/tools/maf/vcf_to_maf_customtrack.py
Python | 151 lines | 145 code | 5 blank | 1 comment | 6 complexity | 0742547dcd8aa3cdd628b0d172156e3d MD5 | raw file
- #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()