def sqlComparator( self, sqlrow, out_splt ) : (chrom1,pos1,ref1,mut1) = sqlrow[1], sqlrow[2],sqlrow[3],sqlrow[4] coord = out_splt[ self.indexOf["coordinates"] ].split(',') (chrom2,pos2,strand,refmut) = coord (ref2,mut2) = refmut.split('/') return globes.compareVariants( chrom1,pos1,ref1,mut1,\ chrom2,pos2,ref2,mut2 )
def varListSNPComparator(self,variant,out_splt) : (chrom1,pos1,ref1,mut1) = variant.getPosition() keys = ['chrom','position','reference','change'] (chrom2,pos2,ref2,mut2) = [ out_splt[ self.indexOf[k] ] for k in keys ] #print chrom1, pos1, ref1, mut1, chrom2, pos2, ref2, mut2 return globes.compareVariants( chrom1,pos1,ref1,mut1,\ chrom2,pos2,ref2,mut2 )
def varListINDELComparator( self, variant, out_splt ) : #print 'comparing: %s to %s' % (variant.getPosition(), out_splt ) (chrom1,pos1,ref1,mut1) = variant.getPosition() keys = ['chrom','position','reference','change', "change type"] (chrom2,pos2,ref2,mut2,change_type) = \ [ out_splt[ self.indexOf[k] ] for k in keys ] #if change_type == 'SNP' : return 1 #want to pass over if change_type == 'INS' : #example: # 1 866511 rs60722469 C CCCCT # 1 866512 * +CCCT INS return globes.compareVariants( chrom1, pos1, ref1, mut1[1:], \ chrom2, int(pos2)-1, ref2, mut2[1:] ) elif change_type == 'DEL' : #1 874864 . CT C #1 874865 * -T DEL Het return globes.compareVariants( chrom1, pos1, ref1[1:], mut1, \ chrom2, int(pos2)-1, mut2[1:], ref2 )
def eqkey( self, out_splt ) : if self.switch == 'snp' : keys = ['chrom','position','reference','change'] (chrom,pos,ref,mut) = [ out_splt[ self.indexOf[k] ] for k in keys ] return (globes.chromNum(chrom),pos,ref,mut) elif sel.switch == 'indel' : keys = ['chrom','position','reference','change', "change type"] (chrom2,pos2,ref2,mut2,change_type) = \ [ out_splt[ self.indexOf[k] ] for k in keys ] if change_type == 'INS' : #example: # 1 866511 rs60722469 C CCCCT # 1 866512 * +CCCT INS return globes.compareVariants( chrom1, pos1, ref1, mut1[1:], \ chrom2, int(pos2)-1, ref2, mut2[1:] ) elif change_type == 'DEL' : #1 874864 . CT C #1 874865 * -T DEL Het return globes.compareVariants( chrom1, pos1, ref1[1:], mut1, \ chrom2, int(pos2)-1, mut2[1:], ref2 ) else : assert "change_type %s is not" % change_type == " INS or DEL" else : assert 'switch must be' == ' snp or indel'
def comparator(a,b) : return globes.compareVariants( a[0],a[1],a[2],a[3],b[0],b[1],b[2],b[3] )
def sqlComparator( self, sqlrow, out_splt ) : (chrom1,pos1,ref1,mut1) = sqlrow[1], sqlrow[2],sqlrow[3],sqlrow[4] keys = ['chrom','position','reference','change'] (chrom2,pos2,ref2,mut2) = [ out_splt[ self.indexOf[k] ] for k in keys ] return globes.compareVariants( chrom1,pos1,ref1,mut1,\ chrom2,pos2,ref2,mut2 )