Mercurial > repos > mheinzl > variant_analyzer2

comparison read2mut.py @ 4:386438cd4c3b draft

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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
comparison
equal deleted inserted replaced
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