Mercurial > repos > mheinzl > variant_analyzer2
comparison read2mut.py @ 4:386438cd4c3b draft
planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
| author | mheinzl |
|---|---|
| date | Tue, 27 Oct 2020 12:39:21 +0000 |
| parents | 4fc62ab6e9e8 |
| children | d9cbf833624e |
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| 3:4fc62ab6e9e8 | 4:386438cd4c3b |
|---|---|
| 229 'read median length.ba', 'DCS median length', | 229 'read median length.ba', 'DCS median length', |
| 230 'FS.ab', 'FS.ba', 'FSqc.ab', 'FSqc.ba', 'ref.ab', 'ref.ba', 'alt.ab', 'alt.ba', | 230 'FS.ab', 'FS.ba', 'FSqc.ab', 'FSqc.ba', 'ref.ab', 'ref.ba', 'alt.ab', 'alt.ba', |
| 231 'rel. ref.ab', 'rel. ref.ba', 'rel. alt.ab', 'rel. alt.ba', | 231 'rel. ref.ab', 'rel. ref.ba', 'rel. alt.ab', 'rel. alt.ba', |
| 232 'na.ab', 'na.ba', 'lowq.ab', 'lowq.ba', 'trim.ab', 'trim.ba', | 232 'na.ab', 'na.ba', 'lowq.ab', 'lowq.ba', 'trim.ab', 'trim.ba', |
| 233 'SSCS alt.ab', 'SSCS alt.ba', 'SSCS ref.ab', 'SSCS ref.ba', | 233 'SSCS alt.ab', 'SSCS alt.ba', 'SSCS ref.ab', 'SSCS ref.ba', |
| 234 'other mut', 'chimeric tag') | 234 'in phase', 'chimeric tag') |
| 235 ws1.write_row(0, 0, header_line) | 235 ws1.write_row(0, 0, header_line) |
| 236 | 236 |
| 237 counter_tier11 = 0 | 237 counter_tier11 = 0 |
| 238 counter_tier12 = 0 | 238 counter_tier12 = 0 |
| 239 counter_tier21 = 0 | 239 counter_tier21 = 0 |
| 318 k1 = mut_read_dict[(key2[:-5] + '.ab.1')].keys() | 318 k1 = mut_read_dict[(key2[:-5] + '.ab.1')].keys() |
| 319 add_mut1 = len(k1) | 319 add_mut1 = len(k1) |
| 320 if add_mut1 > 1: | 320 if add_mut1 > 1: |
| 321 for k, v in mut_read_dict[(key2[:-5] + '.ab.1')].items(): | 321 for k, v in mut_read_dict[(key2[:-5] + '.ab.1')].items(): |
| 322 if k != key1: | 322 if k != key1: |
| 323 new_mut = str(k).split("#")[0] + "-" + str(int(str(k).split("#")[1]) + 1) + "-" + v[1] + "-" + v[0] | |
| 323 if len(add_mut14) == 0: | 324 if len(add_mut14) == 0: |
| 324 add_mut14 = str(k) + "_" + v | 325 add_mut14 = new_mut |
| 325 else: | 326 else: |
| 326 add_mut14 = add_mut14 + ", " + str(k) + "_" + v | 327 add_mut14 = add_mut14 + ", " + new_mut |
| 327 else: | 328 else: |
| 328 k1 = [] | 329 k1 = [] |
| 329 else: | 330 else: |
| 330 total1 = total1new = na1 = lowq1 = 0 | 331 total1 = total1new = na1 = lowq1 = 0 |
| 331 ref1 = alt1 = ref1f = alt1f = 0 | 332 ref1 = alt1 = ref1f = alt1f = 0 |
| 360 k2 = mut_read_dict[(key2[:-5] + '.ab.2')].keys() | 361 k2 = mut_read_dict[(key2[:-5] + '.ab.2')].keys() |
| 361 add_mut2 = len(k2) | 362 add_mut2 = len(k2) |
| 362 if add_mut2 > 1: | 363 if add_mut2 > 1: |
| 363 for k, v in mut_read_dict[(key2[:-5] + '.ab.2')].items(): | 364 for k, v in mut_read_dict[(key2[:-5] + '.ab.2')].items(): |
| 364 if k != key1: | 365 if k != key1: |
| 366 new_mut = str(k).split("#")[0] + "-" + str(int(str(k).split("#")[1]) + 1) + "-" + v[1] + "-" + v[0] | |
| 365 if len(add_mut23) == 0: | 367 if len(add_mut23) == 0: |
| 366 add_mut23 = str(k) + "_" + v | 368 add_mut23 = new_mut |
| 367 else: | 369 else: |
| 368 add_mut23 = add_mut23 + ", " + str(k) + "_" + v | 370 add_mut23 = add_mut23 + ", " + new_mut |
| 369 else: | 371 else: |
| 370 k2 = [] | 372 k2 = [] |
| 371 else: | 373 else: |
| 372 total2 = total2new = na2 = lowq2 = 0 | 374 total2 = total2new = na2 = lowq2 = 0 |
| 373 ref2 = alt2 = ref2f = alt2f = 0 | 375 ref2 = alt2 = ref2f = alt2f = 0 |
| 401 if (key2[:-5] + '.ba.1') in mut_read_dict.keys(): | 403 if (key2[:-5] + '.ba.1') in mut_read_dict.keys(): |
| 402 add_mut3 = len(mut_read_dict[(key2[:-5] + '.ba.1')].keys()) | 404 add_mut3 = len(mut_read_dict[(key2[:-5] + '.ba.1')].keys()) |
| 403 if add_mut3 > 1: | 405 if add_mut3 > 1: |
| 404 for k, v in mut_read_dict[(key2[:-5] + '.ba.1')].items(): | 406 for k, v in mut_read_dict[(key2[:-5] + '.ba.1')].items(): |
| 405 if k != key1 and k not in k2: | 407 if k != key1 and k not in k2: |
| 408 new_mut = str(k).split("#")[0] + "-" + str(int(str(k).split("#")[1]) + 1) + "-" + v[1] + "-" + v[0] | |
| 406 if len(add_mut23) == 0: | 409 if len(add_mut23) == 0: |
| 407 add_mut23 = str(k) + "_" + v | 410 add_mut23 = new_mut |
| 408 else: | 411 else: |
| 409 add_mut23 = add_mut23 + ", " + str(k) + "_" + v | 412 add_mut23 = add_mut23 + ", " + new_mut |
| 410 else: | 413 else: |
| 411 total3 = total3new = na3 = lowq3 = 0 | 414 total3 = total3new = na3 = lowq3 = 0 |
| 412 ref3 = alt3 = ref3f = alt3f = 0 | 415 ref3 = alt3 = ref3f = alt3f = 0 |
| 413 | 416 |
| 414 if key2[:-5] + '.ba.2' in mut_dict[key1].keys(): | 417 if key2[:-5] + '.ba.2' in mut_dict[key1].keys(): |
| 439 if (key2[:-5] + '.ba.2') in mut_read_dict.keys(): | 442 if (key2[:-5] + '.ba.2') in mut_read_dict.keys(): |
| 440 add_mut4 = len(mut_read_dict[(key2[:-5] + '.ba.2')].keys()) | 443 add_mut4 = len(mut_read_dict[(key2[:-5] + '.ba.2')].keys()) |
| 441 if add_mut4 > 1: | 444 if add_mut4 > 1: |
| 442 for k, v in mut_read_dict[(key2[:-5] + '.ba.2')].items(): | 445 for k, v in mut_read_dict[(key2[:-5] + '.ba.2')].items(): |
| 443 if k != key1 and k not in k1: | 446 if k != key1 and k not in k1: |
| 447 new_mut = str(k).split("#")[0] + "-" + str(int(str(k).split("#")[1]) + 1) + "-" + v[1] + "-" + v[0] | |
| 444 if len(add_mut14) == 0: | 448 if len(add_mut14) == 0: |
| 445 add_mut14 = str(k) + "_" + v | 449 add_mut14 = new_mut |
| 446 else: | 450 else: |
| 447 add_mut14 = add_mut14 + ", " + str(k) + "_" + v | 451 add_mut14 = add_mut14 + ", " + new_mut |
| 448 else: | 452 else: |
| 449 total4 = total4new = na4 = lowq4 = 0 | 453 total4 = total4new = na4 = lowq4 = 0 |
| 450 ref4 = alt4 = ref4f = alt4f = 0 | 454 ref4 = alt4 = ref4f = alt4f = 0 |
| 451 | 455 |
| 452 read_pos1 = read_pos2 = read_pos3 = read_pos4 = -1 | 456 read_pos1 = read_pos2 = read_pos3 = read_pos4 = -1 |