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Use nucmer diagdiff #15

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merged 3 commits into from
May 28, 2015
Merged

Use nucmer diagdiff #15

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46f9206
Add diagdiff option
May 28, 2015
75d6268
Update minimum dependency version
May 28, 2015
d99b04c
Version bump
May 28, 2015
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2 changes: 1 addition & 1 deletion circlator/common.py
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
import sys
import subprocess

version = '0.12.1'
version = '0.13.0'

def syscall(cmd, allow_fail=False, verbose=False):
if verbose:
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3 changes: 3 additions & 0 deletions circlator/merge.py
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Expand Up @@ -15,6 +15,7 @@ def __init__(
reassembly,
outprefix,
reads=None,
nucmer_diagdiff=25,
nucmer_min_id=95,
nucmer_min_length=500,
nucmer_min_length_for_merges=4000,
Expand All @@ -34,6 +35,7 @@ def __init__(
self.reassembly_fasta = reassembly
self.reads = reads
self.outprefix = outprefix
self.nucmer_diagdiff = nucmer_diagdiff
self.nucmer_min_id = nucmer_min_id
self.nucmer_min_length = nucmer_min_length
self.nucmer_min_length_for_merges = nucmer_min_length_for_merges
Expand All @@ -59,6 +61,7 @@ def _run_nucmer(self, ref, qry, outfile):
outfile,
min_id=self.nucmer_min_id,
min_length=self.nucmer_min_length,
diagdiff=self.nucmer_diagdiff,
maxmatch=True,
breaklen=self.nucmer_breaklen,
simplify=False,
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2 changes: 2 additions & 0 deletions circlator/tasks/all.py
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Expand Up @@ -32,6 +32,7 @@ def run():
#assemble_group = parser.add_argument_group('assemble_group')

merge_group = parser.add_argument_group('merge options')
merge_group.add_argument('--merge_diagdiff', type=int, help='Nucmer diagdiff option [%(default)s]', metavar='INT', default=25)
merge_group.add_argument('--merge_min_id', type=float, help='Nucmer minimum percent identity [%(default)s]', metavar='FLOAT', default=95)
merge_group.add_argument('--merge_min_length', type=int, help='Minimum length of hit for nucmer to report [%(default)s]', metavar='INT', default=500)
merge_group.add_argument('--merge_min_length_merge', type=int, help='Minimum length of nucmer hit to use when merging [%(default)s]', metavar='INT', default=4000)
Expand Down Expand Up @@ -122,6 +123,7 @@ def run():
original_assembly,
reassembly,
merge_prefix,
nucmer_diagdiff=options.merge_diagdiff,
nucmer_min_id=options.merge_min_id,
nucmer_min_length=options.merge_min_length,
nucmer_min_length_for_merges=options.merge_min_length_merge,
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2 changes: 2 additions & 0 deletions circlator/tasks/merge.py
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Expand Up @@ -7,6 +7,7 @@ def run():
usage = 'circlator merge [options] <original.fasta> <new.fasta> <outprefix>'
)

parser.add_argument('--diagdiff', type=int, help='Nucmer diagdiff option [%(default)s]', metavar='INT', default=25)
parser.add_argument('--min_id', type=float, help='Nucmer minimum percent identity [%(default)s]', metavar='FLOAT', default=95)
parser.add_argument('--min_length', type=int, help='Minimum length of hit for nucmer to report [%(default)s]', metavar='INT', default=500)
parser.add_argument('--min_length_merge', type=int, help='Minimum length of nucmer hit to use when merging [%(default)s]', metavar='INT', default=4000)
Expand All @@ -26,6 +27,7 @@ def run():
options.original_assembly,
options.new_assembly,
options.outprefix,
nucmer_diagdiff=options.diagdiff,
nucmer_min_id=options.min_id,
nucmer_min_length=options.min_length,
nucmer_min_length_for_merges=options.min_length_merge,
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6 changes: 3 additions & 3 deletions setup.py
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Expand Up @@ -7,7 +7,7 @@

setup(
name='circlator',
version='0.12.1',
version='0.13.0',
description='circlator: a tool to circularise bacterial genome assemblies',
packages = find_packages(),
package_data={'circlator': ['data/*']},
Expand All @@ -21,8 +21,8 @@
'openpyxl',
'pyfastaq >= 3.5.0',
'pysam >= 0.8.1',
'pymummer>=0.2.0',
'bio_assembly_refinement>=0.1.0',
'pymummer>=0.4.0',
'bio_assembly_refinement>=0.3.2',
],
license='GPLv3',
classifiers=[
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