Mercurial > repos > mheinzl > variant_analyzer2
comparison mut2read.py @ 8:ced1a529e7cd draft
planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
| author | mheinzl |
|---|---|
| date | Thu, 04 Feb 2021 08:55:35 +0000 |
| parents | ded0dc6a20d3 |
| children | 5800e3acb06d |
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| 7:ded0dc6a20d3 | 8:ced1a529e7cd |
|---|---|
| 72 for variant in VCF(file1): | 72 for variant in VCF(file1): |
| 73 chrom = variant.CHROM | 73 chrom = variant.CHROM |
| 74 stop_pos = variant.start | 74 stop_pos = variant.start |
| 75 #chrom_stop_pos = str(chrom) + "#" + str(stop_pos) | 75 #chrom_stop_pos = str(chrom) + "#" + str(stop_pos) |
| 76 ref = variant.REF | 76 ref = variant.REF |
| 77 alt = variant.ALT[0] | 77 if len(variant.ALT) > 0: |
| 78 alt = variant.ALT[0] | |
| 79 else: | |
| 80 alt = variant.ALT | |
| 78 chrom_stop_pos = str(chrom) + "#" + str(stop_pos) + "#" + ref + "#" + alt | 81 chrom_stop_pos = str(chrom) + "#" + str(stop_pos) + "#" + ref + "#" + alt |
| 79 | 82 |
| 80 | 83 |
| 81 dcs_len = [] | 84 dcs_len = [] |
| 82 if len(ref) == len(alt): | 85 if len(ref) == len(alt): |
| 83 for pileupcolumn in bam.pileup(chrom, stop_pos - 1, stop_pos + 1, max_depth=100000000): | 86 for pileupcolumn in bam.pileup(chrom, stop_pos - 1, stop_pos + 1, max_depth=100000000): |
| 84 | |
| 85 if pileupcolumn.reference_pos == stop_pos: | 87 if pileupcolumn.reference_pos == stop_pos: |
| 86 count_alt = 0 | 88 count_alt = 0 |
| 87 count_ref = 0 | 89 count_ref = 0 |
| 88 count_indel = 0 | 90 count_indel = 0 |
| 89 count_n = 0 | 91 count_n = 0 |