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comparison defuse_results_to_vcf.py @ 28:f51a95bdc38e

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Add breakpoints.bam output derived from breakpoints.genome.psl
author Jim Johnson <jj@umn.edu>
date Tue, 03 Sep 2013 06:41:19 -0500
parents d57fcac025e2
children 8027fc53f3f9
comparison
equal deleted inserted replaced
27:d57fcac025e2 28:f51a95bdc38e
256 if inversion: 256 if inversion:
257 info.append('INVERSION') 257 info.append('INVERSION')
258 info1 = [svtype,'MATEID=%s' % mate_id2] + info 258 info1 = [svtype,'MATEID=%s' % mate_id2] + info
259 info2 = [svtype,'MATEID=%s' % mate_id1] + info 259 info2 = [svtype,'MATEID=%s' % mate_id1] + info
260 qual = int(float(fields[columns.index('probability')]) * 255) if columns.index('probability') else '.' 260 qual = int(float(fields[columns.index('probability')]) * 255) if columns.index('probability') else '.'
261 vcf1 = '%s\t%d\t%s\t%s\t%s\t%s\t%s\t%s'% (gene_chromosome1,genomic_break_pos1, mate_id1, ref1, alt1, qual, filt, ';'.join(info1) ) 261 vcf1 = '%s\t%d\t%s\t%s\t%s\t%s\t%d\t%s'% (gene_chromosome1,genomic_break_pos1, mate_id1, ref1, alt1, qual, filt, ';'.join(info1) )
262 vcf2 = '%s\t%d\t%s\t%s\t%s\t%s\t%s\t%s'% (gene_chromosome2,genomic_break_pos2, mate_id2, ref2, alt2, qual, filt, ';'.join(info2) ) 262 vcf2 = '%s\t%d\t%s\t%s\t%s\t%s\t%d\t%s'% (gene_chromosome2,genomic_break_pos2, mate_id2, ref2, alt2, qual, filt, ';'.join(info2) )
263 add_vcf_line(gene_chromosome1,genomic_break_pos1,mate_id1,vcf1) 263 add_vcf_line(gene_chromosome1,genomic_break_pos1,mate_id1,vcf1)
264 add_vcf_line(gene_chromosome2,genomic_break_pos2,mate_id2,vcf2) 264 add_vcf_line(gene_chromosome2,genomic_break_pos2,mate_id2,vcf2)
265 write_vcf() 265 write_vcf()
266 except Exception, e: 266 except Exception, e:
267 print >> sys.stderr, "failed: %s" % e 267 print >> sys.stderr, "failed: %s" % e