Merge pull request #109 from martinghunt/end_extend_assemble_flag_bug

End extend assemble flag bug
sanger-pathogens · Jul 28, 2016 · a499fd3 · a499fd3
2 parents d6b0184 + efc2b23
commit a499fd3
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Showing 14 changed files with 503 additions and 15 deletions.
diff --git a/ariba/assembly_compare.py b/ariba/assembly_compare.py
@@ -33,6 +33,7 @@ def __init__(self,
         self.assembled_threshold = assembled_threshold
         self.unique_threshold = unique_threshold
         self.max_gene_nt_extend = max_gene_nt_extend
+        self.scaff_name_matching_ref = None
         self.gene_matching_ref = None
         self.gene_matching_ref_type = None
         self.gene_start_bases_added = None
@@ -309,7 +310,7 @@ def _get_gene_matching_ref(nucmer_hits, contigs, max_end_nt_extend):
         if longest_match is None:
             return None, 'NO_MATCH', None, None
         else:
-            return AssemblyCompare._gene_from_nucmer_match(longest_match, contigs[longest_match.qry_name], max_end_nt_extend)
+            return (longest_match.qry_name,) + AssemblyCompare._gene_from_nucmer_match(longest_match, contigs[longest_match.qry_name], max_end_nt_extend)
 
 
     @staticmethod
@@ -334,8 +335,8 @@ def update_flag(self, flag):
         if self._ref_has_region_assembled_twice(self.nucmer_hits, self.ref_sequence, self.unique_threshold):
             flag.add('region_assembled_twice')
 
-        ref_seq_type = self.refdata.sequence_type(self.ref_sequence.id)
-        if ref_seq_type != 'non_coding' and self.gene_matching_ref_type == 'GENE_FOUND':
+        ref_seq_type, is_variant_only = self.refdata.sequence_type(self.ref_sequence.id)
+        if ref_seq_type == 'p' and self.gene_matching_ref_type == 'GENE_FOUND':
             flag.add('complete_gene')
 
         if len(self.nucmer_hits) == 1:
@@ -362,10 +363,10 @@ def run(self):
         self.nucmer_hits = self._parse_nucmer_coords_file(self.nucmer_coords_file, self.ref_sequence.id)
         self.percent_identities = self._nucmer_hits_to_percent_identity(self.nucmer_hits)
         self.assembled_reference_sequences = self._get_assembled_reference_sequences(self.nucmer_hits, self.ref_sequence, self.assembly_sequences)
-        ref_seq_type = self.refdata.sequence_type(self.ref_sequence.id)
+        ref_seq_type, is_variant_only = self.refdata.sequence_type(self.ref_sequence.id)
         if self._ref_covered_by_at_least_one_full_length_contig(self.nucmer_hits, self.assembled_threshold, self.max_gene_nt_extend):
             self.assembled_into_one_contig = True
-            if ref_seq_type != 'non_coding':
-                self.gene_matching_ref, self.gene_matching_ref_type, self.gene_start_bases_added, self.gene_end_bases_added = self._get_gene_matching_ref(self.nucmer_hits, self.assembly_sequences, self.max_gene_nt_extend)
+            if ref_seq_type == 'p':
+                self.scaff_name_matching_ref, self.gene_matching_ref, self.gene_matching_ref_type, self.gene_start_bases_added, self.gene_end_bases_added = self._get_gene_matching_ref(self.nucmer_hits, self.assembly_sequences, self.max_gene_nt_extend)
         else:
             self.assembled_into_one_contig = False
diff --git a/ariba/report.py b/ariba/report.py
@@ -136,6 +136,13 @@ def _report_lines_for_one_contig(cluster, contig_name, ref_cov_per_contig, pymum
     lines = []
     contig_length = len(cluster.assembly.sequences[contig_name])
     assert contig_length != 0
+    if contig_name in ref_cov_per_contig:
+        if contig_name == cluster.assembly_compare.scaff_name_matching_ref:
+            ref_cov = len(cluster.ref_sequence)
+        else:
+            ref_cov = ref_cov_per_contig[contig_name]
+    else:
+        ref_cov = 0
 
     common_first_columns = [
         cluster.ref_sequence.id,
@@ -145,7 +152,7 @@ def _report_lines_for_one_contig(cluster, contig_name, ref_cov_per_contig, pymum
         str(cluster.total_reads),
         cluster.name,
         str(len(cluster.ref_sequence)),
-        str(ref_cov_per_contig[contig_name]) if contig_name in ref_cov_per_contig else '0', # 6 ref bases assembled
+        str(ref_cov),
         str(cluster.assembly_compare.percent_identities[contig_name]) if contig_name in cluster.assembly_compare.percent_identities else '0',
         contig_name,
         str(contig_length),  # 9 length of scaffold matching reference

diff --git a/ariba/tests/assembly_compare_test.py b/ariba/tests/assembly_compare_test.py
@@ -324,7 +324,7 @@ def test_get_gene_matching_ref(self):
         }
 
         got = assembly_compare.AssemblyCompare._get_gene_matching_ref(nucmer_hits, contigs, 10)
-        expected = (pyfastaq.sequences.Fasta('contig.2-16', 'ATGAAATTTCCCTAG'), 'GENE_FOUND', 1, 2)
+        expected = ('contig', pyfastaq.sequences.Fasta('contig.2-16', 'ATGAAATTTCCCTAG'), 'GENE_FOUND', 1, 2)
         self.assertEqual(expected, got)
 
