Mercurial > repos > mheinzl > variant_analyzer2

comparison read2mut.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 ced1a529e7cd
children 84a1a3f70407
comparison
equal deleted inserted replaced
9:5800e3acb06d 10:e18c5293aac7
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 if len(variant.ALT) > 0: 135 if len(variant.ALT) == 0:
136 continue
137 else:
136 alt = variant.ALT[0] 138 alt = variant.ALT[0]
137 else:
138 alt = variant.ALT
139 chrom_stop_pos = str(chrom) + "#" + str(stop_pos) + "#" + ref + "#" + alt 139 chrom_stop_pos = str(chrom) + "#" + str(stop_pos) + "#" + ref + "#" + alt
140 140
141 if len(ref) == len(alt): 141 if len(ref) == len(alt):
142 mut_array.append([chrom, stop_pos, ref, alt]) 142 mut_array.append([chrom, stop_pos, ref, alt])
143 i += 1 143 i += 1