Mercurial > repos > mheinzl > variant_analyzer2

comparison mut2read.py @ 10:e18c5293aac7 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 Thu, 04 Feb 2021 09:01:43 +0000
parents 5800e3acb06d
children 84a1a3f70407
comparison
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9:5800e3acb06d 10:e18c5293aac7
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 if len(variant.ALT) > 0: 77 if len(variant.ALT) == 0:
78 continue
79 else:
78 alt = variant.ALT[0] 80 alt = variant.ALT[0]
79 else:
80 alt = variant.ALT
81 print(alt) 81 print(alt)
82 chrom_stop_pos = str(chrom) + "#" + str(stop_pos) + "#" + ref + "#" + alt 82 chrom_stop_pos = str(chrom) + "#" + str(stop_pos) + "#" + ref + "#" + alt
83 83
84 84
85 dcs_len = [] 85 dcs_len = []