 

diff --git a/ariba/tests/cluster_test.py b/ariba/tests/cluster_test.py
@@ -184,12 +184,12 @@ def test_full_run_ok_presence_absence(self):
         c.run()
 
         expected = [
-            'presence_absence1\t1\t0\t539\t64\tcluster_name\t96\t96\t97.92\tcluster_name.scaffold.1\t158\t17.4\t1\tSNP\tp\tA10V\t1\tA10V\tNONSYN\t28\t28\tC\t83\t83\tT\t22\t.\t22\tpresence_absence1:1:0:A10V:.:Ref has wild, reads have variant so report\tGeneric description of presence_absence1',
-            'presence_absence1\t1\t0\t539\t64\tcluster_name\t96\t96\t97.92\tcluster_name.scaffold.1\t158\t17.4\t0\t.\tp\t.\t0\t.\tSYN\t53\t53\tT\t108\t108\tC\t32\t.\t32\t.\tGeneric description of presence_absence1',
+            'presence_absence1\t1\t0\t539\t64\tcluster_name\t96\t96\t97.92\tcluster_name.scaffold.1\t213\t15.0\t1\tSNP\tp\tA10V\t1\tA10V\tNONSYN\t28\t28\tC\t83\t83\tT\t22\t.\t22\tpresence_absence1:1:0:A10V:.:Ref has wild, reads have variant so report\tGeneric description of presence_absence1',
+            'presence_absence1\t1\t0\t539\t64\tcluster_name\t96\t96\t97.92\tcluster_name.scaffold.1\t213\t15.0\t0\t.\tp\t.\t0\t.\tSYN\t53\t53\tT\t108\t108\tC\t32\t.\t32\t.\tGeneric description of presence_absence1',
 
-            'presence_absence1\t1\t0\t539\t64\tcluster_name\t96\t96\t97.92\tcluster_name.scaffold.1\t158\t17.4\t1\tSNP\tp\tR3S\t0\t.\t.\t7\t9\tC;G;C\t62\t64\tC;G;C\t18;17;17\t.;.;.\t18;17;17\tpresence_absence1:1:0:R3S:.:Ref and assembly have wild type\tGeneric description of presence_absence1',
+            'presence_absence1\t1\t0\t539\t64\tcluster_name\t96\t96\t97.92\tcluster_name.scaffold.1\t213\t15.0\t1\tSNP\tp\tR3S\t0\t.\t.\t7\t9\tC;G;C\t62\t64\tC;G;C\t18;17;17\t.;.;.\t18;17;17\tpresence_absence1:1:0:R3S:.:Ref and assembly have wild type\tGeneric description of presence_absence1',
 
-            'presence_absence1\t1\t0\t539\t64\tcluster_name\t96\t96\t97.92\tcluster_name.scaffold.1\t158\t17.4\t1\tSNP\tp\tI5A\t1\t.\t.\t13\t15\tG;C;G\t68\t70\tG;C;G\t18;20;20\t.;.;.\t18;20;20\tpresence_absence1:1:0:I5A:.:Ref and reads have variant so report\tGeneric description of presence_absence1',
+            'presence_absence1\t1\t0\t539\t64\tcluster_name\t96\t96\t97.92\tcluster_name.scaffold.1\t213\t15.0\t1\tSNP\tp\tI5A\t1\t.\t.\t13\t15\tG;C;G\t68\t70\tG;C;G\t18;20;20\t.;.;.\t18;20;20\tpresence_absence1:1:0:I5A:.:Ref and reads have variant so report\tGeneric description of presence_absence1',
         ]
 
