Mercurial > repos > artbio > repenrich

comparison RepEnrich.py @ 2:15e3e29f310e draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit c89c33e5ea8fc63f3ea5c0f66ebc5fa822ac734b
author artbio
date Tue, 19 Sep 2017 17:23:15 -0400
parents f6f0f1e5e940
children d1f7ab78f7b5
comparison
equal deleted inserted replaced
1:51b4590a972d 2:15e3e29f310e
429 print('Writing final output and removing intermediate files...') 429 print('Writing final output and removing intermediate files...')
430 # print output to file of the categorized counts and total overlapping counts: 430 # print output to file of the categorized counts and total overlapping counts:
431 if allcountmethod == "TRUE": 431 if allcountmethod == "TRUE":
432 fout1 = open(outputfolder + os.path.sep + outputfile_prefix 432 fout1 = open(outputfolder + os.path.sep + outputfile_prefix
433 + '_total_counts.txt', 'w') 433 + '_total_counts.txt', 'w')
434 for key in reptotalcounts.keys(): 434 for key in sorted(reptotalcounts.keys()):
435 fout1.write(str(key) + '\t' + repeatclass[key] + '\t' + 435 fout1.write(str(key) + '\t' + repeatclass[key] + '\t' +
436 repeatfamily[key] + '\t' + str(reptotalcounts[key]) 436 repeatfamily[key] + '\t' + str(reptotalcounts[key])
437 + '\n') 437 + '\n')
438 fout2 = open(outputfolder + os.path.sep + outputfile_prefix 438 fout2 = open(outputfolder + os.path.sep + outputfile_prefix
439 + '_class_total_counts.txt', 'w') 439 + '_class_total_counts.txt', 'w')
440 for key in classtotalcounts.keys(): 440 for key in sorted(classtotalcounts.keys()):
441 fout2.write(str(key) + '\t' + str(classtotalcounts[key]) + '\n') 441 fout2.write(str(key) + '\t' + str(classtotalcounts[key]) + '\n')
442 fout3 = open(outputfolder + os.path.sep + outputfile_prefix 442 fout3 = open(outputfolder + os.path.sep + outputfile_prefix
443 + '_family_total_counts.txt', 'w') 443 + '_family_total_counts.txt', 'w')
444 for key in familytotalcounts.keys(): 444 for key in sorted(familytotalcounts.keys()):
445 fout3.write(str(key) + '\t' + str(familytotalcounts[key]) + '\n') 445 fout3.write(str(key) + '\t' + str(familytotalcounts[key]) + '\n')
446 fout4 = open(outputfolder + os.path.sep + outputfile_prefix + 446 fout4 = open(outputfolder + os.path.sep + outputfile_prefix +
447 '_unique_counts.txt', 'w') 447 '_unique_counts.txt', 'w')
448 for key in repcounts2.keys(): 448 for key in sorted(repcounts2.keys()):
449 fout4.write(str(key) + '\t' + repeatclass[key] + '\t' + 449 fout4.write(str(key) + '\t' + repeatclass[key] + '\t' +
450 repeatfamily[key] + '\t' + str(repcounts2[key]) + '\n') 450 repeatfamily[key] + '\t' + str(repcounts2[key]) + '\n')
451 fout5 = open(outputfolder + os.path.sep + outputfile_prefix 451 fout5 = open(outputfolder + os.path.sep + outputfile_prefix
452 + '_class_fraction_counts.txt', 'w') 452 + '_class_fraction_counts.txt', 'w')
453 for key in classfractionalcounts.keys(): 453 for key in sorted(classfractionalcounts.keys()):
454 fout5.write(str(key) + '\t' + str(classfractionalcounts[key]) + '\n') 454 fout5.write(str(key) + '\t' + str(classfractionalcounts[key]) + '\n')
455 fout6 = open(outputfolder + os.path.sep + outputfile_prefix + 455 fout6 = open(outputfolder + os.path.sep + outputfile_prefix +
456 '_family_fraction_counts.txt', 'w') 456 '_family_fraction_counts.txt', 'w')
457 for key in familyfractionalcounts.keys(): 457 for key in sorted(familyfractionalcounts.keys()):
458 fout6.write(str(key) + '\t' + str(familyfractionalcounts[key]) + '\n') 458 fout6.write(str(key) + '\t' + str(familyfractionalcounts[key]) + '\n')
459 fout7 = open(outputfolder + os.path.sep + outputfile_prefix 459 fout7 = open(outputfolder + os.path.sep + outputfile_prefix
460 + '_fraction_counts.txt', 'w') 460 + '_fraction_counts.txt', 'w')
461 for key in fractionalcounts.keys(): 461 for key in sorted(fractionalcounts.keys()):
462 fout7.write(str(key) + '\t' + repeatclass[key] + '\t' + 462 fout7.write(str(key) + '\t' + repeatclass[key] + '\t' +
463 repeatfamily[key] + '\t' + str(int(fractionalcounts[key])) 463 repeatfamily[key] + '\t' + str(int(fractionalcounts[key]))
464 + '\n') 464 + '\n')
465 fout1.close() 465 fout1.close()
466 fout2.close() 466 fout2.close()
470 fout6.close() 470 fout6.close()
471 fout7.close() 471 fout7.close()
472 else: 472 else:
473 fout1 = open(outputfolder + os.path.sep + outputfile_prefix + 473 fout1 = open(outputfolder + os.path.sep + outputfile_prefix +
474 '_class_fraction_counts.txt', 'w') 474 '_class_fraction_counts.txt', 'w')
475 for key in classfractionalcounts.keys(): 475 for key in sorted(classfractionalcounts.keys()):
476 fout1.write(str(key) + '\t' + str(classfractionalcounts[key]) + '\n') 476 fout1.write(str(key) + '\t' + str(classfractionalcounts[key]) + '\n')
477 fout2 = open(outputfolder + os.path.sep + outputfile_prefix + 477 fout2 = open(outputfolder + os.path.sep + outputfile_prefix +
478 '_family_fraction_counts.txt', 'w') 478 '_family_fraction_counts.txt', 'w')
479 for key in familyfractionalcounts.keys(): 479 for key in sorted(familyfractionalcounts.keys()):
480 fout2.write(str(key) + '\t' + str(familyfractionalcounts[key]) + '\n') 480 fout2.write(str(key) + '\t' + str(familyfractionalcounts[key]) + '\n')
481 fout3 = open(outputfolder + os.path.sep + outputfile_prefix + 481 fout3 = open(outputfolder + os.path.sep + outputfile_prefix +
482 '_fraction_counts.txt', 'w') 482 '_fraction_counts.txt', 'w')
483 for key in fractionalcounts.keys(): 483 for key in sorted(fractionalcounts.keys()):
484 fout3.write(str(key) + '\t' + repeatclass[key] + '\t' + 484 fout3.write(str(key) + '\t' + repeatclass[key] + '\t' +
485 repeatfamily[key] + '\t' + str(int(fractionalcounts[key])) 485 repeatfamily[key] + '\t' + str(int(fractionalcounts[key]))
486 + '\n') 486 + '\n')
487 fout1.close() 487 fout1.close()
488 fout2.close() 488 fout2.close()