Mercurial > repos > mheinzl > variant_analyzer2
comparison mut2sscs.py @ 7:ded0dc6a20d3 draft
planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
| author | mheinzl |
|---|---|
| date | Mon, 25 Jan 2021 13:21:55 +0000 |
| parents | 11a2a34f8a2b |
| children | ced1a529e7cd |
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| 6:11a2a34f8a2b | 7:ded0dc6a20d3 |
|---|---|
| 64 ref_pos_dict = {} | 64 ref_pos_dict = {} |
| 65 | 65 |
| 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 alt = variant.ALT[0] |
| 72 # nc = variant.format('NC') | 72 chrom_stop_pos = str(chrom) + "#" + str(stop_pos) + "#" + ref + "#" + alt |
| 73 ad = variant.format('AD') | |
| 74 | 73 |
| 75 if len(ref) == len(alt): | 74 if len(ref) == len(alt): |
| 76 | 75 |
| 77 for pileupcolumn in bam.pileup(chrom, stop_pos - 1, stop_pos + 1, max_depth=1000000000): | 76 for pileupcolumn in bam.pileup(chrom, stop_pos - 1, stop_pos + 1, max_depth=1000000000): |
| 78 if pileupcolumn.reference_pos == stop_pos: | 77 if pileupcolumn.reference_pos == stop_pos: |