Mercurial > repos > mheinzl > variant_analyzer2

comparison read2mut.py @ 67:60e813039aae 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, 18 Mar 2021 10:42:19 +0000
parents d20be7e66378
children 4dfed0998184
comparison
equal deleted inserted replaced
66:d20be7e66378 67:60e813039aae
1193 'format': format2, 1193 'format': format2,
1194 'multi_range': 'L{}:M{} T{}:U{} B{}'.format(row_number + 1, row_number + 2, row_number + 1, row_number + 2, row_number + 1, row_number + 2)}) 1194 'multi_range': 'L{}:M{} T{}:U{} B{}'.format(row_number + 1, row_number + 2, row_number + 1, row_number + 2, row_number + 1, row_number + 2)})
1195 1195
1196 # sheet 2 1196 # sheet 2
1197 if chimera_correction: 1197 if chimera_correction:
1198 header_line2 = ('variant ID', 'cvrg', 'AC alt (all tiers)', 'AF (all tiers)', 'cvrg (tiers 1.1-2.5)', 'AC alt (tiers 1.1-2.5)', 'AF (tiers 1.1-2.5)', 'chimeras in AC alt (tiers 1.1-2.5)', 'chimera-corrected cvrg (tiers 1.1-2.5)', 'chimera-corrected AF (tiers 1.1-2.5)', 'AC alt (orginal DCS)', 'AF (original DCS)', 1198 header_line2 = ('variant ID', 'cvrg', 'AC alt (all tiers)', 'AF (all tiers)', 'cvrg (tiers 1.1-2.5)', 'AC alt (tiers 1.1-2.5)', 'AF (tiers 1.1-2.5)', 'chimera-corrected cvrg (tiers 1.1-2.5)', 'chimeras in AC alt (tiers 1.1-2.5)', 'chimera-corrected AF (tiers 1.1-2.5)', 'AC alt (orginal DCS)', 'AF (original DCS)',
1199 'tier 1.1', 'tier 1.2', 'tier 2.1', 'tier 2.2', 'tier 2.3', 'tier 2.4', 'tier 2.5', 1199 'tier 1.1', 'tier 1.2', 'tier 2.1', 'tier 2.2', 'tier 2.3', 'tier 2.4', 'tier 2.5',
1200 'tier 3.1', 'tier 3.2', 'tier 4', 'tier 5.1', 'tier 5.2', 'tier 5.3', 'tier 5.4', 'tier 5.5', 'tier 6', 'tier 7', 'AF 1.1-1.2', 'AF 1.1-2.1', 'AF 1.1-2.2', 1200 'tier 3.1', 'tier 3.2', 'tier 4', 'tier 5.1', 'tier 5.2', 'tier 5.3', 'tier 5.4', 'tier 5.5', 'tier 6', 'tier 7', 'AF 1.1-1.2', 'AF 1.1-2.1', 'AF 1.1-2.2',
1201 'AF 1.1-2.3', 'AF 1.1-2.4', 'AF 1.1-2.5', 'AF 1.1-3.1', 'AF 1.1-3.2', 'AF 1.1-4', 'AF 1.1-5.1', 'AF 1.1-5.2', 'AF 1.1-5.3', 'AF 1.1-5.4', 'AF 1.1-5.5', 'AF 1.1-6', 'AF 1.1-7') 1201 'AF 1.1-2.3', 'AF 1.1-2.4', 'AF 1.1-2.5', 'AF 1.1-3.1', 'AF 1.1-3.2', 'AF 1.1-4', 'AF 1.1-5.1', 'AF 1.1-5.2', 'AF 1.1-5.3', 'AF 1.1-5.4', 'AF 1.1-5.5', 'AF 1.1-6', 'AF 1.1-7')
1202 else: 1202 else:
1203 header_line2 = ('variant ID', 'cvrg', 'AC alt (all tiers)', 'AF (all tiers)', 'cvrg (tiers 1.1-2.5)', 'AC alt (tiers 1.1-2.5)', 'AF (tiers 1.1-2.5)', 'AC alt (orginal DCS)', 'AF (original DCS)', 1203 header_line2 = ('variant ID', 'cvrg', 'AC alt (all tiers)', 'AF (all tiers)', 'cvrg (tiers 1.1-2.5)', 'AC alt (tiers 1.1-2.5)', 'AF (tiers 1.1-2.5)', 'AC alt (orginal DCS)', 'AF (original DCS)',
1238 new_alt = sum(used_tiers[0:7]) - chimeras_all 1238 new_alt = sum(used_tiers[0:7]) - chimeras_all
1239 fraction_chimeras = safe_div(chimeras_all, float(sum(used_tiers[0:7]))) 1239 fraction_chimeras = safe_div(chimeras_all, float(sum(used_tiers[0:7])))
1240 if fraction_chimeras is None: 1240 if fraction_chimeras is None:
1241 fraction_chimeras = 0. 1241 fraction_chimeras = 0.
1242 new_cvrg = (cvrg - sum(used_tiers[-10:])) * (1. - fraction_chimeras) 1242 new_cvrg = (cvrg - sum(used_tiers[-10:])) * (1. - fraction_chimeras)
1243 lst.extend([chimeras_all, new_cvrg, safe_div(new_alt, new_cvrg)]) 1243 lst.extend([new_cvrg, chimeras_all, safe_div(new_alt, new_cvrg)])
1244 lst.extend([alt_count, safe_div(alt_count, cvrg)]) 1244 lst.extend([alt_count, safe_div(alt_count, cvrg)])
1245 lst.extend(used_tiers) 1245 lst.extend(used_tiers)
1246 lst.extend(cum_af) 1246 lst.extend(cum_af)
1247 lst = tuple(lst) 1247 lst = tuple(lst)
1248 ws2.write_row(row + 1, 0, lst) 1248 ws2.write_row(row + 1, 0, lst)