Mercurial > repos > mheinzl > variant_analyzer2
diff mut2sscs.py @ 75:6ccff403db8a draft
planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
author | mheinzl |
---|---|
date | Tue, 23 Mar 2021 15:18:17 +0000 |
parents | d21960b45a6b |
children | fdfe9a919ff7 |
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--- a/mut2sscs.py Fri Mar 19 14:16:31 2021 +0000 +++ b/mut2sscs.py Tue Mar 23 15:18:17 2021 +0000 @@ -66,16 +66,13 @@ for variant in VCF(file1): chrom = variant.CHROM stop_pos = variant.start - #chrom_stop_pos = str(chrom) + "#" + str(stop_pos) ref = variant.REF if len(variant.ALT) == 0: continue else: alt = variant.ALT[0] chrom_stop_pos = str(chrom) + "#" + str(stop_pos) + "#" + ref + "#" + alt - if len(ref) == len(alt): - for pileupcolumn in bam.pileup(chrom, stop_pos - 1, stop_pos + 1, max_depth=1000000000): if pileupcolumn.reference_pos == stop_pos: count_alt = 0 @@ -137,4 +134,3 @@ if __name__ == '__main__': sys.exit(mut2sscs(sys.argv)) -