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comparison tools/naive_variant_caller.py @ 0:0095f76a5d05 draft

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planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit cf5c0f6fb2651adf72e317a1cf77805fca30d84e
author blankenberg
date Thu, 17 Sep 2015 11:13:08 -0400
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children cbb8bfd46a80
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-1:000000000000 0:0095f76a5d05
1 #Dan Blankenberg
2 import sys
3 import optparse
4
5 from pyBamParser.bam import Reader
6 from pyBamTools.genotyping.naive import VCFReadGroupGenotyper
7
8 def main():
9 #Parse Command Line
10 parser = optparse.OptionParser()
11 parser.add_option( '-b', '--bam', dest='bam_file', action='append', type="string", default=[], help='BAM filename, optionally index filename. Multiple allowed.' )
12 parser.add_option( '-i', '--index', dest='index_file', action='append', type="string", default=[], help='optionally index filename. Multiple allowed.' )
13 parser.add_option( '-o', '--output_vcf_filename', dest='output_vcf_filename', action='store', default = None, type="string", help='Output VCF filename' )
14 parser.add_option( '-r', '--reference_genome_filename', dest='reference_genome_filename', action='store', default = None, type="string", help='Input reference file' )
15 parser.add_option( '-v', '--variants_only', dest='variants_only', action='store_true', default = False, help='Report only sites with a possible variant allele.' )
16 parser.add_option( '-s', '--use_strand', dest='use_strand', action='store_true', default = False, help='Report counts by strand' )
17 parser.add_option( '-p', '--ploidy', dest='ploidy', action='store', type="int", default=2, help='Ploidy. Default=2.' )
18 parser.add_option( '-d', '--min_support_depth', dest='min_support_depth', action='store', type="int", default=0, help='Minimum number of reads needed to consider a REF/ALT. Default=0.' )
19 parser.add_option( '-q', '--min_base_quality', dest='min_base_quality', action='store', type="int", default=None, help='Minimum base quality.' )
20 parser.add_option( '-m', '--min_mapping_quality', dest='min_mapping_quality', action='store', type="int", default=None, help='Minimum mapping.' )
21 parser.add_option( '-t', '--coverage_dtype', dest='coverage_dtype', action='store', type="string", default=None, help='dtype to use for coverage array' )
22 parser.add_option( '--allow_out_of_bounds_positions', dest='allow_out_of_bounds_positions', action='store_true', default = False, help='Allows out of bounds positions to not throw fatal errors' )
23 parser.add_option( '--safe', dest='safe', action='store_true', default = False, help='Perform checks to prevent certain errors. Is slower.' )
24 parser.add_option( '--region', dest='region', action='append', type="string", default=[], help='region' )
25 (options, args) = parser.parse_args()
26
27 if len( options.bam_file ) == 0:
28 print >>sys.stderr, 'You must provide at least one bam (-b) file.'
29 parser.print_help( sys.stderr )
30 sys.exit( 1 )
31 if options.index_file:
32 assert len( options.index_file ) == len( options.bam_file ), "If you provide a name for an index file, you must provide the index name for all bam files."
33 bam_files = zip( options.bam_file, options.index_file )
34 else:
35 bam_files = [ ( x, ) for x in options.bam_file ]
36 if not options.reference_genome_filename:
37 print >> sys.stderr, "Warning: Reference file has not been specified. Providing a reference genome is highly recommended."
38 if options.output_vcf_filename:
39 out = open( options.output_vcf_filename, 'wb' )
40 else:
41 out = sys.stdout
42
43 regions = []
44 if options.region:
45 for region in options.region:
46 region_split = region.split( ":" )
47 region = region_split.pop( 0 )
48 if region_split:
49 region_split = filter( bool, region_split[0].split( '-' ) )
50 if region_split:
51 if len( region_split ) != 2:
52 print >> sys.stderr, "You must specify both a start and an end, or only a chromosome when specifying regions."
53 cleanup_before_exit( tmp_dir )
54 sys.exit( 1 )
55 region = tuple( [ region ] + map( int, region_split ) )
56 regions.append( region )
57
58 coverage = VCFReadGroupGenotyper( map( lambda x: Reader( *x ), bam_files ), options.reference_genome_filename, dtype=options.coverage_dtype,
59 min_support_depth=options.min_support_depth, min_base_quality=options.min_base_quality,
60 min_mapping_quality=options.min_mapping_quality, restrict_regions=regions, use_strand=options.use_strand,
61 allow_out_of_bounds_positions=options.allow_out_of_bounds_positions, safe=options.safe )
62 for line in coverage.iter_vcf( ploidy=options.ploidy, variants_only=options.variants_only ):
63 out.write( "%s\n" % line )
64 out.close()
65
66 if __name__ == "__main__": main()