#Dan Blankenberg from optparse import OptionParser import sys import galaxy_utils.sequence.vcf from galaxy import eggs import pkg_resources; pkg_resources.require( "bx-python" ) import bx.align.maf UNKNOWN_NUCLEOTIDE = '*' class PopulationVCFParser( object ): def __init__( self, reader, name ): self.reader = reader self.name = name self.counter = 0 def next( self ): rval = [] vc = self.reader.next() for i, allele in enumerate( vc.alt ): rval.append( ( '%s_%i.%i' % ( self.name, i + 1, self.counter + 1 ), allele ) ) self.counter += 1 return ( vc, rval ) def __iter__( self ): while True: yield self.next() class SampleVCFParser( object ): def __init__( self, reader ): self.reader = reader self.counter = 0 def next( self ): rval = [] vc = self.reader.next() alleles = [ vc.ref ] + vc.alt if 'GT' in vc.format: gt_index = vc.format.index( 'GT' ) for sample_name, sample_value in zip( vc.sample_names, vc.sample_values ): gt_indexes = [] for i in sample_value[ gt_index ].replace( '|', '/' ).replace( '\\', '/' ).split( '/' ): #Do we need to consider phase here? try: gt_indexes.append( int( i ) ) except: gt_indexes.append( None ) for i, allele_i in enumerate( gt_indexes ): if allele_i is not None: rval.append( ( '%s_%i.%i' % ( sample_name, i + 1, self.counter + 1 ), alleles[ allele_i ] ) ) self.counter += 1 return ( vc, rval ) def __iter__( self ): while True: yield self.next() def main(): usage = "usage: %prog [options] output_file dbkey inputfile pop_name" parser = OptionParser( usage=usage ) parser.add_option( "-p", "--population", action="store_true", dest="population", default=False, help="Create MAF on a per population basis") parser.add_option( "-s", "--sample", action="store_true", dest="sample", default=False, help="Create MAF on a per sample basis") parser.add_option( "-n", "--name", dest="name", default='Unknown Custom Track', help="Name for Custom Track") parser.add_option( "-g", "--galaxy", action="store_true", dest="galaxy", default=False, help="Tool is being executed by Galaxy (adds extra error messaging).") ( options, args ) = parser.parse_args() if len ( args ) < 3: if options.galaxy: print >>sys.stderr, "It appears that you forgot to specify an input VCF file, click 'Add new VCF...' to add at least input.\n" parser.error( "Need to specify an output file, a dbkey and at least one input file" ) if not ( options.population ^ options.sample ): parser.error( 'You must specify either a per population conversion or a per sample conversion, but not both' ) out = open( args.pop(0), 'wb' ) out.write( 'track name="%s" visibility=pack\n' % options.name.replace( "\"", "'" ) ) maf_writer = bx.align.maf.Writer( out ) dbkey = args.pop(0) vcf_files = [] if options.population: i = 0 while args: filename = args.pop( 0 ) pop_name = args.pop( 0 ).replace( ' ', '_' ) if not pop_name: pop_name = 'population_%i' % ( i + 1 ) vcf_files.append( PopulationVCFParser( galaxy_utils.sequence.vcf.Reader( open( filename ) ), pop_name ) ) i += 1 else: while args: filename = args.pop( 0 ) vcf_files.append( SampleVCFParser( galaxy_utils.sequence.vcf.Reader( open( filename ) ) ) ) non_spec_skipped = 0 for vcf_file in vcf_files: for vc, variants in vcf_file: num_ins = 0 num_dels = 0 for variant_name, variant_text in variants: if 'D' in variant_text: num_dels = max( num_dels, int( variant_text[1:] ) ) elif 'I' in variant_text: num_ins = max( num_ins, len( variant_text ) - 1 ) alignment = bx.align.maf.Alignment() ref_text = vc.ref + '-' * num_ins + UNKNOWN_NUCLEOTIDE * ( num_dels - len( vc.ref ) ) start_pos = vc.pos - 1 if num_dels and start_pos: ref_text = UNKNOWN_NUCLEOTIDE + ref_text start_pos -= 1 alignment.add_component( bx.align.maf.Component( src='%s.%s%s' % ( dbkey, ("chr" if not vc.chrom.startswith("chr") else ""), vc.chrom ), start = start_pos, size = len( ref_text.replace( '-', '' ) ), strand = '+', src_size = start_pos + len( ref_text ), text = ref_text ) ) for variant_name, variant_text in variants: #FIXME: ## skip non-spec. compliant data, see: http://1000genomes.org/wiki/doku.php?id=1000_genomes:analysis:vcf3.3 for format spec ## this check is due to data having indels not represented in the published format spec, ## e.g. 1000 genomes pilot 1 indel data: ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/pilot_data/release/2010_03/pilot1/indels/CEU.SRP000031.2010_03.indels.sites.vcf.gz if variant_text and variant_text[0] in [ '-', '+' ]: non_spec_skipped += 1 continue #do we need a left padding unknown nucleotide (do we have deletions)? if num_dels and start_pos: var_text = UNKNOWN_NUCLEOTIDE else: var_text = '' if 'D' in variant_text: cur_num_del = int( variant_text[1:] ) pre_del = min( len( vc.ref ), cur_num_del ) post_del = cur_num_del - pre_del var_text = var_text + '-' * pre_del + '-' * num_ins + '-' * post_del var_text = var_text + UNKNOWN_NUCLEOTIDE * ( len( ref_text ) - len( var_text ) ) elif 'I' in variant_text: cur_num_ins = len( variant_text ) - 1 var_text = var_text + vc.ref + variant_text[1:] + '-' * ( num_ins - cur_num_ins ) + UNKNOWN_NUCLEOTIDE * max( 0, ( num_dels - 1 ) ) else: var_text = var_text + variant_text + '-' * num_ins + UNKNOWN_NUCLEOTIDE * ( num_dels - len( vc.ref ) ) alignment.add_component( bx.align.maf.Component( src=variant_name, start = 0, size = len( var_text.replace( '-', '' ) ), strand = '+', src_size = len( var_text.replace( '-', '' ) ), text = var_text ) ) maf_writer.write( alignment ) maf_writer.close() if non_spec_skipped: print 'Skipped %i non-specification compliant indels.' % non_spec_skipped if __name__ == "__main__": main()