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annotate tools/naive_variant_caller.py @ 12:ac0235d2d459 draft

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planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit ce964ed3ab7e390754fa03bb32a593fbe79dcf04
author blankenberg
date Thu, 17 Sep 2015 14:56:15 -0400
parents d5f866df45ae
children
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ac0235d2d459 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit ce964ed3ab7e390754fa03bb32a593fbe79dcf04
blankenberg
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1 #!/usr/bin/env python
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2 #Dan Blankenberg
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3 import sys
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4 import optparse
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6 from pyBamParser.bam import Reader
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ac0235d2d459 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit ce964ed3ab7e390754fa03bb32a593fbe79dcf04
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7 from pyBamTools.genotyping.naive import VCFReadGroupGenotyper, PROGRAM_NAME, PROGRAM_VERSION
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9 def main():
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10 #Parse Command Line
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11 parser = optparse.OptionParser()
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12 parser.add_option( '-b', '--bam', dest='bam_file', action='append', type="string", default=[], help='BAM filename, optionally index filename. Multiple allowed.' )
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13 parser.add_option( '-i', '--index', dest='index_file', action='append', type="string", default=[], help='optionally index filename. Multiple allowed.' )
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14 parser.add_option( '-o', '--output_vcf_filename', dest='output_vcf_filename', action='store', default = None, type="string", help='Output VCF filename' )
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15 parser.add_option( '-r', '--reference_genome_filename', dest='reference_genome_filename', action='store', default = None, type="string", help='Input reference file' )
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16 parser.add_option( '-v', '--variants_only', dest='variants_only', action='store_true', default = False, help='Report only sites with a possible variant allele.' )
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17 parser.add_option( '-s', '--use_strand', dest='use_strand', action='store_true', default = False, help='Report counts by strand' )
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18 parser.add_option( '-p', '--ploidy', dest='ploidy', action='store', type="int", default=2, help='Ploidy. Default=2.' )
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19 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.' )
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20 parser.add_option( '-q', '--min_base_quality', dest='min_base_quality', action='store', type="int", default=None, help='Minimum base quality.' )
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21 parser.add_option( '-m', '--min_mapping_quality', dest='min_mapping_quality', action='store', type="int", default=None, help='Minimum mapping.' )
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22 parser.add_option( '-t', '--coverage_dtype', dest='coverage_dtype', action='store', type="string", default=None, help='dtype to use for coverage array' )
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23 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' )
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24 parser.add_option( '--safe', dest='safe', action='store_true', default = False, help='Perform checks to prevent certain errors. Is slower.' )
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25 parser.add_option( '--region', dest='region', action='append', type="string", default=[], help='region' )
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26 parser.add_option( '', '--version', dest='version', action='store_true', default = False, help='Report version and quit' )
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27 (options, args) = parser.parse_args()
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28
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29 if options.version:
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30 print "%s version %s" % ( PROGRAM_NAME, PROGRAM_VERSION )
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31 sys.exit(0)
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32
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33 if len( options.bam_file ) == 0:
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34 print >>sys.stderr, 'You must provide at least one bam (-b) file.'
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35 parser.print_help( sys.stderr )
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36 sys.exit( 1 )
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37 if options.index_file:
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38 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."
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39 bam_files = zip( options.bam_file, options.index_file )
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40 else:
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41 bam_files = [ ( x, ) for x in options.bam_file ]
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42 if not options.reference_genome_filename:
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43 print >> sys.stderr, "Warning: Reference file has not been specified. Providing a reference genome is highly recommended."
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44 if options.output_vcf_filename:
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45 out = open( options.output_vcf_filename, 'wb' )
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46 else:
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47 out = sys.stdout
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48
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49 regions = []
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50 if options.region:
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51 for region in options.region:
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52 region_split = region.split( ":" )
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53 region = region_split.pop( 0 )
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54 if region_split:
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55 region_split = filter( bool, region_split[0].split( '-' ) )
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56 if region_split:
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57 if len( region_split ) != 2:
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58 print >> sys.stderr, "You must specify both a start and an end, or only a chromosome when specifying regions."
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59 cleanup_before_exit( tmp_dir )
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60 sys.exit( 1 )
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61 region = tuple( [ region ] + map( int, region_split ) )
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62 regions.append( region )
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63
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64 coverage = VCFReadGroupGenotyper( map( lambda x: Reader( *x ), bam_files ), options.reference_genome_filename, dtype=options.coverage_dtype,
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65 min_support_depth=options.min_support_depth, min_base_quality=options.min_base_quality,
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66 min_mapping_quality=options.min_mapping_quality, restrict_regions=regions, use_strand=options.use_strand,
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67 allow_out_of_bounds_positions=options.allow_out_of_bounds_positions, safe=options.safe )
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68 for line in coverage.iter_vcf( ploidy=options.ploidy, variants_only=options.variants_only ):
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69 out.write( "%s\n" % line )
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70 out.close()
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71
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72 if __name__ == "__main__": main()