diff --git a/prob2020/python/indel.py b/prob2020/python/indel.py index 9b17106..22d62d0 100644 --- a/prob2020/python/indel.py +++ b/prob2020/python/indel.py @@ -106,10 +106,8 @@ def counts2maf(num_indels, myindel_lens, myindel_types, gene_bed, seed=None): var_class = 'Frame_Shift_Ins' if is_frame_shift[i] else 'In_Frame_Ins' dna_change = 'c.{0}_{1}ins'.format(pos[i], pos[i]) prot_change = 'p.?' - print(i) - print(myindel_lens) tmp = [gene_bed.gene_name, gene_bed.strand, gene_bed.chrom, - gpos, gpos, '-', 'N'*myindel_lens[i], '-', dna_change, + gpos, gpos, '-', 'N'*int(myindel_lens[i]), '-', dna_change, prot_change, var_class] maf_list.append(tmp) else: @@ -117,7 +115,7 @@ def counts2maf(num_indels, myindel_lens, myindel_types, gene_bed, seed=None): dna_change = 'c.{0}_{1}del'.format(pos[i], pos[i]+myindel_lens[i]) prot_change = 'p.?' tmp = [gene_bed.gene_name, gene_bed.strand, gene_bed.chrom, - gpos+1, gpos+myindel_lens[i], 'N'*myindel_lens[i], '-', '-', dna_change, + gpos+1, gpos+myindel_lens[i], 'N'*int(myindel_lens[i]), '-', '-', dna_change, prot_change, var_class] maf_list.append(tmp)