Mercurial > repos > mheinzl > variant_analyzer2

comparison read2mut.py @ 8:ced1a529e7cd 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 08:55:35 +0000
parents ded0dc6a20d3
children e18c5293aac7
comparison
equal deleted inserted replaced
7:ded0dc6a20d3 8:ced1a529e7cd
130 # break 130 # break
131 chrom = variant.CHROM 131 chrom = variant.CHROM
132 stop_pos = variant.start 132 stop_pos = variant.start
133 #chrom_stop_pos = str(chrom) + "#" + str(stop_pos) 133 #chrom_stop_pos = str(chrom) + "#" + str(stop_pos)
134 ref = variant.REF 134 ref = variant.REF
135 alt = variant.ALT[0] 135 if len(variant.ALT) > 0:
136 alt = variant.ALT[0]
137 else:
138 alt = variant.ALT
136 chrom_stop_pos = str(chrom) + "#" + str(stop_pos) + "#" + ref + "#" + alt 139 chrom_stop_pos = str(chrom) + "#" + str(stop_pos) + "#" + ref + "#" + alt
137 140
138 if len(ref) == len(alt): 141 if len(ref) == len(alt):
139 mut_array.append([chrom, stop_pos, ref, alt]) 142 mut_array.append([chrom, stop_pos, ref, alt])
140 i += 1 143 i += 1