGCCGTTGTTGGGCATGTCGAGTTATCCATCCGCGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:502:1070:1355/1 -TGGGAAGGGGATGACCACGAAACCGAGATCGCCCAGTTTTTCGCCGGAGCCCTGGCCGAGCCCAACGAAGTGCTGGTAGCCCATGATGATGCGGGGGCCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:503:1250:1569/1 -TACATCGAGGAGGCCCATCGCTCGTCCAGCGTCGCGACGCAGTTACTACGGCACTCCGAGCAATGGGCCCAAAGTCAGGGATGCCGGGCGTTTGCATCGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:504:962:1239/1 -TGCCGTGGGGAGATTGGGCTGATTGTTTAGCTTCAACTTATGCAGTACTCCATTCGCTCGGTTCGTGTTTCGGATACATCTGATTGGTTACGCCTTCGCA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:513:1191:1460/1 -CCATCCGCGAGGATGTCGCAGGGCTGGAAGGCATCAGAGCGGGCTATATCGAAGGCCTGTACATCGAGGAGGCCCATCGCTCGTCCAGCGTCGCGACGCA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:516:888:1181/1 -TATCACCAGGATGGCAAACGGCGGGTTAGGGTAGCGTACAGGTCGTAGTTCCTGAACCTAAATCTCCAAATGTTTGCCGTGGGGAGATTGGGCTGATTGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:518:1306:1596/1 -CGAGCAATGGGCCCAAAGTCAGGGATGCCGGGCGTTTGCATCGGATCGAGAGGATCGCCTGATCATCCATAAGCGGTTTTCTGTGAGTCCGCTTTCTAAC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:520:1038:1354/1 -CATCTGATTGGTTACGCCTTCGCAATCTCCTGTGGGAAGGGGATGACCACGAAACCGAGATCGCCCAGTTTTTCGCCGGAGCCCTGGCCGAGCCCAACGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:523:913:1223/1 -TTAGGGTAGCGTACAGGTCGTAGTTCCTGAACCTAAATCTCCAAATGTTTGCCGTGGGGAGATTGGGCTGATTGTTTAGCTTCAACTTATGCAGTACTCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:530:730:1063/1 -ATGGATATCGCAAAAAGTGGAACGGTGGGCGGGCTAAGCTGATAAGCGCTGTGCTCAGTCTTGCTTACTAGAAGGAACCCCGACAAGCGACGTAGGGTCT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:535:784:1113/1 -TCAGTCTTGCTTACTAGAAGGAACCCCGACAAGCGACGTAGGGTCTGCCTTATCGTCACGGATTCCGGCTACGCTGCACGGTTTCTGAGCTACGTCCATT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:536:789:1104/1 -CTTGCTTACTAGAAGGAACCCCGACAAGCGACGTAGGGTCTGCCTTATCGTCACGGATTCCGGCTACGCTGCACGGTTTCTGAGCTACGTCCATTGGTAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:538:1000:1308/1 -TATGCAGTACTCCATTCGCTCGGTTCGTGTTTCGGATACATCTGATTGGTTACGCCTTCGCAATCTCCTGTGGGAAGGGGATGACCACGAAACCGAGATC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:540:767:1051/1 -GCTGATAAGCGCTGTGCTCAGTCTTGCTTACTAGAAGGAACCCCGACAAGCGACGTAGGGTCTGCCTTATCGTCACGGATTCCGGCTACGCTGCACGGTT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:541:1178:1470/1 -CATGTCGAGTTATCCATCCGCGAGGATGTCGCAGGGCTGGAAGGCATCAGAGCGGGCTATATCGAAGGCCTGTACATCGAGGAGGCCCATCGCTCGTCCA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:545:1278:1573/1 -GCGTCGCGACGCAGTTACTACGGCACTCCGAGCAATGGGCCCAAAGTCAGGGATGCCGGGCGTTTGCATCGGATCGAGAGGATCGCCTGATCATCCATAA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:552:868:1153/1 -CTGAGCTACGTCCATTGGTATATCACCAGGATGGCAAACGGCGGGTTAGGGTAGCGTACAGGTCGTAGTTCCTGAACCTAAATCTCCAAATGTTTGCCGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:553:870:1175/1 -GAGCTACGTCCATTGGTATATCACCAGGATGGCAAACGGCGGGTTAGGGTAGCGTACAGGTCGTAGTTCCTGAACCTAAATCTCCAAATGTTTGCCGTGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:555:1081:1375/1 -TGACCACGAAACCGAGATCGCCCAGTTTTTCGCCGGAGCCCTGGCCGAGCCCAACGAAGTGCTGGTAGCCCATGATGATGCGGGGGCCGTTGTTGGGCAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:556:941:1243/1 -GAACCTAAATCTCCAAATGTTTGCCGTGGGGAGATTGGGCTGATTGTTTAGCTTCAACTTATGCAGTACTCCATTCGCTCGGTTCGTGTTTCGGATACAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:559:735:1063/1 -TATCGCAAAAAGTGGAACGGTGGGCGGGCTAAGCTGATAAGCGCTGTGCTCAGTCTTGCTTACTAGAAGGAACCCCGACAAGCGACGTAGGGTCTGCCTT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:561:834:1121/1 -TATCGTCACGGATTCCGGCTACGCTGCACGGTTTCTGAGCTACGTCCATTGGTATATCACCAGGATGGCAAACGGCGGGTTAGGGTAGCGTACAGGTCGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:564:1098:1400/1 -TCGCCCAGTTTTTCGCCGGAGCCCTGGCCGAGCCCAACGAAGTGCTGGTAGCCCATGATGATGCGGGGGCCGTTGTTGGGCATGTCGAGTTATCCATCCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:568:1312:1631/1 -ATGGGCCCAAAGTCAGGGATGCCGGGCGTTTGCATCGGATCGAGAGGATCGCCTGATCATCCATAAGCGGTTTTCTGTGAGTCCGCTTTCTAACCCTTCA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:575:894:1174/1 -CAGGATGGCAAACGGCGGGTTAGGGTAGCGTACAGGTCGTAGTTCCTGAACCTAAATCTCCAAATGTTTGCCGTGGGGAGATTGGGCTGATTGTTTAGCT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:579:1186:1521/1 -GTTATCCATCCGCGAGGATGTCGCAGGGCTGGAAGGCATCAGAGCGGGCTATATCGAAGGCCTGTACATCGAGGAGGCCCATCGCTCGTCCAGCGTCGCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:585:900:1209/1 -GGCAAACGGCGGGTTAGGGTAGCGTACAGGTCGTAGTTCCTGAACCTAAATCTCCAAATGTTTGCCGTGGGGAGATTGGGCTGATTGTTTAGCTTCAACT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:586:1305:1589/1 -CCGAGCAATGGGCCCAAAGTCAGGGATGCCGGGCGTTTGCATCGGATCGAGAGGATCGCCTGATCATCCATAAGCGGTTTTCTGTGAGTCCGCTTTCTAA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:593:778:1063/1 -CTGTGCTCAGTCTTGCTTACTAGAAGGAACCCCGACAAGCGACGTAGGGTCTGCCTTATCGTCACGGATTCCGGCTACGCTGCACGGTTTCTGAGCTACG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:597:659:1016/1 -CGTACCCCTTTAGTCAAGGGTCTCAACGTGGGACTGTCTTCTAACCGTGTCTACGGCCGCGCGCTGTCCTAATGGATATCGCAAAAAGTGGAACGGTGGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:598:1043:1318/1 -GATTGGTTACGCCTTCGCAATCTCCTGTGGGAAGGGGATGACCACGAAACCGAGATCGCCCAGTTTTTCGCCGGAGCCCTGGCCGAGCCCAACGAAGTGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:599:824:1109/1 -GGGTCTGCCTTATCGTCACGGATTCCGGCTACGCTGCACGGTTTCTGAGCTACGTCCATTGGTATATCACCAGGATGGCAAACGGCGGGTTAGGGTAGCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:602:842:1134/1 -CGGATTCCGGCTACGCTGCACGGTTTCTGAGCTACGTCCATTGGTATATCACCAGGATGGCAAACGGCGGGTTAGGGTAGCGTACAGGTCGTAGTTCCTG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:606:963:1237/1 -GCCGTGGGGAGATTGGGCTGATTGTTTAGCTTCAACTTATGCAGTACTCCATTCGCTCGGTTCGTGTTTCGGATACATCTGATTGGTTACGCCTTCGCAA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:607:1139:1448/1 -GTGCTGGTAGCCCATGATGATGCGGGGGCCGTTGTTGGGCATGTCGAGTTATCCATCCGCGAGGATGTCGCAGGGCTGGAAGGCATCAGAGCGGGCTATA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:610:873:1156/1 -CTACGTCCATTGGTATATCACCAGGATGGCAAACGGCGGGTTAGGGTAGCGTACAGGTCGTAGTTCCTGAACCTAAATCTCCAAATGTTTGCCGTGGGGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII diff --git a/ariba/tests/data/cluster_test_assemble_with_velvet/reads_2.fq b/ariba/tests/data/cluster_test_assemble_with_velvet/reads_2.fq deleted file mode 100644 index de63a352..00000000 --- a/ariba/tests/data/cluster_test_assemble_with_velvet/reads_2.fq +++ /dev/null @@ -1,772 +0,0 @@ -@test_2__02__aac_6prime__1_AY553333:3:932:1260/2 -TCCTCTCGATCCGATGCAAACGCCCGGCATCCCTGACTTTGGGCCCATTGCTCGGAGTGCCGTAGTAACTGCGTCGCGACGCTGGACGAGCGATGGGCCT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:9:1187:1470/2 -AACCTTCGACTCCTTAGATTTCGCCCGGAAGGTCGCGATCTTCCTTGGTGCACGTACAGCGGCCAAATAGGATTGAAAAGTGGACGAAATTCTTACACCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:11:1034:1339/2 -GCGGCCGCCGAAGGCGGTCCGCTGGAATGAAGGGTTAGAAAGCGGACTCACAGAAAACCGCTTATGGATGATCAGGCGATCCTCTCGATCCGATGCAAAC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:12:813:1107/2 -ACATCCTCGCGGATGGATAACTCGACATGCCCAACAACGGCCCCCGCATCATCATGGGCTACCAGCACTTCGTTGGGCTCGGCCAGGGCTCCGGCGAAAA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:18:809:1111/2 -TGCGACATCCTCGCGGATGGATAACTCGACATGCCCAACAACGGCCCCCGCATCATCATGGGCTACCAGCACTTCGTTGGGCTCGGCCAGGGCTCCGGCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:21:1340:1603/2 -TGATTTATTGTAGCGCCAACAACCCCTTTGTGCCTTGGTAGCATCGCATCTGGGTATGTTATTAGTGGCTTGGCGTAGTCCCTCCTGCCTCAATCGTCTC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:22:889:1173/2 -GAGCGATGGGCCTCCTCGATGTACAGGCCTTCGATATAGCCCGCTCTGATGCCTTCCAGCCCTGCGACATCCTCGCGGATGGATAACTCGACATGCCCAA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:26:1286:1595/2 -TGTAGCGCCAACAACCCCTTTGTGCCTTGGTAGCATCGCATCTGGGTATGTTATTAGTGGCTTGGCGTAGTCCCTCCTGCCTCAATCGTCTCTAGCCGCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:34:921:1212/2 -TGCTCGGAGTGCCGTAGTAACTGCGTCGCGACGCTGGACGAGCGATGGGCCTCCTCGATGTACAGGCCTTCGATATAGCCCGCTCTGATGCCTTCCAGCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:39:1078:1369/2 -GGACAAGTATCCGGAAAGAACTATATCTCAGCGGCCGCCGAAGGCGGTCCGCTGGAATGAAGGGTTAGAAAGCGGACTCACAGAAAACCGCTTATGGATG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:40:723:1004/2 -GGGCGATCTCGGTTTCGTGGTCATCCCCTTCCCACAGGAGATTGCGAAGGCGTAACCAATCAGATGTATCCGAAACACGAACCGAGCGAATGGAGTACTG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:41:753:1013/2 -CGAAAAACTGGGCGATCTCGGTTTCGTGGTCATCCCCTTCCCACAGGAGATTGCGAAGGCGTAACCAATCAGATGTATCCGAAACACGAACCGAGCGAAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:45:976:1267/2 -CAGGCGATCCTCTCGATCCGATGCAAACGCCCGGCATCCCTGACTTTGGGCCCATTGCTCGGAGTGCCGTAGTAACTGCGTCGCGACGCTGGACGAGCGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:46:859:1166/2 -GGGCCTCCTCGATGTACAGGCCTTCGATATAGCCCGCTCTGATGCCTTCCAGCCCTGCGACATCCTCGCGGATGGATAACTCGACATGCCCAACAACGGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:52:1024:1314/2 -AATGAAGGGTTAGAAAGCGGACTCACAGAAAACCGCTTATGGATGATCAGGCGATCCTCTCGATCCGATGCAAACGCCCGGCATCCCTGACTTTGGGCCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:57:1294:1584/2 -CAACCCCTTTGTGCCTTGGTAGCATCGCATCTGGGTATGTTATTAGTGGCTTGGCGTAGTCCCTCCTGCCTCAATCGTCTCTAGCCGCCAATTATGGTTG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:60:883:1191/2 -TGCGTCGCGACGCTGGACGAGCGATGGGCCTCCTCGATGTACAGGCCTTCGATATAGCCCGCTCTGATGCCTTCCAGCCCTGCGACATCCTCGCGGATGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:61:1296:1576/2 -TTGTGCCTTGGTAGCATCGCATCTGGGTATGTTATTAGTGGCTTGGCGTAGTCCCTCCTGCCTCAATCGTCTCTAGCCGCCAATTATGGTTGTTTCAGTA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:63:904:1200/2 -CGTAGTAACTGCGTCGCGACGCTGGACGAGCGATGGGCCTCCTCGATGTACAGGCCTTCGATATAGCCCGCTCTGATGCCTTCCAGCCCTGCGACATCCT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:67:999:1285/2 -AAACCGCTTATGGATGATCAGGCGATCCTCTCGATCCGATGCAAACGCCCGGCATCCCTGACTTTGGGCCCATTGCTCGGAGTGCCGTAGTAACTGCGTC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:69:1081:1387/2 -ACGAAATTCTTACACCGTGGACAAGTATCCGGAAAGAACTATATCTCAGCGGCCGCCGAAGGCGGTCCGCTGGAATGAAGGGTTAGAAAGCGGACTCACA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:81:1336:1630/2 -AACGGCTTTTGGACCCCGCTCTAGCCCTGATTTATTGTAGCGCCAACAACCCCTTTGTGCCTTGGTAGCATCGCATCTGGGTATGTTATTAGTGGCTTGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:82:1029:1311/2 -GAAGGGTTAGAAAGCGGACTCACAGAAAACCGCTTATGGATGATCAGGCGATCCTCTCGATCCGATGCAAACGCCCGGCATCCCTGACTTTGGGCCCATT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:86:1220:1507/2 -TCTCTAGCCGCCAATTATGGTTGTTTCAGTACGTTAAAACCTTCGACTCCTTAGATTTCGCCCGGAAGGTCGCGATCTTCCTTGGTGCACGTACAGCGGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:89:1202:1509/2 -CGTCTCTAGCCGCCAATTATGGTTGTTTCAGTACGTTAAAACCTTCGACTCCTTAGATTTCGCCCGGAAGGTCGCGATCTTCCTTGGTGCACGTACAGCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:92:877:1170/2 -CGATGGGCCTCCTCGATGTACAGGCCTTCGATATAGCCCGCTCTGATGCCTTCCAGCCCTGCGACATCCTCGCGGATGGATAACTCGACATGCCCAACAA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:95:678:1005/2 -TGGGCGATCTCGGTTTCGTGGTCATCCCCTTCCCACAGGAGATTGCGAAGGCGTAACCAATCAGATGTATCCGAAACACGAACCGAGCGAATGGAGTACT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:96:887:1206/2 -GAGTGCCGTAGTAACTGCGTCGCGACGCTGGACGAGCGATGGGCCTCCTCGATGTACAGGCCTTCGATATAGCCCGCTCTGATGCCTTCCAGCCCTGCGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:97:698:998/2 -TCTCGGTTTCGTGGTCATCCCCTTCCCACAGGAGATTGCGAAGGCGTAACCAATCAGATGTATCCGAAACACGAACCGAGCGAATGGAGTACTGCATAAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:98:1304:1593/2 -TAGCGCCAACAACCCCTTTGTGCCTTGGTAGCATCGCATCTGGGTATGTTATTAGTGGCTTGGCGTAGTCCCTCCTGCCTCAATCGTCTCTAGCCGCCAA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:101:960:1249/2 -CGATGCAAACGCCCGGCATCCCTGACTTTGGGCCCATTGCTCGGAGTGCCGTAGTAACTGCGTCGCGACGCTGGACGAGCGATGGGCCTCCTCGATGTAC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:104:860:1179/2 -CTGGACGAGCGATGGGCCTCCTCGATGTACAGGCCTTCGATATAGCCCGCTCTGATGCCTTCCAGCCCTGCGACATCCTCGCGGATGGATAACTCGACAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:106:990:1295/2 -GACTCACAGAAAACCGCTTATGGATGATCAGGCGATCCTCTCGATCCGATGCAAACGCCCGGCATCCCTGACTTTGGGCCCATTGCTCGGAGTGCCGTAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:110:910:1245/2 -GCAAACGCCCGGCATCCCTGACTTTGGGCCCATTGCTCGGAGTGCCGTAGTAACTGCGTCGCGACGCTGGACGAGCGATGGGCCTCCTCGATGTACAGGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:111:914:1201/2 -CCGTAGTAACTGCGTCGCGACGCTGGACGAGCGATGGGCCTCCTCGATGTACAGGCCTTCGATATAGCCCGCTCTGATGCCTTCCAGCCCTGCGACATCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:114:820:1136/2 -AGCCCGCTCTGATGCCTTCCAGCCCTGCGACATCCTCGCGGATGGATAACTCGACATGCCCAACAACGGCCCCCGCATCATCATGGGCTACCAGCACTTC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:116:711:1053/2 -TGGGCTACCAGCACTTCGTTGGGCTCGGCCAGGGCTCCGGCGAAAAACTGGGCGATCTCGGTTTCGTGGTCATCCCCTTCCCACAGGAGATTGCGAAGGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:118:753:1075/2 -AACAACGGCCCCCGCATCATCATGGGCTACCAGCACTTCGTTGGGCTCGGCCAGGGCTCCGGCGAAAAACTGGGCGATCTCGGTTTCGTGGTCATCCCCT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:119:1249:1552/2 -GGGTATGTTATTAGTGGCTTGGCGTAGTCCCTCCTGCCTCAATCGTCTCTAGCCGCCAATTATGGTTGTTTCAGTACGTTAAAACCTTCGACTCCTTAGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:124:1178:1459/2 -CCTTAGATTTCGCCCGGAAGGTCGCGATCTTCCTTGGTGCACGTACAGCGGCCAAATAGGATTGAAAAGTGGACGAAATTCTTACACCGTGGACAAGTAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:125:1304:1614/2 -CGCTCTAGCCCTGATTTATTGTAGCGCCAACAACCCCTTTGTGCCTTGGTAGCATCGCATCTGGGTATGTTATTAGTGGCTTGGCGTAGTCCCTCCTGCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:126:1011:1349/2 -CTATATCTCAGCGGCCGCCGAAGGCGGTCCGCTGGAATGAAGGGTTAGAAAGCGGACTCACAGAAAACCGCTTATGGATGATCAGGCGATCCTCTCGATC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:128:1031:1347/2 -ATATCTCAGCGGCCGCCGAAGGCGGTCCGCTGGAATGAAGGGTTAGAAAGCGGACTCACAGAAAACCGCTTATGGATGATCAGGCGATCCTCTCGATCCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:134:788:1094/2 -TGGATAACTCGACATGCCCAACAACGGCCCCCGCATCATCATGGGCTACCAGCACTTCGTTGGGCTCGGCCAGGGCTCCGGCGAAAAACTGGGCGATCTC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:135:1146:1445/2 -CGGAAGGTCGCGATCTTCCTTGGTGCACGTACAGCGGCCAAATAGGATTGAAAAGTGGACGAAATTCTTACACCGTGGACAAGTATCCGGAAAGAACTAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:139:750:1022/2 -GGGCTCCGGCGAAAAACTGGGCGATCTCGGTTTCGTGGTCATCCCCTTCCCACAGGAGATTGCGAAGGCGTAACCAATCAGATGTATCCGAAACACGAAC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:140:989:1305/2 -TTAGAAAGCGGACTCACAGAAAACCGCTTATGGATGATCAGGCGATCCTCTCGATCCGATGCAAACGCCCGGCATCCCTGACTTTGGGCCCATTGCTCGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:143:1194:1463/2 -GACTCCTTAGATTTCGCCCGGAAGGTCGCGATCTTCCTTGGTGCACGTACAGCGGCCAAATAGGATTGAAAAGTGGACGAAATTCTTACACCGTGGACAA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:146:1036:1342/2 -TCAGCGGCCGCCGAAGGCGGTCCGCTGGAATGAAGGGTTAGAAAGCGGACTCACAGAAAACCGCTTATGGATGATCAGGCGATCCTCTCGATCCGATGCA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:147:1013:1292/2 -TCACAGAAAACCGCTTATGGATGATCAGGCGATCCTCTCGATCCGATGCAAACGCCCGGCATCCCTGACTTTGGGCCCATTGCTCGGAGTGCCGTAGTAA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:149:1042:1340/2 -AGCGGCCGCCGAAGGCGGTCCGCTGGAATGAAGGGTTAGAAAGCGGACTCACAGAAAACCGCTTATGGATGATCAGGCGATCCTCTCGATCCGATGCAAA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:152:1003:1295/2 -GACTCACAGAAAACCGCTTATGGATGATCAGGCGATCCTCTCGATCCGATGCAAACGCCCGGCATCCCTGACTTTGGGCCCATTGCTCGGAGTGCCGTAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:158:937:1237/2 -CCGGCATCCCTGACTTTGGGCCCATTGCTCGGAGTGCCGTAGTAACTGCGTCGCGACGCTGGACGAGCGATGGGCCTCCTCGATGTACAGGCCTTCGATA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:160:903:1174/2 -CGAGCGATGGGCCTCCTCGATGTACAGGCCTTCGATATAGCCCGCTCTGATGCCTTCCAGCCCTGCGACATCCTCGCGGATGGATAACTCGACATGCCCA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:164:1150:1445/2 -CGGAAGGTCGCGATCTTCCTTGGTGCACGTACAGCGGCCAAATAGGATTGAAAAGTGGACGAAATTCTTACACCGTGGACAAGTATCCGGAAAGAACTAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:166:1229:1535/2 -CTTGGCGTAGTCCCTCCTGCCTCAATCGTCTCTAGCCGCCAATTATGGTTGTTTCAGTACGTTAAAACCTTCGACTCCTTAGATTTCGCCCGGAAGGTCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:172:1026:1354/2 -AAGAACTATATCTCAGCGGCCGCCGAAGGCGGTCCGCTGGAATGAAGGGTTAGAAAGCGGACTCACAGAAAACCGCTTATGGATGATCAGGCGATCCTCT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:173:1210:1516/2 -CCTCAATCGTCTCTAGCCGCCAATTATGGTTGTTTCAGTACGTTAAAACCTTCGACTCCTTAGATTTCGCCCGGAAGGTCGCGATCTTCCTTGGTGCACG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:174:706:1004/2 -GGGCGATCTCGGTTTCGTGGTCATCCCCTTCCCACAGGAGATTGCGAAGGCGTAACCAATCAGATGTATCCGAAACACGAACCGAGCGAATGGAGTACTG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:176:1114:1396/2 -GAAAAGTGGACGAAATTCTTACACCGTGGACAAGTATCCGGAAAGAACTATATCTCAGCGGCCGCCGAAGGCGGTCCGCTGGAATGAAGGGTTAGAAAGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:182:822:1094/2 -TGGATAACTCGACATGCCCAACAACGGCCCCCGCATCATCATGGGCTACCAGCACTTCGTTGGGCTCGGCCAGGGCTCCGGCGAAAAACTGGGCGATCTC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:186:813:1128/2 -CTGATGCCTTCCAGCCCTGCGACATCCTCGCGGATGGATAACTCGACATGCCCAACAACGGCCCCCGCATCATCATGGGCTACCAGCACTTCGTTGGGCT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:187:1048:1359/2 -CCGGAAAGAACTATATCTCAGCGGCCGCCGAAGGCGGTCCGCTGGAATGAAGGGTTAGAAAGCGGACTCACAGAAAACCGCTTATGGATGATCAGGCGAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:189:891:1195/2 -TAACTGCGTCGCGACGCTGGACGAGCGATGGGCCTCCTCGATGTACAGGCCTTCGATATAGCCCGCTCTGATGCCTTCCAGCCCTGCGACATCCTCGCGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:193:796:1112/2 -CTGCGACATCCTCGCGGATGGATAACTCGACATGCCCAACAACGGCCCCCGCATCATCATGGGCTACCAGCACTTCGTTGGGCTCGGCCAGGGCTCCGGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:196:1088:1394/2 -AAAGTGGACGAAATTCTTACACCGTGGACAAGTATCCGGAAAGAACTATATCTCAGCGGCCGCCGAAGGCGGTCCGCTGGAATGAAGGGTTAGAAAGCGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:200:1270:1573/2 -TGCCTTGGTAGCATCGCATCTGGGTATGTTATTAGTGGCTTGGCGTAGTCCCTCCTGCCTCAATCGTCTCTAGCCGCCAATTATGGTTGTTTCAGTACGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:203:802:1108/2 -GACATCCTCGCGGATGGATAACTCGACATGCCCAACAACGGCCCCCGCATCATCATGGGCTACCAGCACTTCGTTGGGCTCGGCCAGGGCTCCGGCGAAA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:207:1322:1624/2 -TTTTGGACCCCGCTCTAGCCCTGATTTATTGTAGCGCCAACAACCCCTTTGTGCCTTGGTAGCATCGCATCTGGGTATGTTATTAGTGGCTTGGCGTAGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:209:1269:1584/2 -CAACCCCTTTGTGCCTTGGTAGCATCGCATCTGGGTATGTTATTAGTGGCTTGGCGTAGTCCCTCCTGCCTCAATCGTCTCTAGCCGCCAATTATGGTTG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:210:798:1129/2 -TCTGATGCCTTCCAGCCCTGCGACATCCTCGCGGATGGATAACTCGACATGCCCAACAACGGCCCCCGCATCATCATGGGCTACCAGCACTTCGTTGGGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:212:998:1292/2 -TCACAGAAAACCGCTTATGGATGATCAGGCGATCCTCTCGATCCGATGCAAACGCCCGGCATCCCTGACTTTGGGCCCATTGCTCGGAGTGCCGTAGTAA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:213:896:1212/2 -TGCTCGGAGTGCCGTAGTAACTGCGTCGCGACGCTGGACGAGCGATGGGCCTCCTCGATGTACAGGCCTTCGATATAGCCCGCTCTGATGCCTTCCAGCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:214:1235:1523/2 -CCTCCTGCCTCAATCGTCTCTAGCCGCCAATTATGGTTGTTTCAGTACGTTAAAACCTTCGACTCCTTAGATTTCGCCCGGAAGGTCGCGATCTTCCTTG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:218:879:1145/2 -CTTCGATATAGCCCGCTCTGATGCCTTCCAGCCCTGCGACATCCTCGCGGATGGATAACTCGACATGCCCAACAACGGCCCCCGCATCATCATGGGCTAC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:219:752:1070/2 -CGGCCCCCGCATCATCATGGGCTACCAGCACTTCGTTGGGCTCGGCCAGGGCTCCGGCGAAAAACTGGGCGATCTCGGTTTCGTGGTCATCCCCTTCCCA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:221:1194:1529/2 -GTAGTCCCTCCTGCCTCAATCGTCTCTAGCCGCCAATTATGGTTGTTTCAGTACGTTAAAACCTTCGACTCCTTAGATTTCGCCCGGAAGGTCGCGATCT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:223:838:1151/2 -ACAGGCCTTCGATATAGCCCGCTCTGATGCCTTCCAGCCCTGCGACATCCTCGCGGATGGATAACTCGACATGCCCAACAACGGCCCCCGCATCATCATG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:225:1188:1495/2 -AATTATGGTTGTTTCAGTACGTTAAAACCTTCGACTCCTTAGATTTCGCCCGGAAGGTCGCGATCTTCCTTGGTGCACGTACAGCGGCCAAATAGGATTG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:229:808:1086/2 -TCGACATGCCCAACAACGGCCCCCGCATCATCATGGGCTACCAGCACTTCGTTGGGCTCGGCCAGGGCTCCGGCGAAAAACTGGGCGATCTCGGTTTCGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:231:1239:1521/2 -TCCTGCCTCAATCGTCTCTAGCCGCCAATTATGGTTGTTTCAGTACGTTAAAACCTTCGACTCCTTAGATTTCGCCCGGAAGGTCGCGATCTTCCTTGGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:236:1104:1410/2 -GGCCAAATAGGATTGAAAAGTGGACGAAATTCTTACACCGTGGACAAGTATCCGGAAAGAACTATATCTCAGCGGCCGCCGAAGGCGGTCCGCTGGAATG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:237:818:1098/2 -CGGATGGATAACTCGACATGCCCAACAACGGCCCCCGCATCATCATGGGCTACCAGCACTTCGTTGGGCTCGGCCAGGGCTCCGGCGAAAAACTGGGCGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:241:1297:1582/2 -ACCCCTTTGTGCCTTGGTAGCATCGCATCTGGGTATGTTATTAGTGGCTTGGCGTAGTCCCTCCTGCCTCAATCGTCTCTAGCCGCCAATTATGGTTGTT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:246:726:1048/2 -TACCAGCACTTCGTTGGGCTCGGCCAGGGCTCCGGCGAAAAACTGGGCGATCTCGGTTTCGTGGTCATCCCCTTCCCACAGGAGATTGCGAAGGCGTAAC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:247:863:1164/2 -GCCTCCTCGATGTACAGGCCTTCGATATAGCCCGCTCTGATGCCTTCCAGCCCTGCGACATCCTCGCGGATGGATAACTCGACATGCCCAACAACGGCCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:250:1208:1522/2 -CTCCTGCCTCAATCGTCTCTAGCCGCCAATTATGGTTGTTTCAGTACGTTAAAACCTTCGACTCCTTAGATTTCGCCCGGAAGGTCGCGATCTTCCTTGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:251:1123:1421/2 -GCACGTACAGCGGCCAAATAGGATTGAAAAGTGGACGAAATTCTTACACCGTGGACAAGTATCCGGAAAGAACTATATCTCAGCGGCCGCCGAAGGCGGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:252:1305:1584/2 -CAACCCCTTTGTGCCTTGGTAGCATCGCATCTGGGTATGTTATTAGTGGCTTGGCGTAGTCCCTCCTGCCTCAATCGTCTCTAGCCGCCAATTATGGTTG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:253:711:1007/2 -ACTGGGCGATCTCGGTTTCGTGGTCATCCCCTTCCCACAGGAGATTGCGAAGGCGTAACCAATCAGATGTATCCGAAACACGAACCGAGCGAATGGAGTA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:254:1229:1536/2 -GCTTGGCGTAGTCCCTCCTGCCTCAATCGTCTCTAGCCGCCAATTATGGTTGTTTCAGTACGTTAAAACCTTCGACTCCTTAGATTTCGCCCGGAAGGTC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:255:817:1158/2 -TCGATGTACAGGCCTTCGATATAGCCCGCTCTGATGCCTTCCAGCCCTGCGACATCCTCGCGGATGGATAACTCGACATGCCCAACAACGGCCCCCGCAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:258:989:1263/2 -CGATCCTCTCGATCCGATGCAAACGCCCGGCATCCCTGACTTTGGGCCCATTGCTCGGAGTGCCGTAGTAACTGCGTCGCGACGCTGGACGAGCGATGGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:259:796:1115/2 -GCCCTGCGACATCCTCGCGGATGGATAACTCGACATGCCCAACAACGGCCCCCGCATCATCATGGGCTACCAGCACTTCGTTGGGCTCGGCCAGGGCTCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:263:1225:1525/2 -TCCCTCCTGCCTCAATCGTCTCTAGCCGCCAATTATGGTTGTTTCAGTACGTTAAAACCTTCGACTCCTTAGATTTCGCCCGGAAGGTCGCGATCTTCCT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:272:1297:1568/2 -TGGTAGCATCGCATCTGGGTATGTTATTAGTGGCTTGGCGTAGTCCCTCCTGCCTCAATCGTCTCTAGCCGCCAATTATGGTTGTTTCAGTACGTTAAAA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:279:1192:1472/2 -AAAACCTTCGACTCCTTAGATTTCGCCCGGAAGGTCGCGATCTTCCTTGGTGCACGTACAGCGGCCAAATAGGATTGAAAAGTGGACGAAATTCTTACAC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:282:806:1102/2 -CTCGCGGATGGATAACTCGACATGCCCAACAACGGCCCCCGCATCATCATGGGCTACCAGCACTTCGTTGGGCTCGGCCAGGGCTCCGGCGAAAAACTGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:283:893:1209/2 -TCGGAGTGCCGTAGTAACTGCGTCGCGACGCTGGACGAGCGATGGGCCTCCTCGATGTACAGGCCTTCGATATAGCCCGCTCTGATGCCTTCCAGCCCTG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:285:740:1046/2 -CCAGCACTTCGTTGGGCTCGGCCAGGGCTCCGGCGAAAAACTGGGCGATCTCGGTTTCGTGGTCATCCCCTTCCCACAGGAGATTGCGAAGGCGTAACCA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:290:1181:1498/2 -GCCAATTATGGTTGTTTCAGTACGTTAAAACCTTCGACTCCTTAGATTTCGCCCGGAAGGTCGCGATCTTCCTTGGTGCACGTACAGCGGCCAAATAGGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:292:867:1178/2 -TGGACGAGCGATGGGCCTCCTCGATGTACAGGCCTTCGATATAGCCCGCTCTGATGCCTTCCAGCCCTGCGACATCCTCGCGGATGGATAACTCGACATG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:294:1200:1519/2 -CTGCCTCAATCGTCTCTAGCCGCCAATTATGGTTGTTTCAGTACGTTAAAACCTTCGACTCCTTAGATTTCGCCCGGAAGGTCGCGATCTTCCTTGGTGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:307:1190:1498/2 -GCCAATTATGGTTGTTTCAGTACGTTAAAACCTTCGACTCCTTAGATTTCGCCCGGAAGGTCGCGATCTTCCTTGGTGCACGTACAGCGGCCAAATAGGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:310:1041:1359/2 -CCGGAAAGAACTATATCTCAGCGGCCGCCGAAGGCGGTCCGCTGGAATGAAGGGTTAGAAAGCGGACTCACAGAAAACCGCTTATGGATGATCAGGCGAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:312:1104:1399/2 -ATTGAAAAGTGGACGAAATTCTTACACCGTGGACAAGTATCCGGAAAGAACTATATCTCAGCGGCCGCCGAAGGCGGTCCGCTGGAATGAAGGGTTAGAA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:325:728:1039/2 -TTCGTTGGGCTCGGCCAGGGCTCCGGCGAAAAACTGGGCGATCTCGGTTTCGTGGTCATCCCCTTCCCACAGGAGATTGCGAAGGCGTAACCAATCAGAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:328:792:1067/2 -CCCCCGCATCATCATGGGCTACCAGCACTTCGTTGGGCTCGGCCAGGGCTCCGGCGAAAAACTGGGCGATCTCGGTTTCGTGGTCATCCCCTTCCCACAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:329:1138:1431/2 -CTTCCTTGGTGCACGTACAGCGGCCAAATAGGATTGAAAAGTGGACGAAATTCTTACACCGTGGACAAGTATCCGGAAAGAACTATATCTCAGCGGCCGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:333:1153:1462/2 -ACTCCTTAGATTTCGCCCGGAAGGTCGCGATCTTCCTTGGTGCACGTACAGCGGCCAAATAGGATTGAAAAGTGGACGAAATTCTTACACCGTGGACAAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:336:1317:1605/2 -CCTGATTTATTGTAGCGCCAACAACCCCTTTGTGCCTTGGTAGCATCGCATCTGGGTATGTTATTAGTGGCTTGGCGTAGTCCCTCCTGCCTCAATCGTC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:337:894:1172/2 -AGCGATGGGCCTCCTCGATGTACAGGCCTTCGATATAGCCCGCTCTGATGCCTTCCAGCCCTGCGACATCCTCGCGGATGGATAACTCGACATGCCCAAC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:342:1180:1488/2 -GTTGTTTCAGTACGTTAAAACCTTCGACTCCTTAGATTTCGCCCGGAAGGTCGCGATCTTCCTTGGTGCACGTACAGCGGCCAAATAGGATTGAAAAGTG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:348:1329:1637/2 -AATGCTTAACGGCTTTTGGACCCCGCTCTAGCCCTGATTTATTGTAGCGCCAACAACCCCTTTGTGCCTTGGTAGCATCGCATCTGGGTATGTTATTAGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:355:698:1022/2 -GGGCTCCGGCGAAAAACTGGGCGATCTCGGTTTCGTGGTCATCCCCTTCCCACAGGAGATTGCGAAGGCGTAACCAATCAGATGTATCCGAAACACGAAC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:356:1032:1341/2 -CAGCGGCCGCCGAAGGCGGTCCGCTGGAATGAAGGGTTAGAAAGCGGACTCACAGAAAACCGCTTATGGATGATCAGGCGATCCTCTCGATCCGATGCAA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:357:1051:1345/2 -ATCTCAGCGGCCGCCGAAGGCGGTCCGCTGGAATGAAGGGTTAGAAAGCGGACTCACAGAAAACCGCTTATGGATGATCAGGCGATCCTCTCGATCCGAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:358:862:1183/2 -GACGCTGGACGAGCGATGGGCCTCCTCGATGTACAGGCCTTCGATATAGCCCGCTCTGATGCCTTCCAGCCCTGCGACATCCTCGCGGATGGATAACTCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:360:1242:1552/2 -GGGTATGTTATTAGTGGCTTGGCGTAGTCCCTCCTGCCTCAATCGTCTCTAGCCGCCAATTATGGTTGTTTCAGTACGTTAAAACCTTCGACTCCTTAGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:361:869:1189/2 -CGTCGCGACGCTGGACGAGCGATGGGCCTCCTCGATGTACAGGCCTTCGATATAGCCCGCTCTGATGCCTTCCAGCCCTGCGACATCCTCGCGGATGGAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:362:1321:1634/2 -GCTTAACGGCTTTTGGACCCCGCTCTAGCCCTGATTTATTGTAGCGCCAACAACCCCTTTGTGCCTTGGTAGCATCGCATCTGGGTATGTTATTAGTGGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:363:936:1248/2 -GATGCAAACGCCCGGCATCCCTGACTTTGGGCCCATTGCTCGGAGTGCCGTAGTAACTGCGTCGCGACGCTGGACGAGCGATGGGCCTCCTCGATGTACA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:364:1150:1465/2 -TCGACTCCTTAGATTTCGCCCGGAAGGTCGCGATCTTCCTTGGTGCACGTACAGCGGCCAAATAGGATTGAAAAGTGGACGAAATTCTTACACCGTGGAC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:373:1177:1458/2 -CTTAGATTTCGCCCGGAAGGTCGCGATCTTCCTTGGTGCACGTACAGCGGCCAAATAGGATTGAAAAGTGGACGAAATTCTTACACCGTGGACAAGTATC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:376:853:1184/2 -CGACGCTGGACGAGCGATGGGCCTCCTCGATGTACAGGCCTTCGATATAGCCCGCTCTGATGCCTTCCAGCCCTGCGACATCCTCGCGGATGGATAACTC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:383:1127:1415/2 -ACAGCGGCCAAATAGGATTGAAAAGTGGACGAAATTCTTACACCGTGGACAAGTATCCGGAAAGAACTATATCTCAGCGGCCGCCGAAGGCGGTCCGCTG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:390:1350:1638/2 -CAATGCTTAACGGCTTTTGGACCCCGCTCTAGCCCTGATTTATTGTAGCGCCAACAACCCCTTTGTGCCTTGGTAGCATCGCATCTGGGTATGTTATTAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:398:1074:1387/2 -ACGAAATTCTTACACCGTGGACAAGTATCCGGAAAGAACTATATCTCAGCGGCCGCCGAAGGCGGTCCGCTGGAATGAAGGGTTAGAAAGCGGACTCACA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:399:853:1153/2 -GTACAGGCCTTCGATATAGCCCGCTCTGATGCCTTCCAGCCCTGCGACATCCTCGCGGATGGATAACTCGACATGCCCAACAACGGCCCCCGCATCATCA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:400:1202:1493/2 -TTATGGTTGTTTCAGTACGTTAAAACCTTCGACTCCTTAGATTTCGCCCGGAAGGTCGCGATCTTCCTTGGTGCACGTACAGCGGCCAAATAGGATTGAA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:404:1056:1331/2 -CGAAGGCGGTCCGCTGGAATGAAGGGTTAGAAAGCGGACTCACAGAAAACCGCTTATGGATGATCAGGCGATCCTCTCGATCCGATGCAAACGCCCGGCA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:407:821:1100/2 -CGCGGATGGATAACTCGACATGCCCAACAACGGCCCCCGCATCATCATGGGCTACCAGCACTTCGTTGGGCTCGGCCAGGGCTCCGGCGAAAAACTGGGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:414:1329:1613/2 -GCTCTAGCCCTGATTTATTGTAGCGCCAACAACCCCTTTGTGCCTTGGTAGCATCGCATCTGGGTATGTTATTAGTGGCTTGGCGTAGTCCCTCCTGCCT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:420:977:1281/2 -CGCTTATGGATGATCAGGCGATCCTCTCGATCCGATGCAAACGCCCGGCATCCCTGACTTTGGGCCCATTGCTCGGAGTGCCGTAGTAACTGCGTCGCGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:426:818:1076/2 -CAACAACGGCCCCCGCATCATCATGGGCTACCAGCACTTCGTTGGGCTCGGCCAGGGCTCCGGCGAAAAACTGGGCGATCTCGGTTTCGTGGTCATCCCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:427:956:1269/2 -ATCAGGCGATCCTCTCGATCCGATGCAAACGCCCGGCATCCCTGACTTTGGGCCCATTGCTCGGAGTGCCGTAGTAACTGCGTCGCGACGCTGGACGAGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:436:940:1228/2 -CTGACTTTGGGCCCATTGCTCGGAGTGCCGTAGTAACTGCGTCGCGACGCTGGACGAGCGATGGGCCTCCTCGATGTACAGGCCTTCGATATAGCCCGCT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:437:1129:1432/2 -TCTTCCTTGGTGCACGTACAGCGGCCAAATAGGATTGAAAAGTGGACGAAATTCTTACACCGTGGACAAGTATCCGGAAAGAACTATATCTCAGCGGCCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:439:941:1262/2 -GATCCTCTCGATCCGATGCAAACGCCCGGCATCCCTGACTTTGGGCCCATTGCTCGGAGTGCCGTAGTAACTGCGTCGCGACGCTGGACGAGCGATGGGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:440:769:1085/2 -CGACATGCCCAACAACGGCCCCCGCATCATCATGGGCTACCAGCACTTCGTTGGGCTCGGCCAGGGCTCCGGCGAAAAACTGGGCGATCTCGGTTTCGTG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:444:692:1038/2 -TCGTTGGGCTCGGCCAGGGCTCCGGCGAAAAACTGGGCGATCTCGGTTTCGTGGTCATCCCCTTCCCACAGGAGATTGCGAAGGCGTAACCAATCAGATG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:446:923:1207/2 -GGAGTGCCGTAGTAACTGCGTCGCGACGCTGGACGAGCGATGGGCCTCCTCGATGTACAGGCCTTCGATATAGCCCGCTCTGATGCCTTCCAGCCCTGCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:447:879:1188/2 -GTCGCGACGCTGGACGAGCGATGGGCCTCCTCGATGTACAGGCCTTCGATATAGCCCGCTCTGATGCCTTCCAGCCCTGCGACATCCTCGCGGATGGATA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:450:1323:1611/2 -TCTAGCCCTGATTTATTGTAGCGCCAACAACCCCTTTGTGCCTTGGTAGCATCGCATCTGGGTATGTTATTAGTGGCTTGGCGTAGTCCCTCCTGCCTCA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:452:1340:1636/2 -ATGCTTAACGGCTTTTGGACCCCGCTCTAGCCCTGATTTATTGTAGCGCCAACAACCCCTTTGTGCCTTGGTAGCATCGCATCTGGGTATGTTATTAGTG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:459:782:1089/2 -AACTCGACATGCCCAACAACGGCCCCCGCATCATCATGGGCTACCAGCACTTCGTTGGGCTCGGCCAGGGCTCCGGCGAAAAACTGGGCGATCTCGGTTT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:462:1137:1404/2 -ATAGGATTGAAAAGTGGACGAAATTCTTACACCGTGGACAAGTATCCGGAAAGAACTATATCTCAGCGGCCGCCGAAGGCGGTCCGCTGGAATGAAGGGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:463:1306:1584/2 -CAACCCCTTTGTGCCTTGGTAGCATCGCATCTGGGTATGTTATTAGTGGCTTGGCGTAGTCCCTCCTGCCTCAATCGTCTCTAGCCGCCAATTATGGTTG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:468:894:1162/2 -CTCCTCGATGTACAGGCCTTCGATATAGCCCGCTCTGATGCCTTCCAGCCCTGCGACATCCTCGCGGATGGATAACTCGACATGCCCAACAACGGCCCCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:470:844:1125/2 -ATGCCTTCCAGCCCTGCGACATCCTCGCGGATGGATAACTCGACATGCCCAACAACGGCCCCCGCATCATCATGGGCTACCAGCACTTCGTTGGGCTCGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:473:930:1213/2 -TTGCTCGGAGTGCCGTAGTAACTGCGTCGCGACGCTGGACGAGCGATGGGCCTCCTCGATGTACAGGCCTTCGATATAGCCCGCTCTGATGCCTTCCAGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:478:813:1078/2 -CCCAACAACGGCCCCCGCATCATCATGGGCTACCAGCACTTCGTTGGGCTCGGCCAGGGCTCCGGCGAAAAACTGGGCGATCTCGGTTTCGTGGTCATCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:479:886:1205/2 -AGTGCCGTAGTAACTGCGTCGCGACGCTGGACGAGCGATGGGCCTCCTCGATGTACAGGCCTTCGATATAGCCCGCTCTGATGCCTTCCAGCCCTGCGAC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:482:819:1130/2 -CTCTGATGCCTTCCAGCCCTGCGACATCCTCGCGGATGGATAACTCGACATGCCCAACAACGGCCCCCGCATCATCATGGGCTACCAGCACTTCGTTGGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:486:844:1161/2 -TCCTCGATGTACAGGCCTTCGATATAGCCCGCTCTGATGCCTTCCAGCCCTGCGACATCCTCGCGGATGGATAACTCGACATGCCCAACAACGGCCCCCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:487:1005:1316/2 -GGAATGAAGGGTTAGAAAGCGGACTCACAGAAAACCGCTTATGGATGATCAGGCGATCCTCTCGATCCGATGCAAACGCCCGGCATCCCTGACTTTGGGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:489:1179:1492/2 -TATGGTTGTTTCAGTACGTTAAAACCTTCGACTCCTTAGATTTCGCCCGGAAGGTCGCGATCTTCCTTGGTGCACGTACAGCGGCCAAATAGGATTGAAA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:490:1101:1398/2 -TTGAAAAGTGGACGAAATTCTTACACCGTGGACAAGTATCCGGAAAGAACTATATCTCAGCGGCCGCCGAAGGCGGTCCGCTGGAATGAAGGGTTAGAAA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:502:1070:1355/2 -AAAGAACTATATCTCAGCGGCCGCCGAAGGCGGTCCGCTGGAATGAAGGGTTAGAAAGCGGACTCACAGAAAACCGCTTATGGATGATCAGGCGATCCTC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:503:1250:1569/2 -TTGGTAGCATCGCATCTGGGTATGTTATTAGTGGCTTGGCGTAGTCCCTCCTGCCTCAATCGTCTCTAGCCGCCAATTATGGTTGTTTCAGTACGTTAAA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:504:962:1239/2 -GCCCGGCATCCCTGACTTTGGGCCCATTGCTCGGAGTGCCGTAGTAACTGCGTCGCGACGCTGGACGAGCGATGGGCCTCCTCGATGTACAGGCCTTCGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:513:1191:1460/2 -TCCTTAGATTTCGCCCGGAAGGTCGCGATCTTCCTTGGTGCACGTACAGCGGCCAAATAGGATTGAAAAGTGGACGAAATTCTTACACCGTGGACAAGTA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:516:888:1181/2 -CGCTGGACGAGCGATGGGCCTCCTCGATGTACAGGCCTTCGATATAGCCCGCTCTGATGCCTTCCAGCCCTGCGACATCCTCGCGGATGGATAACTCGAC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:518:1306:1596/2 -TTGTAGCGCCAACAACCCCTTTGTGCCTTGGTAGCATCGCATCTGGGTATGTTATTAGTGGCTTGGCGTAGTCCCTCCTGCCTCAATCGTCTCTAGCCGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:520:1038:1354/2 -AAGAACTATATCTCAGCGGCCGCCGAAGGCGGTCCGCTGGAATGAAGGGTTAGAAAGCGGACTCACAGAAAACCGCTTATGGATGATCAGGCGATCCTCT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:523:913:1223/2 -TTTGGGCCCATTGCTCGGAGTGCCGTAGTAACTGCGTCGCGACGCTGGACGAGCGATGGGCCTCCTCGATGTACAGGCCTTCGATATAGCCCGCTCTGAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:530:730:1063/2 -CGCATCATCATGGGCTACCAGCACTTCGTTGGGCTCGGCCAGGGCTCCGGCGAAAAACTGGGCGATCTCGGTTTCGTGGTCATCCCCTTCCCACAGGAGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:535:784:1113/2 -CCTGCGACATCCTCGCGGATGGATAACTCGACATGCCCAACAACGGCCCCCGCATCATCATGGGCTACCAGCACTTCGTTGGGCTCGGCCAGGGCTCCGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:536:789:1104/2 -TCCTCGCGGATGGATAACTCGACATGCCCAACAACGGCCCCCGCATCATCATGGGCTACCAGCACTTCGTTGGGCTCGGCCAGGGCTCCGGCGAAAAACT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:538:1000:1308/2 -GGGTTAGAAAGCGGACTCACAGAAAACCGCTTATGGATGATCAGGCGATCCTCTCGATCCGATGCAAACGCCCGGCATCCCTGACTTTGGGCCCATTGCT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:540:767:1051/2 -GGCTACCAGCACTTCGTTGGGCTCGGCCAGGGCTCCGGCGAAAAACTGGGCGATCTCGGTTTCGTGGTCATCCCCTTCCCACAGGAGATTGCGAAGGCGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:541:1178:1470/2 -AACCTTCGACTCCTTAGATTTCGCCCGGAAGGTCGCGATCTTCCTTGGTGCACGTACAGCGGCCAAATAGGATTGAAAAGTGGACGAAATTCTTACACCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:545:1278:1573/2 -TGCCTTGGTAGCATCGCATCTGGGTATGTTATTAGTGGCTTGGCGTAGTCCCTCCTGCCTCAATCGTCTCTAGCCGCCAATTATGGTTGTTTCAGTACGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:552:868:1153/2 -GTACAGGCCTTCGATATAGCCCGCTCTGATGCCTTCCAGCCCTGCGACATCCTCGCGGATGGATAACTCGACATGCCCAACAACGGCCCCCGCATCATCA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:553:870:1175/2 -ACGAGCGATGGGCCTCCTCGATGTACAGGCCTTCGATATAGCCCGCTCTGATGCCTTCCAGCCCTGCGACATCCTCGCGGATGGATAACTCGACATGCCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:555:1081:1375/2 -CACCGTGGACAAGTATCCGGAAAGAACTATATCTCAGCGGCCGCCGAAGGCGGTCCGCTGGAATGAAGGGTTAGAAAGCGGACTCACAGAAAACCGCTTA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:556:941:1243/2 -AAACGCCCGGCATCCCTGACTTTGGGCCCATTGCTCGGAGTGCCGTAGTAACTGCGTCGCGACGCTGGACGAGCGATGGGCCTCCTCGATGTACAGGCCT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:559:735:1063/2 -CGCATCATCATGGGCTACCAGCACTTCGTTGGGCTCGGCCAGGGCTCCGGCGAAAAACTGGGCGATCTCGGTTTCGTGGTCATCCCCTTCCCACAGGAGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:561:834:1121/2 -CTTCCAGCCCTGCGACATCCTCGCGGATGGATAACTCGACATGCCCAACAACGGCCCCCGCATCATCATGGGCTACCAGCACTTCGTTGGGCTCGGCCAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:564:1098:1400/2 -GATTGAAAAGTGGACGAAATTCTTACACCGTGGACAAGTATCCGGAAAGAACTATATCTCAGCGGCCGCCGAAGGCGGTCCGCTGGAATGAAGGGTTAGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:568:1312:1631/2 -TAACGGCTTTTGGACCCCGCTCTAGCCCTGATTTATTGTAGCGCCAACAACCCCTTTGTGCCTTGGTAGCATCGCATCTGGGTATGTTATTAGTGGCTTG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:575:894:1174/2 -CGAGCGATGGGCCTCCTCGATGTACAGGCCTTCGATATAGCCCGCTCTGATGCCTTCCAGCCCTGCGACATCCTCGCGGATGGATAACTCGACATGCCCA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:579:1186:1521/2 -TCCTGCCTCAATCGTCTCTAGCCGCCAATTATGGTTGTTTCAGTACGTTAAAACCTTCGACTCCTTAGATTTCGCCCGGAAGGTCGCGATCTTCCTTGGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:585:900:1209/2 -TCGGAGTGCCGTAGTAACTGCGTCGCGACGCTGGACGAGCGATGGGCCTCCTCGATGTACAGGCCTTCGATATAGCCCGCTCTGATGCCTTCCAGCCCTG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:586:1305:1589/2 -GCCAACAACCCCTTTGTGCCTTGGTAGCATCGCATCTGGGTATGTTATTAGTGGCTTGGCGTAGTCCCTCCTGCCTCAATCGTCTCTAGCCGCCAATTAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:593:778:1063/2 -CGCATCATCATGGGCTACCAGCACTTCGTTGGGCTCGGCCAGGGCTCCGGCGAAAAACTGGGCGATCTCGGTTTCGTGGTCATCCCCTTCCCACAGGAGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:597:659:1016/2 -CGGCGAAAAACTGGGCGATCTCGGTTTCGTGGTCATCCCCTTCCCACAGGAGATTGCGAAGGCGTAACCAATCAGATGTATCCGAAACACGAACCGAGCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:598:1043:1318/2 -CTGGAATGAAGGGTTAGAAAGCGGACTCACAGAAAACCGCTTATGGATGATCAGGCGATCCTCTCGATCCGATGCAAACGCCCGGCATCCCTGACTTTGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:599:824:1109/2 -CGACATCCTCGCGGATGGATAACTCGACATGCCCAACAACGGCCCCCGCATCATCATGGGCTACCAGCACTTCGTTGGGCTCGGCCAGGGCTCCGGCGAA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:602:842:1134/2 -CCCGCTCTGATGCCTTCCAGCCCTGCGACATCCTCGCGGATGGATAACTCGACATGCCCAACAACGGCCCCCGCATCATCATGGGCTACCAGCACTTCGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:606:963:1237/2 -CCGGCATCCCTGACTTTGGGCCCATTGCTCGGAGTGCCGTAGTAACTGCGTCGCGACGCTGGACGAGCGATGGGCCTCCTCGATGTACAGGCCTTCGATA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:607:1139:1448/2 -GCCCGGAAGGTCGCGATCTTCCTTGGTGCACGTACAGCGGCCAAATAGGATTGAAAAGTGGACGAAATTCTTACACCGTGGACAAGTATCCGGAAAGAAC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_2__02__aac_6prime__1_AY553333:610:873:1156/2 -GATGTACAGGCCTTCGATATAGCCCGCTCTGATGCCTTCCAGCCCTGCGACATCCTCGCGGATGGATAACTCGACATGCCCAACAACGGCCCCCGCATCA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII diff --git a/ariba/tests/data/cluster_test_choose_best_gene.gene.fa b/ariba/tests/data/cluster_test_choose_best_gene.gene.fa new file mode 100644 index 00000000..6d31a2ed --- /dev/null +++ b/ariba/tests/data/cluster_test_choose_best_gene.gene.fa @@ -0,0 +1,6 @@ +>1 +AGCGCCTAGCTTTGGCACTTCAGGAGCGCCCGGAAATAATGGCGGGCGATGAAGGTTCTG +TAGGTACGCAAGATCCCTCTTAATCACAGTGGTGTAATCTGCGGGTCAGACCCTGTTAAC +CCGTGGCTTTCACACTCCCTCCTATGGGTAATCAATCCAGAAAGGGGCCGAAATGCAAAA +GTCTTAAGGACTCTGCGAGGCAAAGTACGGGCGAACTAAACCCCCGTGACAGGTCAGACG +TTGTTTCGGCAATCTGTCGCGCTCCCACACCTATAAGCGTACACCGTCTCTTCTGCCAGC diff --git a/ariba/tests/data/cluster_test_choose_best_gene/genes.fa b/ariba/tests/data/cluster_test_choose_best_gene/genes.fa new file mode 100644 index 00000000..ebf51a01 --- /dev/null +++ b/ariba/tests/data/cluster_test_choose_best_gene/genes.fa @@ -0,0 +1,18 @@ +>1 +AGCGCCTAGCTTTGGCACTTCAGGAGCGCCCGGAAATAATGGCGGGCGATGAAGGTTCTG +TAGGTACGCAAGATCCCTCTTAATCACAGTGGTGTAATCTGCGGGTCAGACCCTGTTAAC +CCGTGGCTTTCACACTCCCTCCTATGGGTAATCAATCCAGAAAGGGGCCGAAATGCAAAA +GTCTTAAGGACTCTGCGAGGCAAAGTACGGGCGAACTAAACCCCCGTGACAGGTCAGACG +TTGTTTCGGCAATCTGTCGCGCTCCCACACCTATAAGCGTACACCGTCTCTTCTGCCAGC +>2 +ATGGTACAAGACGGCCCTTTGCAGTCCTGTGTACTTGCGGGTCGCTCCTTTGCATTGAAT +TATCGAACATCGTCGCGTTCAAGATCCCGCGAAAAAAATTATAGATCGCAGGATATCACT +GCCAGTGGCATCTGTGTAAGCGCTTAGCCACGACGGTTGAGTAGGCCACATCCAAGTTCC +TGACGTTTTTTAGCGAGGTTGTCCGAGCGGCCGGCTGCTAGCTCTCTTATCGTGTGAACT +GATTGTTGTTTCTCAAGAGCTCGTTTTTTGCTTGCGAAG +>3 +AGGTGTACCCGTAAGCCGCTACTAGGTAATGATGAGCTAAGGGTCGACGCCTTCTCCGCA +AGATCCTATCATGATCACAAGTGCAGTACACGCGGACGTTATCGAAGAATGTTGAATTTT +TCATCGGATACAGGCAGGACCAGGTACAGATGGTGAGTTTATTTGTATAATGGCCCCGGT +TAGCTAGTACCGCGCCTGTGCGATATCCCCATTTTGCTCCTGCCGTGCTACTAGCGTCGC +CTCAACATCCGCCTCAGCAAGGACTATAATTGCGCAAAGCAAGTGCCAAGAACATTTGGT diff --git a/ariba/tests/data/cluster_test_choose_best_gene/reads_1.fq b/ariba/tests/data/cluster_test_choose_best_gene/reads_1.fq new file mode 100644 index 00000000..bd98e88d --- /dev/null +++ b/ariba/tests/data/cluster_test_choose_best_gene/reads_1.fq @@ -0,0 +1,180 @@ +@1:1:142:249/1 +CTATGGGTAATCAATCCAGAAAGGGGCCGAAATGCAAAAGTCTTAAGGAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:2:79:164/1 +CTTAATCACAGTGGTGTAATCTGCGGGTCAGACCCTGTTAACCCGTGGCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:3:66:162/1 +ACGCAAGATCCCTCTTAATCACAGTGGTGTAATCTGCGGGTCAGACCCTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:4:113:217/1 +CTGTTAACCCGTGGCTTTCACACTCCCTCCTATGGGTAATCAATCCAGAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:5:69:174/1 +CAAGATCCCTCTTAATCACAGTGGTGTAATCTGCGGGTCAGACCCTGTTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:6:49:156/1 +ATGAAGGTTCTGTAGGTACGCAAGATCCCTCTTAATCACAGTGGTGTAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:7:103:194/1 +GGGTCAGACCCTGTTAACCCGTGGCTTTCACACTCCCTCCTATGGGTAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:8:94:181/1 +GTAATCTGCGGGTCAGACCCTGTTAACCCGTGGCTTTCACACTCCCTCCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:9:100:206/1 +TGCGGGTCAGACCCTGTTAACCCGTGGCTTTCACACTCCCTCCTATGGGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:10:93:185/1 +TGTAATCTGCGGGTCAGACCCTGTTAACCCGTGGCTTTCACACTCCCTCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:11:72:166/1 +GATCCCTCTTAATCACAGTGGTGTAATCTGCGGGTCAGACCCTGTTAACC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:12:98:187/1 +TCTGCGGGTCAGACCCTGTTAACCCGTGGCTTTCACACTCCCTCCTATGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:13:111:229/1 +CCCTGTTAACCCGTGGCTTTCACACTCCCTCCTATGGGTAATCAATCCAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:14:73:170/1 +ATCCCTCTTAATCACAGTGGTGTAATCTGCGGGTCAGACCCTGTTAACCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:15:68:164/1 +GCAAGATCCCTCTTAATCACAGTGGTGTAATCTGCGGGTCAGACCCTGTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:16:130:234/1 +ATCTGTGTAAGCGCTTAGCCACGACGGTTGAGTTGGCCACATCCAAGTTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:17:78:190/1 +TTCAAGATCCCGCGAAAAAAATTATAGATCGCAGGATATCACTGCCAGTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:18:36:130/1 +TGCGCCACGCTCCTTTGCATTGAATTATCGAACATCGTCGCGTTCAAGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:19:31:119/1 +GTACTTGCGCCACGCTCCTTTGCATTGAATTATCGAACATCGTCGCGTTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:20:45:166/1 +CTCCTTTGCATTGAATTATCGAACATCGTCGCGTTCAAGATCCCGCGAAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:21:50:163/1 +TTGCATTGAATTATCGAACATCGTCGCGTTCAAGATCCCGCGAAAAAAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:22:119:227/1 +CTGCCAGTGGCATCTGTGTAAGCGCTTAGCCACGACGGTTGAGTTGGCCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:23:85:191/1 +TCCCGCGAAAAAAATTATAGATCGCAGGATATCACTGCCAGTGGCATCTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:24:34:149/1 +CTTGCGCCACGCTCCTTTGCATTGAATTATCGAACATCGTCGCGTTCAAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:25:139:236/1 +AGCGCTTAGCCACGACGGTTGAGTTGGCCACATCCAAGTTCCTGACGTTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:26:73:145/1 +TCGCGTTCAAGATCCCGCGAAAAAAATTATAGATCGCAGGATATCACTGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:27:39:139/1 +GCCACGCTCCTTTGCATTGAATTATCGAACATCGTCGCGTTCAAGATCCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:28:73:180/1 +TCGCGTTCAAGATCCCGCGAAAAAAATTATAGATCGCAGGATATCACTGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:29:143:216/1 +CTTAGCCACGACGGTTGAGTTGGCCACATCCAAGTTCCTGACGTTTTTTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:30:73:170/1 +TCGCGTTCAAGATCCCGCGAAAAAAATTATAGATCGCAGGATATCACTGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:31:155:249/1 +GAGTTTATTTGTATAATGGCCCCGGTTAGCTAGTACCGCGCCTGTGCGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:32:27:129/1 +TAATGATGAGCTAAGGGTCGACGCCTTCTCCGCAATGGAGATCCTATCAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:33:15:99/1 +GCCGCTACTAGGTAATGATGAGCTAAGGGTCGACGCCTTCTCCGCAATGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:34:81:172/1 +ACAAGTGCAGTACACGCGGACGTTATCGAAGAATGTTGAATCATCGGATA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:35:145:243/1 +TACAGATGGTGAGTTTATTTGTATAATGGCCCCGGTTAGCTAGTACCGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:36:62:163/1 +TGGAGATCCTATCATGATCACAAGTGCAGTACACGCGGACGTTATCGAAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:37:117:219/1 +TGAATCATCGGATACAGGCAGGACCAGGTACAGATGGTGAGTTTATTTGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:38:57:145/1 +CGCAATGGAGATCCTATCATGATCACAAGTGCAGTACACGCGGACGTTAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:39:40:152/1 +AGGGTCGACGCCTTCTCCGCAATGGAGATCCTATCATGATCACAAGTGCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:40:95:200/1 +CGCGGACGTTATCGAAGAATGTTGAATCATCGGATACAGGCAGGACCAGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:41:24:119/1 +AGGTAATGATGAGCTAAGGGTCGACGCCTTCTCCGCAATGGAGATCCTAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:42:41:153/1 +GGGTCGACGCCTTCTCCGCAATGGAGATCCTATCATGATCACAAGTGCAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:43:86:189/1 +TGCAGTACACGCGGACGTTATCGAAGAATGTTGAATCATCGGATACAGGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:44:25:110/1 +GGTAATGATGAGCTAAGGGTCGACGCCTTCTCCGCAATGGAGATCCTATC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:45:99:196/1 +GACGTTATCGAAGAATGTTGAATCATCGGATACAGGCAGGACCAGGTACA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII diff --git a/ariba/tests/data/cluster_test_choose_best_gene/reads_2.fq b/ariba/tests/data/cluster_test_choose_best_gene/reads_2.fq new file mode 100644 index 00000000..23083a69 --- /dev/null +++ b/ariba/tests/data/cluster_test_choose_best_gene/reads_2.fq @@ -0,0 +1,180 @@ +@1:1:142:249/2 +TGGCAGAAGAGACGGTGTACGCTTATAGGTGTGGGAGCGCGACAGATTGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:2:79:164/2 +CGCCCGTACTTTGCCTCGCAGAGTCCTTAAGACTTTTGCATTTCGGCCCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:3:66:162/2 +CCCGTACTTTGCCTCGCAGAGTCCTTAAGACTTTTGCATTTCGGCCCCTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:4:113:217/2 +GGGAGCGCGACAGATTGCCGAAACAACGTCTGACCTGTCACGGGGGTTTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:5:69:174/2 +GGGTTTAGTTCGCCCGTACTTTGCCTCGCAGAGTCCTTAAGACTTTTGCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:6:49:156/2 +CTTTGCCTCGCAGAGTCCTTAAGACTTTTGCATTTCGGCCCCTTTCTGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:7:103:194/2 +CAACGTCTGACCTGTCACGGGGGTTTAGTTCGCCCGTACTTTGCCTCGCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:8:94:181/2 +GTCACGGGGGTTTAGTTCGCCCGTACTTTGCCTCGCAGAGTCCTTAAGAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:9:100:206/2 +AGATTGCCGAAACAACGTCTGACCTGTCACGGGGGTTTAGTTCGCCCGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:10:93:185/2 +ACCTGTCACGGGGGTTTAGTTCGCCCGTACTTTGCCTCGCAGAGTCCTTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:11:72:166/2 +TTCGCCCGTACTTTGCCTCGCAGAGTCCTTAAGACTTTTGCATTTCGGCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:12:98:187/2 +TGACCTGTCACGGGGGTTTAGTTCGCCCGTACTTTGCCTCGCAGAGTCCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:13:111:229/2 +GCTTATAGGTGTGGGAGCGCGACAGATTGCCGAAACAACGTCTGACCTGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:14:73:170/2 +TTAGTTCGCCCGTACTTTGCCTCGCAGAGTCCTTAAGACTTTTGCATTTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:15:68:164/2 +CGCCCGTACTTTGCCTCGCAGAGTCCTTAAGACTTTTGCATTTCGGCCCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:16:130:234/2 +GAACCTTCGCAAGCAAAAAACGAGCTCTTGAGAAACAACAATCAGTTCAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:17:78:190/2 +GTTCACACGATAAGAGAGCTAGCAGCCGGCCGCTCGGACAACCTCGCTAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:18:36:130/2 +GAACTTGGATGTGGCCAACTCAACCGTCGTGGCTAAGCGCTTACACAGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:19:31:119/2 +TGGCCAACTCAACCGTCGTGGCTAAGCGCTTACACAGATGCCACTGGCAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:20:45:166/2 +GCCGGCCGCTCGGACAACCTCGCTAAAAAACGTCAGGAACTTGGATGTGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:21:50:163/2 +GGCCGCTCGGACAACCTCGCTAAAAAACGTCAGGAACTTGGATGTGGCCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:22:119:227/2 +CGCAAGCAAAAAACGAGCTCTTGAGAAACAACAATCAGTTCACACGATAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:23:85:191/2 +AGTTCACACGATAAGAGAGCTAGCAGCCGGCCGCTCGGACAACCTCGCTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:24:34:149/2 +CCTCGCTAAAAAACGTCAGGAACTTGGATGTGGCCAACTCAACCGTCGTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:25:139:236/2 +CGGAACCTTCGCAAGCAAAAAACGAGCTCTTGAGAAACAACAATCAGTTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:26:73:145/2 +GCTAAAAAACGTCAGGAACTTGGATGTGGCCAACTCAACCGTCGTGGCTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:27:39:139/2 +AAACGTCAGGAACTTGGATGTGGCCAACTCAACCGTCGTGGCTAAGCGCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:28:73:180/2 +TAAGAGAGCTAGCAGCCGGCCGCTCGGACAACCTCGCTAAAAAACGTCAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:29:143:216/2 +AACGAGCTCTTGAGAAACAACAATCAGTTCACACGATAAGAGAGCTAGCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:30:73:170/2 +AGCAGCCGGCCGCTCGGACAACCTCGCTAAAAAACGTCAGGAACTTGGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:31:155:249/2 +CAAATGTTCTTGGCACTTGCTTTGCGCAATTATAGTCCTTGCTGAGGCGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:32:27:129/2 +CGGGGCCATTATACAAATAAACTCACCATCTGTACCTGGTCCTGCCTGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:33:15:99/2 +TGTACCTGGTCCTGCCTGTATCCGATGATTCAACATTCTTCGATAACGTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:34:81:172/2 +AGGAGCAAAATGGGGATATCGCACAGGCGCGGTACTAGCTAACCGGGGCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:35:145:243/2 +TTCTTGGCACTTGCTTTGCGCAATTATAGTCCTTGCTGAGGCGGATGTTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:36:62:163/2 +ATGGGGATATCGCACAGGCGCGGTACTAGCTAACCGGGGCCATTATACAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:37:117:219/2 +TATAGTCCTTGCTGAGGCGGATGTTGAGGCGACGCTAGTAGCACGGCAGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:38:57:145/2 +CGCGGTACTAGCTAACCGGGGCCATTATACAAATAAACTCACCATCTGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:39:40:152/2 +GCACAGGCGCGGTACTAGCTAACCGGGGCCATTATACAAATAAACTCACC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:40:95:200/2 +GATGTTGAGGCGACGCTAGTAGCACGGCAGGAGCAAAATGGGGATATCGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:41:24:119/2 +ATACAAATAAACTCACCATCTGTACCTGGTCCTGCCTGTATCCGATGATT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:42:41:153/2 +CGCACAGGCGCGGTACTAGCTAACCGGGGCCATTATACAAATAAACTCAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:43:86:189/2 +GACGCTAGTAGCACGGCAGGAGCAAAATGGGGATATCGCACAGGCGCGGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:44:25:110/2 +AACTCACCATCTGTACCTGGTCCTGCCTGTATCCGATGATTCAACATTCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:45:99:196/2 +TTGAGGCGACGCTAGTAGCACGGCAGGAGCAAAATGGGGATATCGCACAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII diff --git a/ariba/tests/data/cluster_test_fix_contig_orientation/gene.fa b/ariba/tests/data/cluster_test_fix_contig_orientation.gene.fa similarity index 100% rename from ariba/tests/data/cluster_test_fix_contig_orientation/gene.fa rename to ariba/tests/data/cluster_test_fix_contig_orientation.gene.fa diff --git a/ariba/tests/data/cluster_test_fix_contig_orientation/genes.fa b/ariba/tests/data/cluster_test_fix_contig_orientation/genes.fa new file mode 100644 index 00000000..5d5102b8 --- /dev/null +++ b/ariba/tests/data/cluster_test_fix_contig_orientation/genes.fa @@ -0,0 +1,10 @@ +>gene +ACTTACCGGTTCGGGGTCTAAACCAACCATTAAACTGCGACAACCATTCATCCTGGAGTA +CGCTTCGGTCCACCATGATGGAGCGCCATGTGATGGGATTTCCAACCCCGTTGTTTCAGG +ACTCATGGCATTTACCACCGACAACCGTTTATAATCCATGAGCAAGGAATACAGTGGAGA +CAGGATTGGTTGTATTGGACTGAATACATGCCCCACTGTTACCCCGAAAGTTAACACGTA +CCCATAGTTTATTTAAACTAGGCACTCCCGATCAGCCAAGACTTAAAAAGGGGGATAGGA +ATATCAACGTAGTACTTCTCGGTTGATCCGTGTTTTTTAATCTAAAATATAATGTGTAGG +CAGCTATCGTGCTAATCGTTGAAATGAGCAGGCGAAATGCCGTTTACAACGACGCTAAAC +CTCCAAGTCGAATTAAGCCAAATTGTGCCTTCCATATGACCTCCACAGATTTGGGCTGGC +ACTGTCAGCGTAGTTGCGCT diff --git a/ariba/tests/data/cluster_test_generic/gene.fa b/ariba/tests/data/cluster_test_gapfill_with_gapfiller.gene.fa similarity index 100% rename from ariba/tests/data/cluster_test_generic/gene.fa rename to ariba/tests/data/cluster_test_gapfill_with_gapfiller.gene.fa diff --git a/ariba/tests/data/cluster_test_init_no_reads_1/gene.fa b/ariba/tests/data/cluster_test_gapfill_with_gapfiller/genes.fa similarity index 100% rename from ariba/tests/data/cluster_test_init_no_reads_1/gene.fa rename to ariba/tests/data/cluster_test_gapfill_with_gapfiller/genes.fa diff --git a/ariba/tests/data/cluster_test_init_no_reads_2/gene.fa b/ariba/tests/data/cluster_test_generic/genes.fa similarity index 100% rename from ariba/tests/data/cluster_test_init_no_reads_2/gene.fa rename to ariba/tests/data/cluster_test_generic/genes.fa diff --git a/ariba/tests/data/cluster_test_get_best_gene_by_alignment_score/genes.fa b/ariba/tests/data/cluster_test_get_best_gene_by_alignment_score/genes.fa new file mode 100644 index 00000000..ebf51a01 --- /dev/null +++ b/ariba/tests/data/cluster_test_get_best_gene_by_alignment_score/genes.fa @@ -0,0 +1,18 @@ +>1 +AGCGCCTAGCTTTGGCACTTCAGGAGCGCCCGGAAATAATGGCGGGCGATGAAGGTTCTG +TAGGTACGCAAGATCCCTCTTAATCACAGTGGTGTAATCTGCGGGTCAGACCCTGTTAAC +CCGTGGCTTTCACACTCCCTCCTATGGGTAATCAATCCAGAAAGGGGCCGAAATGCAAAA +GTCTTAAGGACTCTGCGAGGCAAAGTACGGGCGAACTAAACCCCCGTGACAGGTCAGACG +TTGTTTCGGCAATCTGTCGCGCTCCCACACCTATAAGCGTACACCGTCTCTTCTGCCAGC +>2 +ATGGTACAAGACGGCCCTTTGCAGTCCTGTGTACTTGCGGGTCGCTCCTTTGCATTGAAT +TATCGAACATCGTCGCGTTCAAGATCCCGCGAAAAAAATTATAGATCGCAGGATATCACT +GCCAGTGGCATCTGTGTAAGCGCTTAGCCACGACGGTTGAGTAGGCCACATCCAAGTTCC +TGACGTTTTTTAGCGAGGTTGTCCGAGCGGCCGGCTGCTAGCTCTCTTATCGTGTGAACT +GATTGTTGTTTCTCAAGAGCTCGTTTTTTGCTTGCGAAG +>3 +AGGTGTACCCGTAAGCCGCTACTAGGTAATGATGAGCTAAGGGTCGACGCCTTCTCCGCA +AGATCCTATCATGATCACAAGTGCAGTACACGCGGACGTTATCGAAGAATGTTGAATTTT +TCATCGGATACAGGCAGGACCAGGTACAGATGGTGAGTTTATTTGTATAATGGCCCCGGT +TAGCTAGTACCGCGCCTGTGCGATATCCCCATTTTGCTCCTGCCGTGCTACTAGCGTCGC +CTCAACATCCGCCTCAGCAAGGACTATAATTGCGCAAAGCAAGTGCCAAGAACATTTGGT diff --git a/ariba/tests/data/cluster_test_get_best_gene_by_alignment_score/reads_1.fq b/ariba/tests/data/cluster_test_get_best_gene_by_alignment_score/reads_1.fq new file mode 100644 index 00000000..bd98e88d --- /dev/null +++ b/ariba/tests/data/cluster_test_get_best_gene_by_alignment_score/reads_1.fq @@ -0,0 +1,180 @@ +@1:1:142:249/1 +CTATGGGTAATCAATCCAGAAAGGGGCCGAAATGCAAAAGTCTTAAGGAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:2:79:164/1 +CTTAATCACAGTGGTGTAATCTGCGGGTCAGACCCTGTTAACCCGTGGCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:3:66:162/1 +ACGCAAGATCCCTCTTAATCACAGTGGTGTAATCTGCGGGTCAGACCCTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:4:113:217/1 +CTGTTAACCCGTGGCTTTCACACTCCCTCCTATGGGTAATCAATCCAGAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:5:69:174/1 +CAAGATCCCTCTTAATCACAGTGGTGTAATCTGCGGGTCAGACCCTGTTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:6:49:156/1 +ATGAAGGTTCTGTAGGTACGCAAGATCCCTCTTAATCACAGTGGTGTAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:7:103:194/1 +GGGTCAGACCCTGTTAACCCGTGGCTTTCACACTCCCTCCTATGGGTAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:8:94:181/1 +GTAATCTGCGGGTCAGACCCTGTTAACCCGTGGCTTTCACACTCCCTCCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:9:100:206/1 +TGCGGGTCAGACCCTGTTAACCCGTGGCTTTCACACTCCCTCCTATGGGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:10:93:185/1 +TGTAATCTGCGGGTCAGACCCTGTTAACCCGTGGCTTTCACACTCCCTCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:11:72:166/1 +GATCCCTCTTAATCACAGTGGTGTAATCTGCGGGTCAGACCCTGTTAACC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:12:98:187/1 +TCTGCGGGTCAGACCCTGTTAACCCGTGGCTTTCACACTCCCTCCTATGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:13:111:229/1 +CCCTGTTAACCCGTGGCTTTCACACTCCCTCCTATGGGTAATCAATCCAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:14:73:170/1 +ATCCCTCTTAATCACAGTGGTGTAATCTGCGGGTCAGACCCTGTTAACCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:15:68:164/1 +GCAAGATCCCTCTTAATCACAGTGGTGTAATCTGCGGGTCAGACCCTGTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:16:130:234/1 +ATCTGTGTAAGCGCTTAGCCACGACGGTTGAGTTGGCCACATCCAAGTTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:17:78:190/1 +TTCAAGATCCCGCGAAAAAAATTATAGATCGCAGGATATCACTGCCAGTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:18:36:130/1 +TGCGCCACGCTCCTTTGCATTGAATTATCGAACATCGTCGCGTTCAAGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:19:31:119/1 +GTACTTGCGCCACGCTCCTTTGCATTGAATTATCGAACATCGTCGCGTTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:20:45:166/1 +CTCCTTTGCATTGAATTATCGAACATCGTCGCGTTCAAGATCCCGCGAAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:21:50:163/1 +TTGCATTGAATTATCGAACATCGTCGCGTTCAAGATCCCGCGAAAAAAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:22:119:227/1 +CTGCCAGTGGCATCTGTGTAAGCGCTTAGCCACGACGGTTGAGTTGGCCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:23:85:191/1 +TCCCGCGAAAAAAATTATAGATCGCAGGATATCACTGCCAGTGGCATCTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:24:34:149/1 +CTTGCGCCACGCTCCTTTGCATTGAATTATCGAACATCGTCGCGTTCAAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:25:139:236/1 +AGCGCTTAGCCACGACGGTTGAGTTGGCCACATCCAAGTTCCTGACGTTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:26:73:145/1 +TCGCGTTCAAGATCCCGCGAAAAAAATTATAGATCGCAGGATATCACTGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:27:39:139/1 +GCCACGCTCCTTTGCATTGAATTATCGAACATCGTCGCGTTCAAGATCCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:28:73:180/1 +TCGCGTTCAAGATCCCGCGAAAAAAATTATAGATCGCAGGATATCACTGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:29:143:216/1 +CTTAGCCACGACGGTTGAGTTGGCCACATCCAAGTTCCTGACGTTTTTTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:30:73:170/1 +TCGCGTTCAAGATCCCGCGAAAAAAATTATAGATCGCAGGATATCACTGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:31:155:249/1 +GAGTTTATTTGTATAATGGCCCCGGTTAGCTAGTACCGCGCCTGTGCGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:32:27:129/1 +TAATGATGAGCTAAGGGTCGACGCCTTCTCCGCAATGGAGATCCTATCAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:33:15:99/1 +GCCGCTACTAGGTAATGATGAGCTAAGGGTCGACGCCTTCTCCGCAATGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:34:81:172/1 +ACAAGTGCAGTACACGCGGACGTTATCGAAGAATGTTGAATCATCGGATA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:35:145:243/1 +TACAGATGGTGAGTTTATTTGTATAATGGCCCCGGTTAGCTAGTACCGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:36:62:163/1 +TGGAGATCCTATCATGATCACAAGTGCAGTACACGCGGACGTTATCGAAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:37:117:219/1 +TGAATCATCGGATACAGGCAGGACCAGGTACAGATGGTGAGTTTATTTGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:38:57:145/1 +CGCAATGGAGATCCTATCATGATCACAAGTGCAGTACACGCGGACGTTAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:39:40:152/1 +AGGGTCGACGCCTTCTCCGCAATGGAGATCCTATCATGATCACAAGTGCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:40:95:200/1 +CGCGGACGTTATCGAAGAATGTTGAATCATCGGATACAGGCAGGACCAGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:41:24:119/1 +AGGTAATGATGAGCTAAGGGTCGACGCCTTCTCCGCAATGGAGATCCTAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:42:41:153/1 +GGGTCGACGCCTTCTCCGCAATGGAGATCCTATCATGATCACAAGTGCAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:43:86:189/1 +TGCAGTACACGCGGACGTTATCGAAGAATGTTGAATCATCGGATACAGGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:44:25:110/1 +GGTAATGATGAGCTAAGGGTCGACGCCTTCTCCGCAATGGAGATCCTATC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:45:99:196/1 +GACGTTATCGAAGAATGTTGAATCATCGGATACAGGCAGGACCAGGTACA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII diff --git a/ariba/tests/data/cluster_test_get_best_gene_by_alignment_score/reads_2.fq b/ariba/tests/data/cluster_test_get_best_gene_by_alignment_score/reads_2.fq new file mode 100644 index 00000000..23083a69 --- /dev/null +++ b/ariba/tests/data/cluster_test_get_best_gene_by_alignment_score/reads_2.fq @@ -0,0 +1,180 @@ +@1:1:142:249/2 +TGGCAGAAGAGACGGTGTACGCTTATAGGTGTGGGAGCGCGACAGATTGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:2:79:164/2 +CGCCCGTACTTTGCCTCGCAGAGTCCTTAAGACTTTTGCATTTCGGCCCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:3:66:162/2 +CCCGTACTTTGCCTCGCAGAGTCCTTAAGACTTTTGCATTTCGGCCCCTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:4:113:217/2 +GGGAGCGCGACAGATTGCCGAAACAACGTCTGACCTGTCACGGGGGTTTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:5:69:174/2 +GGGTTTAGTTCGCCCGTACTTTGCCTCGCAGAGTCCTTAAGACTTTTGCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:6:49:156/2 +CTTTGCCTCGCAGAGTCCTTAAGACTTTTGCATTTCGGCCCCTTTCTGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:7:103:194/2 +CAACGTCTGACCTGTCACGGGGGTTTAGTTCGCCCGTACTTTGCCTCGCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:8:94:181/2 +GTCACGGGGGTTTAGTTCGCCCGTACTTTGCCTCGCAGAGTCCTTAAGAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:9:100:206/2 +AGATTGCCGAAACAACGTCTGACCTGTCACGGGGGTTTAGTTCGCCCGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:10:93:185/2 +ACCTGTCACGGGGGTTTAGTTCGCCCGTACTTTGCCTCGCAGAGTCCTTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:11:72:166/2 +TTCGCCCGTACTTTGCCTCGCAGAGTCCTTAAGACTTTTGCATTTCGGCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:12:98:187/2 +TGACCTGTCACGGGGGTTTAGTTCGCCCGTACTTTGCCTCGCAGAGTCCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:13:111:229/2 +GCTTATAGGTGTGGGAGCGCGACAGATTGCCGAAACAACGTCTGACCTGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:14:73:170/2 +TTAGTTCGCCCGTACTTTGCCTCGCAGAGTCCTTAAGACTTTTGCATTTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:15:68:164/2 +CGCCCGTACTTTGCCTCGCAGAGTCCTTAAGACTTTTGCATTTCGGCCCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:16:130:234/2 +GAACCTTCGCAAGCAAAAAACGAGCTCTTGAGAAACAACAATCAGTTCAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:17:78:190/2 +GTTCACACGATAAGAGAGCTAGCAGCCGGCCGCTCGGACAACCTCGCTAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:18:36:130/2 +GAACTTGGATGTGGCCAACTCAACCGTCGTGGCTAAGCGCTTACACAGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:19:31:119/2 +TGGCCAACTCAACCGTCGTGGCTAAGCGCTTACACAGATGCCACTGGCAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:20:45:166/2 +GCCGGCCGCTCGGACAACCTCGCTAAAAAACGTCAGGAACTTGGATGTGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:21:50:163/2 +GGCCGCTCGGACAACCTCGCTAAAAAACGTCAGGAACTTGGATGTGGCCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:22:119:227/2 +CGCAAGCAAAAAACGAGCTCTTGAGAAACAACAATCAGTTCACACGATAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:23:85:191/2 +AGTTCACACGATAAGAGAGCTAGCAGCCGGCCGCTCGGACAACCTCGCTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:24:34:149/2 +CCTCGCTAAAAAACGTCAGGAACTTGGATGTGGCCAACTCAACCGTCGTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:25:139:236/2 +CGGAACCTTCGCAAGCAAAAAACGAGCTCTTGAGAAACAACAATCAGTTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:26:73:145/2 +GCTAAAAAACGTCAGGAACTTGGATGTGGCCAACTCAACCGTCGTGGCTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:27:39:139/2 +AAACGTCAGGAACTTGGATGTGGCCAACTCAACCGTCGTGGCTAAGCGCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:28:73:180/2 +TAAGAGAGCTAGCAGCCGGCCGCTCGGACAACCTCGCTAAAAAACGTCAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:29:143:216/2 +AACGAGCTCTTGAGAAACAACAATCAGTTCACACGATAAGAGAGCTAGCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:30:73:170/2 +AGCAGCCGGCCGCTCGGACAACCTCGCTAAAAAACGTCAGGAACTTGGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:31:155:249/2 +CAAATGTTCTTGGCACTTGCTTTGCGCAATTATAGTCCTTGCTGAGGCGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:32:27:129/2 +CGGGGCCATTATACAAATAAACTCACCATCTGTACCTGGTCCTGCCTGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:33:15:99/2 +TGTACCTGGTCCTGCCTGTATCCGATGATTCAACATTCTTCGATAACGTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:34:81:172/2 +AGGAGCAAAATGGGGATATCGCACAGGCGCGGTACTAGCTAACCGGGGCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:35:145:243/2 +TTCTTGGCACTTGCTTTGCGCAATTATAGTCCTTGCTGAGGCGGATGTTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:36:62:163/2 +ATGGGGATATCGCACAGGCGCGGTACTAGCTAACCGGGGCCATTATACAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:37:117:219/2 +TATAGTCCTTGCTGAGGCGGATGTTGAGGCGACGCTAGTAGCACGGCAGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:38:57:145/2 +CGCGGTACTAGCTAACCGGGGCCATTATACAAATAAACTCACCATCTGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:39:40:152/2 +GCACAGGCGCGGTACTAGCTAACCGGGGCCATTATACAAATAAACTCACC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:40:95:200/2 +GATGTTGAGGCGACGCTAGTAGCACGGCAGGAGCAAAATGGGGATATCGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:41:24:119/2 +ATACAAATAAACTCACCATCTGTACCTGGTCCTGCCTGTATCCGATGATT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:42:41:153/2 +CGCACAGGCGCGGTACTAGCTAACCGGGGCCATTATACAAATAAACTCAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:43:86:189/2 +GACGCTAGTAGCACGGCAGGAGCAAAATGGGGATATCGCACAGGCGCGGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:44:25:110/2 +AACTCACCATCTGTACCTGGTCCTGCCTGTATCCGATGATTCAACATTCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:45:99:196/2 +TTGAGGCGACGCTAGTAGCACGGCAGGAGCAAAATGGGGATATCGCACAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII diff --git a/ariba/tests/data/cluster_test_get_gene/gene.fa b/ariba/tests/data/cluster_test_get_gene/gene.fa deleted file mode 100644 index c20d11d8..00000000 --- a/ariba/tests/data/cluster_test_get_gene/gene.fa +++ /dev/null @@ -1,2 +0,0 @@ ->name_of_gene -CATGCGAAAGAAAAC diff --git a/ariba/tests/data/cluster_test_get_gene/reads_1.fq b/ariba/tests/data/cluster_test_get_gene/reads_1.fq deleted file mode 100644 index 6ff1e12f..00000000 --- a/ariba/tests/data/cluster_test_get_gene/reads_1.fq +++ /dev/null @@ -1,4 +0,0 @@ -@read1/1 -ACGTACGT -+ -IIIIIIII diff --git a/ariba/tests/data/cluster_test_get_gene/reads_2.fq b/ariba/tests/data/cluster_test_get_gene/reads_2.fq deleted file mode 100644 index 2eb387ff..00000000 --- a/ariba/tests/data/cluster_test_get_gene/reads_2.fq +++ /dev/null @@ -1,4 +0,0 @@ -@read1/2 -ACGTACGT -+ -IIIIIIII diff --git a/ariba/tests/data/cluster_test_get_total_alignment_score/genes.fa b/ariba/tests/data/cluster_test_get_total_alignment_score/genes.fa new file mode 100644 index 00000000..ebf51a01 --- /dev/null +++ b/ariba/tests/data/cluster_test_get_total_alignment_score/genes.fa @@ -0,0 +1,18 @@ +>1 +AGCGCCTAGCTTTGGCACTTCAGGAGCGCCCGGAAATAATGGCGGGCGATGAAGGTTCTG +TAGGTACGCAAGATCCCTCTTAATCACAGTGGTGTAATCTGCGGGTCAGACCCTGTTAAC +CCGTGGCTTTCACACTCCCTCCTATGGGTAATCAATCCAGAAAGGGGCCGAAATGCAAAA +GTCTTAAGGACTCTGCGAGGCAAAGTACGGGCGAACTAAACCCCCGTGACAGGTCAGACG +TTGTTTCGGCAATCTGTCGCGCTCCCACACCTATAAGCGTACACCGTCTCTTCTGCCAGC +>2 +ATGGTACAAGACGGCCCTTTGCAGTCCTGTGTACTTGCGGGTCGCTCCTTTGCATTGAAT +TATCGAACATCGTCGCGTTCAAGATCCCGCGAAAAAAATTATAGATCGCAGGATATCACT +GCCAGTGGCATCTGTGTAAGCGCTTAGCCACGACGGTTGAGTAGGCCACATCCAAGTTCC +TGACGTTTTTTAGCGAGGTTGTCCGAGCGGCCGGCTGCTAGCTCTCTTATCGTGTGAACT +GATTGTTGTTTCTCAAGAGCTCGTTTTTTGCTTGCGAAG +>3 +AGGTGTACCCGTAAGCCGCTACTAGGTAATGATGAGCTAAGGGTCGACGCCTTCTCCGCA +AGATCCTATCATGATCACAAGTGCAGTACACGCGGACGTTATCGAAGAATGTTGAATTTT +TCATCGGATACAGGCAGGACCAGGTACAGATGGTGAGTTTATTTGTATAATGGCCCCGGT +TAGCTAGTACCGCGCCTGTGCGATATCCCCATTTTGCTCCTGCCGTGCTACTAGCGTCGC +CTCAACATCCGCCTCAGCAAGGACTATAATTGCGCAAAGCAAGTGCCAAGAACATTTGGT diff --git a/ariba/tests/data/cluster_test_get_total_alignment_score/reads_1.fq b/ariba/tests/data/cluster_test_get_total_alignment_score/reads_1.fq new file mode 100644 index 00000000..bd98e88d --- /dev/null +++ b/ariba/tests/data/cluster_test_get_total_alignment_score/reads_1.fq @@ -0,0 +1,180 @@ +@1:1:142:249/1 +CTATGGGTAATCAATCCAGAAAGGGGCCGAAATGCAAAAGTCTTAAGGAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:2:79:164/1 +CTTAATCACAGTGGTGTAATCTGCGGGTCAGACCCTGTTAACCCGTGGCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:3:66:162/1 +ACGCAAGATCCCTCTTAATCACAGTGGTGTAATCTGCGGGTCAGACCCTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:4:113:217/1 +CTGTTAACCCGTGGCTTTCACACTCCCTCCTATGGGTAATCAATCCAGAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:5:69:174/1 +CAAGATCCCTCTTAATCACAGTGGTGTAATCTGCGGGTCAGACCCTGTTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:6:49:156/1 +ATGAAGGTTCTGTAGGTACGCAAGATCCCTCTTAATCACAGTGGTGTAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:7:103:194/1 +GGGTCAGACCCTGTTAACCCGTGGCTTTCACACTCCCTCCTATGGGTAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:8:94:181/1 +GTAATCTGCGGGTCAGACCCTGTTAACCCGTGGCTTTCACACTCCCTCCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:9:100:206/1 +TGCGGGTCAGACCCTGTTAACCCGTGGCTTTCACACTCCCTCCTATGGGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:10:93:185/1 +TGTAATCTGCGGGTCAGACCCTGTTAACCCGTGGCTTTCACACTCCCTCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:11:72:166/1 +GATCCCTCTTAATCACAGTGGTGTAATCTGCGGGTCAGACCCTGTTAACC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:12:98:187/1 +TCTGCGGGTCAGACCCTGTTAACCCGTGGCTTTCACACTCCCTCCTATGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:13:111:229/1 +CCCTGTTAACCCGTGGCTTTCACACTCCCTCCTATGGGTAATCAATCCAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:14:73:170/1 +ATCCCTCTTAATCACAGTGGTGTAATCTGCGGGTCAGACCCTGTTAACCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:15:68:164/1 +GCAAGATCCCTCTTAATCACAGTGGTGTAATCTGCGGGTCAGACCCTGTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:16:130:234/1 +ATCTGTGTAAGCGCTTAGCCACGACGGTTGAGTTGGCCACATCCAAGTTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:17:78:190/1 +TTCAAGATCCCGCGAAAAAAATTATAGATCGCAGGATATCACTGCCAGTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:18:36:130/1 +TGCGCCACGCTCCTTTGCATTGAATTATCGAACATCGTCGCGTTCAAGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:19:31:119/1 +GTACTTGCGCCACGCTCCTTTGCATTGAATTATCGAACATCGTCGCGTTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:20:45:166/1 +CTCCTTTGCATTGAATTATCGAACATCGTCGCGTTCAAGATCCCGCGAAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:21:50:163/1 +TTGCATTGAATTATCGAACATCGTCGCGTTCAAGATCCCGCGAAAAAAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:22:119:227/1 +CTGCCAGTGGCATCTGTGTAAGCGCTTAGCCACGACGGTTGAGTTGGCCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:23:85:191/1 +TCCCGCGAAAAAAATTATAGATCGCAGGATATCACTGCCAGTGGCATCTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:24:34:149/1 +CTTGCGCCACGCTCCTTTGCATTGAATTATCGAACATCGTCGCGTTCAAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:25:139:236/1 +AGCGCTTAGCCACGACGGTTGAGTTGGCCACATCCAAGTTCCTGACGTTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:26:73:145/1 +TCGCGTTCAAGATCCCGCGAAAAAAATTATAGATCGCAGGATATCACTGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:27:39:139/1 +GCCACGCTCCTTTGCATTGAATTATCGAACATCGTCGCGTTCAAGATCCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:28:73:180/1 +TCGCGTTCAAGATCCCGCGAAAAAAATTATAGATCGCAGGATATCACTGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:29:143:216/1 +CTTAGCCACGACGGTTGAGTTGGCCACATCCAAGTTCCTGACGTTTTTTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:30:73:170/1 +TCGCGTTCAAGATCCCGCGAAAAAAATTATAGATCGCAGGATATCACTGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:31:155:249/1 +GAGTTTATTTGTATAATGGCCCCGGTTAGCTAGTACCGCGCCTGTGCGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:32:27:129/1 +TAATGATGAGCTAAGGGTCGACGCCTTCTCCGCAATGGAGATCCTATCAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:33:15:99/1 +GCCGCTACTAGGTAATGATGAGCTAAGGGTCGACGCCTTCTCCGCAATGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:34:81:172/1 +ACAAGTGCAGTACACGCGGACGTTATCGAAGAATGTTGAATCATCGGATA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:35:145:243/1 +TACAGATGGTGAGTTTATTTGTATAATGGCCCCGGTTAGCTAGTACCGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:36:62:163/1 +TGGAGATCCTATCATGATCACAAGTGCAGTACACGCGGACGTTATCGAAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:37:117:219/1 +TGAATCATCGGATACAGGCAGGACCAGGTACAGATGGTGAGTTTATTTGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:38:57:145/1 +CGCAATGGAGATCCTATCATGATCACAAGTGCAGTACACGCGGACGTTAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:39:40:152/1 +AGGGTCGACGCCTTCTCCGCAATGGAGATCCTATCATGATCACAAGTGCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:40:95:200/1 +CGCGGACGTTATCGAAGAATGTTGAATCATCGGATACAGGCAGGACCAGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:41:24:119/1 +AGGTAATGATGAGCTAAGGGTCGACGCCTTCTCCGCAATGGAGATCCTAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:42:41:153/1 +GGGTCGACGCCTTCTCCGCAATGGAGATCCTATCATGATCACAAGTGCAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:43:86:189/1 +TGCAGTACACGCGGACGTTATCGAAGAATGTTGAATCATCGGATACAGGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:44:25:110/1 +GGTAATGATGAGCTAAGGGTCGACGCCTTCTCCGCAATGGAGATCCTATC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:45:99:196/1 +GACGTTATCGAAGAATGTTGAATCATCGGATACAGGCAGGACCAGGTACA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII diff --git a/ariba/tests/data/cluster_test_get_total_alignment_score/reads_2.fq b/ariba/tests/data/cluster_test_get_total_alignment_score/reads_2.fq new file mode 100644 index 00000000..23083a69 --- /dev/null +++ b/ariba/tests/data/cluster_test_get_total_alignment_score/reads_2.fq @@ -0,0 +1,180 @@ +@1:1:142:249/2 +TGGCAGAAGAGACGGTGTACGCTTATAGGTGTGGGAGCGCGACAGATTGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:2:79:164/2 +CGCCCGTACTTTGCCTCGCAGAGTCCTTAAGACTTTTGCATTTCGGCCCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:3:66:162/2 +CCCGTACTTTGCCTCGCAGAGTCCTTAAGACTTTTGCATTTCGGCCCCTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:4:113:217/2 +GGGAGCGCGACAGATTGCCGAAACAACGTCTGACCTGTCACGGGGGTTTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:5:69:174/2 +GGGTTTAGTTCGCCCGTACTTTGCCTCGCAGAGTCCTTAAGACTTTTGCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:6:49:156/2 +CTTTGCCTCGCAGAGTCCTTAAGACTTTTGCATTTCGGCCCCTTTCTGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:7:103:194/2 +CAACGTCTGACCTGTCACGGGGGTTTAGTTCGCCCGTACTTTGCCTCGCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:8:94:181/2 +GTCACGGGGGTTTAGTTCGCCCGTACTTTGCCTCGCAGAGTCCTTAAGAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:9:100:206/2 +AGATTGCCGAAACAACGTCTGACCTGTCACGGGGGTTTAGTTCGCCCGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:10:93:185/2 +ACCTGTCACGGGGGTTTAGTTCGCCCGTACTTTGCCTCGCAGAGTCCTTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:11:72:166/2 +TTCGCCCGTACTTTGCCTCGCAGAGTCCTTAAGACTTTTGCATTTCGGCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:12:98:187/2 +TGACCTGTCACGGGGGTTTAGTTCGCCCGTACTTTGCCTCGCAGAGTCCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:13:111:229/2 +GCTTATAGGTGTGGGAGCGCGACAGATTGCCGAAACAACGTCTGACCTGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:14:73:170/2 +TTAGTTCGCCCGTACTTTGCCTCGCAGAGTCCTTAAGACTTTTGCATTTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@1:15:68:164/2 +CGCCCGTACTTTGCCTCGCAGAGTCCTTAAGACTTTTGCATTTCGGCCCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:16:130:234/2 +GAACCTTCGCAAGCAAAAAACGAGCTCTTGAGAAACAACAATCAGTTCAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:17:78:190/2 +GTTCACACGATAAGAGAGCTAGCAGCCGGCCGCTCGGACAACCTCGCTAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:18:36:130/2 +GAACTTGGATGTGGCCAACTCAACCGTCGTGGCTAAGCGCTTACACAGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:19:31:119/2 +TGGCCAACTCAACCGTCGTGGCTAAGCGCTTACACAGATGCCACTGGCAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:20:45:166/2 +GCCGGCCGCTCGGACAACCTCGCTAAAAAACGTCAGGAACTTGGATGTGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:21:50:163/2 +GGCCGCTCGGACAACCTCGCTAAAAAACGTCAGGAACTTGGATGTGGCCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:22:119:227/2 +CGCAAGCAAAAAACGAGCTCTTGAGAAACAACAATCAGTTCACACGATAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:23:85:191/2 +AGTTCACACGATAAGAGAGCTAGCAGCCGGCCGCTCGGACAACCTCGCTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:24:34:149/2 +CCTCGCTAAAAAACGTCAGGAACTTGGATGTGGCCAACTCAACCGTCGTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:25:139:236/2 +CGGAACCTTCGCAAGCAAAAAACGAGCTCTTGAGAAACAACAATCAGTTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:26:73:145/2 +GCTAAAAAACGTCAGGAACTTGGATGTGGCCAACTCAACCGTCGTGGCTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:27:39:139/2 +AAACGTCAGGAACTTGGATGTGGCCAACTCAACCGTCGTGGCTAAGCGCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:28:73:180/2 +TAAGAGAGCTAGCAGCCGGCCGCTCGGACAACCTCGCTAAAAAACGTCAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:29:143:216/2 +AACGAGCTCTTGAGAAACAACAATCAGTTCACACGATAAGAGAGCTAGCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2:30:73:170/2 +AGCAGCCGGCCGCTCGGACAACCTCGCTAAAAAACGTCAGGAACTTGGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:31:155:249/2 +CAAATGTTCTTGGCACTTGCTTTGCGCAATTATAGTCCTTGCTGAGGCGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:32:27:129/2 +CGGGGCCATTATACAAATAAACTCACCATCTGTACCTGGTCCTGCCTGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:33:15:99/2 +TGTACCTGGTCCTGCCTGTATCCGATGATTCAACATTCTTCGATAACGTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:34:81:172/2 +AGGAGCAAAATGGGGATATCGCACAGGCGCGGTACTAGCTAACCGGGGCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:35:145:243/2 +TTCTTGGCACTTGCTTTGCGCAATTATAGTCCTTGCTGAGGCGGATGTTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:36:62:163/2 +ATGGGGATATCGCACAGGCGCGGTACTAGCTAACCGGGGCCATTATACAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:37:117:219/2 +TATAGTCCTTGCTGAGGCGGATGTTGAGGCGACGCTAGTAGCACGGCAGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:38:57:145/2 +CGCGGTACTAGCTAACCGGGGCCATTATACAAATAAACTCACCATCTGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:39:40:152/2 +GCACAGGCGCGGTACTAGCTAACCGGGGCCATTATACAAATAAACTCACC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:40:95:200/2 +GATGTTGAGGCGACGCTAGTAGCACGGCAGGAGCAAAATGGGGATATCGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:41:24:119/2 +ATACAAATAAACTCACCATCTGTACCTGGTCCTGCCTGTATCCGATGATT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:42:41:153/2 +CGCACAGGCGCGGTACTAGCTAACCGGGGCCATTATACAAATAAACTCAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:43:86:189/2 +GACGCTAGTAGCACGGCAGGAGCAAAATGGGGATATCGCACAGGCGCGGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:44:25:110/2 +AACTCACCATCTGTACCTGGTCCTGCCTGTATCCGATGATTCAACATTCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3:45:99:196/2 +TTGAGGCGACGCTAGTAGCACGGCAGGAGCAAAATGGGGATATCGCACAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII diff --git a/ariba/tests/data/cluster_test_load_final_contigs/gene.fa b/ariba/tests/data/cluster_test_init_no_reads_1/genes.fa similarity index 100% rename from ariba/tests/data/cluster_test_load_final_contigs/gene.fa rename to ariba/tests/data/cluster_test_init_no_reads_1/genes.fa diff --git a/ariba/tests/data/cluster_test_parse_assembly_bam/gene.fa b/ariba/tests/data/cluster_test_init_no_reads_2/genes.fa similarity index 100% rename from ariba/tests/data/cluster_test_parse_assembly_bam/gene.fa rename to ariba/tests/data/cluster_test_init_no_reads_2/genes.fa diff --git a/ariba/tests/data/cluster_test_rename_scaffolds/gene.fa b/ariba/tests/data/cluster_test_load_final_contigs/genes.fa similarity index 100% rename from ariba/tests/data/cluster_test_rename_scaffolds/gene.fa rename to ariba/tests/data/cluster_test_load_final_contigs/genes.fa diff --git a/ariba/tests/data/cluster_test_scaffold_with_sspace/gene.fa b/ariba/tests/data/cluster_test_parse_assembly_bam/genes.fa similarity index 100% rename from ariba/tests/data/cluster_test_scaffold_with_sspace/gene.fa rename to ariba/tests/data/cluster_test_parse_assembly_bam/genes.fa diff --git a/ariba/tests/data/cluster_test_parse_assembly_vs_gene_coords/gene.fa b/ariba/tests/data/cluster_test_parse_assembly_vs_gene_coords/genes.fa similarity index 100% rename from ariba/tests/data/cluster_test_parse_assembly_vs_gene_coords/gene.fa rename to ariba/tests/data/cluster_test_parse_assembly_vs_gene_coords/genes.fa diff --git a/ariba/tests/data/cluster_test_set_assembly_kmer/gene.fa b/ariba/tests/data/cluster_test_rename_scaffolds/genes.fa similarity index 100% rename from ariba/tests/data/cluster_test_set_assembly_kmer/gene.fa rename to ariba/tests/data/cluster_test_rename_scaffolds/genes.fa diff --git a/ariba/tests/data/cluster_test_scaffold_with_sspace.gene.fa b/ariba/tests/data/cluster_test_scaffold_with_sspace.gene.fa new file mode 100644 index 00000000..042775d6 --- /dev/null +++ b/ariba/tests/data/cluster_test_scaffold_with_sspace.gene.fa @@ -0,0 +1,2 @@ +>name_of_gene +AAACCCGGGTTT diff --git a/ariba/tests/data/cluster_test_scaffold_with_sspace/genes.fa b/ariba/tests/data/cluster_test_scaffold_with_sspace/genes.fa new file mode 100644 index 00000000..042775d6 --- /dev/null +++ b/ariba/tests/data/cluster_test_scaffold_with_sspace/genes.fa @@ -0,0 +1,2 @@ +>name_of_gene +AAACCCGGGTTT diff --git a/ariba/tests/data/cluster_test_set_assembly_kmer/genes.fa b/ariba/tests/data/cluster_test_set_assembly_kmer/genes.fa new file mode 100644 index 00000000..042775d6 --- /dev/null +++ b/ariba/tests/data/cluster_test_set_assembly_kmer/genes.fa @@ -0,0 +1,2 @@ +>name_of_gene +AAACCCGGGTTT diff --git a/ariba/tests/data/clusters_test_write_report.tsv b/ariba/tests/data/clusters_test_write_report.tsv index 0b219c9f..a7180669 100644 --- a/ariba/tests/data/clusters_test_write_report.tsv +++ b/ariba/tests/data/clusters_test_write_report.tsv @@ -1,3 +1,3 @@ -#gene flag gene_len var_type var_effect new_aa gene_start gene_end gene_nt scaffold scaff_len scaff_start scaff_end scaff_nt +#gene flag cluster gene_len var_type var_effect new_aa gene_start gene_end gene_nt scaffold scaff_len scaff_start scaff_end scaff_nt gene1 line1 gene2 line2 diff --git a/ariba/tests/data/faidx_test_write_fa_subset.in.fa b/ariba/tests/data/faidx_test_write_fa_subset.in.fa new file mode 100644 index 00000000..d7a3a928 --- /dev/null +++ b/ariba/tests/data/faidx_test_write_fa_subset.in.fa @@ -0,0 +1,8 @@ +>seq1 +A +>seq2 +G +>seq3 +C +>seq4 +T diff --git a/ariba/tests/data/faidx_test_write_fa_subset.in.fa.fai b/ariba/tests/data/faidx_test_write_fa_subset.in.fa.fai new file mode 100644 index 00000000..0f995e3a --- /dev/null +++ b/ariba/tests/data/faidx_test_write_fa_subset.in.fa.fai @@ -0,0 +1,4 @@ +seq1 1 6 1 2 +seq2 1 14 1 2 +seq3 1 22 1 2 +seq4 1 30 1 2 diff --git a/ariba/tests/data/faidx_test_write_fa_subset.out.fa b/ariba/tests/data/faidx_test_write_fa_subset.out.fa new file mode 100644 index 00000000..ca3257f0 --- /dev/null +++ b/ariba/tests/data/faidx_test_write_fa_subset.out.fa @@ -0,0 +1,6 @@ +>seq1 +A +>seq3 +C +>seq4 +T diff --git a/ariba/tests/data/mapping_test_get_total_alignment_score.bam b/ariba/tests/data/mapping_test_get_total_alignment_score.bam new file mode 100644 index 00000000..e50c639a Binary files /dev/null and b/ariba/tests/data/mapping_test_get_total_alignment_score.bam differ diff --git a/ariba/tests/faidx_test.py b/ariba/tests/faidx_test.py new file mode 100644 index 00000000..ce83af69 --- /dev/null +++ b/ariba/tests/faidx_test.py @@ -0,0 +1,18 @@ +import unittest +import filecmp +import os +from ariba import faidx + +modules_dir = os.path.dirname(os.path.abspath(faidx.__file__)) +data_dir = os.path.join(modules_dir, 'tests', 'data') + + +class TestFaidx(unittest.TestCase): + def test_write_fa_subset(self): + '''test write_fa_subset''' + infile = os.path.join(data_dir, 'faidx_test_write_fa_subset.in.fa') + expected = os.path.join(data_dir, 'faidx_test_write_fa_subset.out.fa') + tmpfile = 'tmp.test_write_fa_subset.out.fa' + faidx.write_fa_subset(['seq1', 'seq3', 'seq4'], infile, tmpfile) + self.assertTrue(filecmp.cmp(expected, tmpfile, shallow=False)) + os.unlink(tmpfile) diff --git a/ariba/tests/mapping_test.py b/ariba/tests/mapping_test.py index 60245d37..5c5f29b2 100644 --- a/ariba/tests/mapping_test.py +++ b/ariba/tests/mapping_test.py @@ -60,3 +60,11 @@ def test_run_smalt_and_sort(self): os.unlink(out_prefix + '.bam.bai') os.unlink(out_prefix + '.unsorted.bam') + + def test_get_total_alignment_score(self): + '''Test get_total_alignment_score''' + bam = os.path.join(data_dir, 'mapping_test_get_total_alignment_score.bam') + expected = 219 + got = mapping.get_total_alignment_score(bam) + self.assertEqual(got, expected) +