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 |
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date | Thu, 04 Feb 2021 08:55:35 +0000 |
parents | ded0dc6a20d3 |
children | 5800e3acb06d |
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7:ded0dc6a20d3 | 8:ced1a529e7cd |
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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 |