Mercurial > repos > mheinzl > variant_analyzer2

comparison mut2read.py @ 7:ded0dc6a20d3 draft

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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
comparison
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6:11a2a34f8a2b 7:ded0dc6a20d3
70 cvrg_dict = {} 70 cvrg_dict = {}
71 71
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 alt = variant.ALT[0]
78 # nc = variant.format('NC') 78 chrom_stop_pos = str(chrom) + "#" + str(stop_pos) + "#" + ref + "#" + alt
79 ad = variant.format('AD') 79
80 80
81 dcs_len = [] 81 dcs_len = []
82 if len(ref) == len(alt): 82 if len(ref) == len(alt):
83 for pileupcolumn in bam.pileup(chrom, stop_pos - 1, stop_pos + 1, max_depth=100000000): 83 for pileupcolumn in bam.pileup(chrom, stop_pos - 1, stop_pos + 1, max_depth=100000000):
84 84