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comparison tools/naive_variant_detector.py @ 5:4a67169be0ee

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Update to allow out of bounds positions to be not be fatal errors.
author Daniel Blankenberg <dan@bx.psu.edu>
date Thu, 16 May 2013 09:27:59 -0400
parents 55b4460cd0ce
children
comparison
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4:1c23da12b768 5:4a67169be0ee
17 parser.add_option( '-p', '--ploidy', dest='ploidy', action='store', type="int", default=2, help='Ploidy. Default=2.' ) 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.' ) 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.' ) 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.' ) 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' ) 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' )
22 parser.add_option( '--region', dest='region', action='append', type="string", default=[], help='region' ) 23 parser.add_option( '--region', dest='region', action='append', type="string", default=[], help='region' )
23 (options, args) = parser.parse_args() 24 (options, args) = parser.parse_args()
24 25
25 if len( options.bam_file ) == 0: 26 if len( options.bam_file ) == 0:
26 print >>sys.stderr, 'You must provide at least one bam (-b) file.' 27 print >>sys.stderr, 'You must provide at least one bam (-b) file.'
53 region = tuple( [ region ] + map( int, region_split ) ) 54 region = tuple( [ region ] + map( int, region_split ) )
54 regions.append( region ) 55 regions.append( region )
55 56
56 coverage = VCFReadGroupGenotyper( map( lambda x: Reader( *x ), bam_files ), options.reference_genome_filename, dtype=options.coverage_dtype, 57 coverage = VCFReadGroupGenotyper( map( lambda x: Reader( *x ), bam_files ), options.reference_genome_filename, dtype=options.coverage_dtype,
57 min_support_depth=options.min_support_depth, min_base_quality=options.min_base_quality, min_mapping_quality=options.min_mapping_quality, 58 min_support_depth=options.min_support_depth, min_base_quality=options.min_base_quality, min_mapping_quality=options.min_mapping_quality,
58 restrict_regions=regions, use_strand=options.use_strand ) 59 restrict_regions=regions, use_strand=options.use_strand, allow_out_of_bounds_positions=options.allow_out_of_bounds_positions )
59 for line in coverage.iter_vcf( ploidy=options.ploidy, variants_only=options.variants_only ): 60 for line in coverage.iter_vcf( ploidy=options.ploidy, variants_only=options.variants_only ):
60 out.write( "%s\n" % line ) 61 out.write( "%s\n" % line )
61 out.close() 62 out.close()
62 63
63 if __name__ == "__main__": main() 64 if __name__ == "__main__": main()