Mercurial > repos > mheinzl > hd
comparison hd.py @ 8:e2596a4e1c56 draft
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
| author | mheinzl |
|---|---|
| date | Tue, 15 May 2018 11:15:22 -0400 |
| parents | 6f124cc95838 |
| children | c81bc96bea1c |
comparison
equal
deleted
inserted
replaced
| 7:6f124cc95838 | 8:e2596a4e1c56 |
|---|---|
| 437 array1_half2 = numpy.array([i[len(i) / 2:len(i)] for i in array1]) # mate1 part 2 | 437 array1_half2 = numpy.array([i[len(i) / 2:len(i)] for i in array1]) # mate1 part 2 |
| 438 | 438 |
| 439 array2_half = numpy.array([i[0:(len(i)) / 2] for i in array2]) # mate2 part1 | 439 array2_half = numpy.array([i[0:(len(i)) / 2] for i in array2]) # mate2 part1 |
| 440 array2_half2 = numpy.array([i[len(i) / 2:len(i)] for i in array2]) # mate2 part2 | 440 array2_half2 = numpy.array([i[len(i) / 2:len(i)] for i in array2]) # mate2 part2 |
| 441 | 441 |
| 442 diff11 = 999 * numpy.ones(len(array2)) | 442 #diff11 = 999 * numpy.ones(len(array2)) |
| 443 relativeDiffList = 999 * numpy.ones(len(array2)) | 443 #relativeDiffList = 999 * numpy.ones(len(array2)) |
| 444 ham1 = 999 * numpy.ones(len(array2)) | 444 #ham1 = 999 * numpy.ones(len(array2)) |
| 445 ham2 = 999 * numpy.ones(len(array2)) | 445 #ham2 = 999 * numpy.ones(len(array2)) |
| 446 min_valueList = 999 * numpy.ones(len(array2)) | 446 #min_valueList = 999 * numpy.ones(len(array2)) |
| 447 min_tagsList = 999 * numpy.ones(len(array2)) | 447 #min_tagsList = 999 * numpy.ones(len(array2)) |
| 448 diff11_zeros = 999 * numpy.ones(len(array2)) | 448 #diff11_zeros = 999 * numpy.ones(len(array2)) |
| 449 min_tagsList_zeros = 999 * numpy.ones(len(array2)) | 449 #min_tagsList_zeros = 999 * numpy.ones(len(array2)) |
| 450 | 450 |
| 451 | 451 |
| 452 #diff11 = [] | 452 diff11 = [] |
| 453 #relativeDiffList = [] | 453 relativeDiffList = [] |
| 454 #ham1 = [] | 454 ham1 = [] |
| 455 #ham2 = [] | 455 ham2 = [] |
| 456 #min_valueList = [] | 456 min_valueList = [] |
| 457 #min_tagsList = [] | 457 min_tagsList = [] |
| 458 #diff11_zeros = [] | 458 diff11_zeros = [] |
| 459 #min_tagsList_zeros = [] | 459 min_tagsList_zeros = [] |
| 460 counter = 0 # counter, only used to see how many HDs of tags were already calculated | 460 i = 0 # counter, only used to see how many HDs of tags were already calculated |
| 461 if mate_b is False: # HD calculation for all a's | 461 if mate_b is False: # HD calculation for all a's |
| 462 half1_mate1 = array1_half | 462 half1_mate1 = array1_half |
| 463 half2_mate1 = array1_half2 | 463 half2_mate1 = array1_half2 |
| 464 half1_mate2 = array2_half | 464 half1_mate2 = array2_half |
| 465 half2_mate2 = array2_half2 | 465 half2_mate2 = array2_half2 |
| 494 d = d_2 | 494 d = d_2 |
| 495 d2 = d_1 | 495 d2 = d_1 |
| 496 else: # half1, corrects the variable of the HD from both halfs if it is a or b | 496 else: # half1, corrects the variable of the HD from both halfs if it is a or b |
| 497 d = d_1 | 497 d = d_1 |
| 498 d2 = d_2 | 498 d2 = d_2 |
| 499 min_valueList[counter] = d + d2 | 499 min_valueList.append(d + d2) |
| 500 min_tagsList[counter] = tag | 500 min_tagsList.append(tag) |
| 501 ham1[counter] = d | 501 ham1.append.append(d) |
| 502 ham2[counter] = d2 | 502 ham2.append.append(d2) |
| 503 difference1 = abs(d - d2) | 503 difference1 = abs(d - d2) |
| 504 diff11[counter] = difference1 | 504 diff11.append(difference1) |
| 505 rel_difference = round(float(difference1) / (d + d2), 1) | 505 rel_difference = round(float(difference1) / (d + d2), 1) |
| 506 relativeDiffList[counter] = rel_difference | 506 relativeDiffList.append(rel_difference) |
| 507 | 507 |
| 508 #### tags which have identical parts: | 508 #### tags which have identical parts: |
| 509 if d == 0 or d2 == 0: | 509 if d == 0 or d2 == 0: |
| 510 min_tagsList_zeros[counter] = tag | 510 min_tagsList_zeros.append(tag) |
| 511 difference1_zeros = abs(d - d2) | 511 difference1_zeros = abs(d - d2) |
| 512 diff11_zeros[counter] = difference1_zeros | 512 diff11_zeros.append(difference1_zeros) |
| 513 | 513 i += 1 |
| 514 counter += 1 | |
| 515 | 514 |
| 516 #print(i) | 515 #print(i) |
| 517 diff11 = [st for st in diff11 if st != 999] | 516 diff11 = [st for st in diff11 if st != 999] |
| 518 ham1 = [st for st in ham1 if st != 999] | 517 ham1 = [st for st in ham1 if st != 999] |
| 519 ham2 = [st for st in ham2 if st != 999] | 518 ham2 = [st for st in ham2 if st != 999] |
| 710 files = [file1] | 709 files = [file1] |
| 711 name1 = name1.split(".tabular")[0] | 710 name1 = name1.split(".tabular")[0] |
| 712 names = [name1] | 711 names = [name1] |
| 713 pdf_files = [title_savedFile_pdf] | 712 pdf_files = [title_savedFile_pdf] |
| 714 csv_files = [title_savedFile_csv] | 713 csv_files = [title_savedFile_csv] |
| 714 | |
| 715 print(type(onlyDuplicates)) | |
| 716 print(onlyDuplicates) | |
| 715 | 717 |
| 716 for f, name_file, pdf_f, csv_f in zip(files, names, pdf_files, csv_files): | 718 for f, name_file, pdf_f, csv_f in zip(files, names, pdf_files, csv_files): |
| 717 with open(csv_f, "w") as output_file, PdfPages(pdf_f) as pdf: | 719 with open(csv_f, "w") as output_file, PdfPages(pdf_f) as pdf: |
| 718 print("dataset: ", name_file) | 720 print("dataset: ", name_file) |
| 719 integers, data_array = readFileReferenceFree(f) | 721 integers, data_array = readFileReferenceFree(f) |