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comparison tools/naive_variant_caller.py @ 1:ae6edc0012ba

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Populate naive_variant_caller repository.
author Daniel Blankenberg <dan@bx.psu.edu>
date Thu, 29 Aug 2013 10:54:14 -0400
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children 8398666758e3
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0:0fa83c466e9d 1:ae6edc0012ba
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='uint8', 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( '--region', dest='region', action='append', type="string", default=[], help='region' )
24 (options, args) = parser.parse_args()
25
26 if len( options.bam_file ) == 0:
27 print >>sys.stderr, 'You must provide at least one bam (-b) file.'
28 parser.print_help( sys.stderr )
29 sys.exit( 1 )
30 if options.index_file:
31 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."
32 bam_files = zip( options.bam_file, options.index_file )
33 else:
34 bam_files = [ ( x, ) for x in options.bam_file ]
35 if not options.reference_genome_filename:
36 print >> sys.stderr, "Warning: Reference file has not been specified. Providing a reference genome is highly recommended."
37 if options.output_vcf_filename:
38 out = open( options.output_vcf_filename, 'wb' )
39 else:
40 out = sys.stdout
41
42 regions = []
43 if options.region:
44 for region in options.region:
45 region_split = region.split( ":" )
46 region = region_split.pop( 0 )
47 if region_split:
48 region_split = filter( bool, region_split[0].split( '-' ) )
49 if region_split:
50 if len( region_split ) != 2:
51 print >> sys.stderr, "You must specify both a start and an end, or only a chromosome when specifying regions."
52 cleanup_before_exit( tmp_dir )
53 sys.exit( 1 )
54 region = tuple( [ region ] + map( int, region_split ) )
55 regions.append( region )
56
57 coverage = VCFReadGroupGenotyper( map( lambda x: Reader( *x ), bam_files ), options.reference_genome_filename, dtype=options.coverage_dtype,
58 min_support_depth=options.min_support_depth, min_base_quality=options.min_base_quality, min_mapping_quality=options.min_mapping_quality,
59 restrict_regions=regions, use_strand=options.use_strand, allow_out_of_bounds_positions=options.allow_out_of_bounds_positions )
60 for line in coverage.iter_vcf( ploidy=options.ploidy, variants_only=options.variants_only ):
61 out.write( "%s\n" % line )
62 out.close()
63
64 if __name__ == "__main__": main()