Mercurial > repos > mheinzl > variant_analyzer2
comparison mut2sscs.py @ 8:ced1a529e7cd draft
planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
author | mheinzl |
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date | Thu, 04 Feb 2021 08:55:35 +0000 |
parents | ded0dc6a20d3 |
children | e18c5293aac7 |
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7:ded0dc6a20d3 | 8:ced1a529e7cd |
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66 for variant in VCF(file1): | 66 for variant in VCF(file1): |
67 chrom = variant.CHROM | 67 chrom = variant.CHROM |
68 stop_pos = variant.start | 68 stop_pos = variant.start |
69 #chrom_stop_pos = str(chrom) + "#" + str(stop_pos) | 69 #chrom_stop_pos = str(chrom) + "#" + str(stop_pos) |
70 ref = variant.REF | 70 ref = variant.REF |
71 alt = variant.ALT[0] | 71 if len(variant.ALT) > 0: |
72 alt = variant.ALT[0] | |
73 else: | |
74 alt = variant.ALT | |
72 chrom_stop_pos = str(chrom) + "#" + str(stop_pos) + "#" + ref + "#" + alt | 75 chrom_stop_pos = str(chrom) + "#" + str(stop_pos) + "#" + ref + "#" + alt |
73 | 76 |
74 if len(ref) == len(alt): | 77 if len(ref) == len(alt): |
75 | 78 |
76 for pileupcolumn in bam.pileup(chrom, stop_pos - 1, stop_pos + 1, max_depth=1000000000): | 79 for pileupcolumn in bam.pileup(chrom, stop_pos - 1, stop_pos + 1, max_depth=1000000000): |