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Set nucmer opts to match nucmers defaults, but add --maxmatch #57

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merged 1 commit into from
Apr 21, 2016
+14 −12
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Set nucmer opts to match nucmers defaults, but add --maxmatch #57

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9 changes: 5 additions & 4 deletions ariba/assembly.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,8 +22,8 @@ def __init__(self,
min_scaff_depth=10,
min_scaff_length=50,
nucmer_min_id=90,
nucmer_min_len=50,
nucmer_breaklen=50,
nucmer_min_len=20,
nucmer_breaklen=200,
spades_other_options=None,
sspace_k=20,
sspace_sd=0.4,
Expand Down Expand Up @@ -214,7 +214,7 @@ def _gap_fill_with_gapfiller(self):


@staticmethod
def _fix_contig_orientation(contigs_fa, ref_fa, outfile, min_id=90, min_length=50, breaklen=50):
def _fix_contig_orientation(contigs_fa, ref_fa, outfile, min_id=90, min_length=20, breaklen=200):
'''Changes orientation of each contig to match the reference, when possible.
Returns a set of names of contigs that had hits in both orientations to the reference'''
if not os.path.exists(contigs_fa):
Expand All @@ -228,6 +228,7 @@ def _fix_contig_orientation(contigs_fa, ref_fa, outfile, min_id=90, min_length=5
min_id=min_id,
min_length=min_length,
breaklen=breaklen,
maxmatch=True,
).run()

to_revcomp = set()
Expand Down Expand Up @@ -289,7 +290,7 @@ def run(self):
self.log_fh = None
return

contigs_both_strands = self._fix_contig_orientation(self.gapfilled_length_filtered, self.ref_fasta, self.final_assembly_fa)
contigs_both_strands = self._fix_contig_orientation(self.gapfilled_length_filtered, self.ref_fasta, self.final_assembly_fa, min_id=self.nucmer_min_id, min_length=self.nucmer_min_len, breaklen=self.nucmer_breaklen)
self.has_contigs_on_both_strands = len(contigs_both_strands) > 0
pyfastaq.tasks.file_to_dict(self.final_assembly_fa, self.sequences)

Expand Down
5 changes: 3 additions & 2 deletions ariba/assembly_compare.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,8 +14,8 @@ def __init__(self,
outprefix,
refdata,
nucmer_min_id=90,
nucmer_min_len=50,
nucmer_breaklen=50,
nucmer_min_len=20,
nucmer_breaklen=200,
assembled_threshold=0.95,
unique_threshold=0.03,
):
Expand Down Expand Up @@ -45,6 +45,7 @@ def _run_nucmer(self):
min_id=self.nucmer_min_id,
min_length=self.nucmer_min_len,
breaklen=self.nucmer_breaklen,
maxmatch=True,
show_snps=True
).run()

Expand Down
4 changes: 2 additions & 2 deletions ariba/cluster.py
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Original file line number Diff line number Diff line change
Expand Up @@ -23,8 +23,8 @@ def __init__(self,
max_insert=1000,
min_scaff_depth=10,
nucmer_min_id=90,
nucmer_min_len=50,
nucmer_breaklen=50,
nucmer_min_len=20,
nucmer_breaklen=200,
reads_insert=500,
sspace_k=20,
sspace_sd=0.4,
Expand Down
4 changes: 2 additions & 2 deletions ariba/clusters.py
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Original file line number Diff line number Diff line change
Expand Up @@ -38,8 +38,8 @@ def __init__(self,
max_insert=1000,
min_scaff_depth=10,
nucmer_min_id=90,
nucmer_min_len=50,
nucmer_breaklen=50,
nucmer_min_len=20,
nucmer_breaklen=200,
assembled_threshold=0.95,
unique_threshold=0.03,
bowtie2_preset='very-sensitive-local',
Expand Down
4 changes: 2 additions & 2 deletions ariba/tasks/run.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,8 +15,8 @@ def run():

nucmer_group = parser.add_argument_group('nucmer options')
nucmer_group.add_argument('--nucmer_min_id', type=int, help='Minimum alignment identity (delta-filter -i) [%(default)s]', default=90, metavar='INT')
nucmer_group.add_argument('--nucmer_min_len', type=int, help='Minimum alignment length (delta-filter -i) [%(default)s]', default=50, metavar='INT')
nucmer_group.add_argument('--nucmer_breaklen', type=int, help='Value to use for -breaklen when running nucmer [%(default)s]', default=50, metavar='INT')
nucmer_group.add_argument('--nucmer_min_len', type=int, help='Minimum alignment length (delta-filter -i) [%(default)s]', default=20, metavar='INT')
nucmer_group.add_argument('--nucmer_breaklen', type=int, help='Value to use for -breaklen when running nucmer [%(default)s]', default=200, metavar='INT')

assembly_group = parser.add_argument_group('Assembly options')
assembly_group.add_argument('--assembly_cov', type=int, help='Target read coverage when sampling reads for assembly [%(default)s]', default=100, metavar='INT')
Expand Down