         self.assertEqual(expected, c.report_lines)
@@ -247,3 +247,20 @@ def test_full_run_ok_variants_only_variant_is_present(self):
         ]
         self.assertEqual(expected, c.report_lines)
         shutil.rmtree(tmpdir)
+
+
+    def test_full_run_ok_gene_start_mismatch(self):
+        '''test complete run where gene extended because too different at end for full nucmer match'''
+        fasta_in = os.path.join(data_dir, 'cluster_test_full_run_ok_gene_start_mismatch.fa')
+        tsv_in = os.path.join(data_dir, 'cluster_test_full_run_ok_gene_start_mismatch.metadata.tsv')
+        refdata = reference_data.ReferenceData([fasta_in], [tsv_in])
+        tmpdir = 'tmp.cluster_test_full_run_ok_gene_start_mismatch'
+        shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_gene_start_mismatch'), tmpdir)
+        c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=112, total_reads_bases=1080)
+        c.run()
+        expected = [
+            'gene\t1\t0\t27\t112\tcluster_name\t96\t96\t100.0\tcluster_name.scaffold.1\t364\t27.0\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\tGeneric description of gene'
+        ]
+        self.assertEqual(expected, c.report_lines)
+        shutil.rmtree(tmpdir)
+
diff --git a/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.fa b/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.fa
@@ -0,0 +1,3 @@
+>gene
+ATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCAT
+ATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
diff --git a/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.metadata.tsv b/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.metadata.tsv
@@ -0,0 +1 @@
+gene	1	0	.	.	Generic description of gene
diff --git a/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.ref_to_make_reads.fa b/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.ref_to_make_reads.fa
@@ -0,0 +1,7 @@
+>gene
+GAGCCAGATCGTAGGAGAGCGTGTCCCGGTCCACAGCTTTTGAAAAACGATACAGGTGAA
+TAAGCGCGGCCAATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGAC
+ATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCAT
+ATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAATGATGCATTAAGTTCGGTGAGCAC
+GACGCCCGAGGCAGTCTGAGCATTCAAAGTTGGCCTGAGCCAGATCGTAGGAGAGCGTGT
+CCCGGTCCACAGCTTTTGAAAAACGATACAGGTGAA
diff --git a/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_1.fq b/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_1.fq
@@ -0,0 +1,224 @@
+@gene:1:71:181/1
+CAATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:2:85:195/1
+TCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:3:43:154/1
+AAAAACGATACAGGTGAATAAGCGCGGCCAATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:4:81:189/1
+AACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:5:69:180/1
+GCCAATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:6:124:234/1
+CGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:7:76:185/1
+CTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:8:98:208/1
+CGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:9:135:247/1
+GATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAATGATGCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:10:13:122/1
+AGGAGAGCGTGTCCCGGTCCACAGCTTTTGAAAAACGATACAGGTGAATAAGCGCGGCCAATTCTCAGAACGTCGCGGATTTCACCGGTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:11:82:191/1
+ACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:12:103:213/1
+ACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:13:72:182/1
+AATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:14:116:226/1
+GAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:15:70:178/1
+CCAATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:16:45:155/1
+AAACGATACAGGTGAATAAGCGCGGCCAATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:17:75:185/1
+TCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:18:51:162/1
+TACAGGTGAATAAGCGCGGCCAATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:19:53:161/1
+CAGGTGAATAAGCGCGGCCAATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:20:116:225/1
+GAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:21:46:155/1
+AACGATACAGGTGAATAAGCGCGGCCAATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:22:59:168/1
+AATAAGCGCGGCCAATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:23:22:132/1
+TGTCCCGGTCCACAGCTTTTGAAAAACGATACAGGTGAATAAGCGCGGCCAATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:24:38:148/1
+TTTTGAAAAACGATACAGGTGAATAAGCGCGGCCAATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:25:35:143/1
+AGCTTTTGAAAAACGATACAGGTGAATAAGCGCGGCCAATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:26:94:205/1
+TCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:27:30:141/1
+TCCACAGCTTTTGAAAAACGATACAGGTGAATAAGCGCGGCCAATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:28:125:236/1
+GTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:29:71:181.dup.2/1
+CAATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:30:16:126/1
+AGAGCGTGTCCCGGTCCACAGCTTTTGAAAAACGATACAGGTGAATAAGCGCGGCCAATTCTCAGAACGTCGCGGATTTCACCGGTCACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:31:73:183/1
+ATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:32:131:241/1
+AAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAATGAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:33:115:226/1
+TGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:34:59:168.dup.2/1
+AATAAGCGCGGCCAATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:35:84:195/1
+GTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:36:95:206/1
+CACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:37:3:113/1
+GCCAGATCGTAGGAGAGCGTGTCCCGGTCCACAGCTTTTGAAAAACGATACAGGTGAATAAGCGCGGCCAATTCTCAGAACGTCGCGGAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:38:33:143/1
+ACAGCTTTTGAAAAACGATACAGGTGAATAAGCGCGGCCAATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:39:9:117/1
+TCGTAGGAGAGCGTGTCCCGGTCCACAGCTTTTGAAAAACGATACAGGTGAATAAGCGCGGCCAATTCTCAGAACGTCGCGGATTTCACC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:40:107:217/1
+GAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:41:83:192/1
+CGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:42:135:246/1
+GATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAATGATGCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:43:130:238/1
+GAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAATGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:44:120:229/1
+CATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:45:59:168.dup.3/1
+AATAAGCGCGGCCAATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:46:92:202/1
+TTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:47:73:183.dup.2/1
+ATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:48:34:144/1
+CAGCTTTTGAAAAACGATACAGGTGAATAAGCGCGGCCAATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:49:72:182.dup.2/1
+AATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:50:86:196/1
+CGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:51:124:232/1
+CGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:52:30:138/1
+TCCACAGCTTTTGAAAAACGATACAGGTGAATAAGCGCGGCCAATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:53:25:134/1
+CCCGGTCCACAGCTTTTGAAAAACGATACAGGTGAATAAGCGCGGCCAATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:54:110:220/1
+GTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:55:95:205/1
+CACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@gene:56:122:231/1
+TGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII