Mercurial > repos > jjjjia > cpo_prediction

comparison cpo_galaxy_prediction.py @ 23:2cca036ceb91 draft

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planemo upload
author jjjjia
date Wed, 29 Aug 2018 01:42:01 -0400
parents e03c8f2d2629
children e5a7da2239af
comparison
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22:e03c8f2d2629 23:2cca036ceb91
581 for keys in rFinder: 581 for keys in rFinder:
582 carbapenamases.append(rFinder[keys].shortGene + "(" + rFinder[keys].source + ")") 582 carbapenamases.append(rFinder[keys].shortGene + "(" + rFinder[keys].source + ")")
583 resfinderCarbas.append(rFinder[keys]) 583 resfinderCarbas.append(rFinder[keys])
584 for keys in rgiAMR: 584 for keys in rgiAMR:
585 if (rgiAMR[keys].Drug_Class.find("carbapenem") > -1 and rgiAMR[keys].AMR_Gene_Family.find("beta-lactamase") > -1): 585 if (rgiAMR[keys].Drug_Class.find("carbapenem") > -1 and rgiAMR[keys].AMR_Gene_Family.find("beta-lactamase") > -1):
586 if (rgiAMR[keys].Best_Hit_ARO not in carbapenamases): 586 if ((rgiAMR[keys].Best_Hit_ARO+ "(" + rgiAMR[keys].source + ")") not in carbapenamases):
587 carbapenamases.append(rgiAMR[keys].Best_Hit_ARO+ "(" + rgiAMR[keys].source + ")") 587 carbapenamases.append(rgiAMR[keys].Best_Hit_ARO+ "(" + rgiAMR[keys].source + ")")
588 else: 588 else:
589 if (rgiAMR[keys].Best_Hit_ARO not in amrGenes): 589 if ((rgiAMR[keys].Best_Hit_ARO+ "(" + rgiAMR[keys].source + ")") not in amrGenes):
590 amrGenes.append(rgiAMR[keys].Best_Hit_ARO+ "(" + rgiAMR[keys].source + ")") 590 amrGenes.append(rgiAMR[keys].Best_Hit_ARO+ "(" + rgiAMR[keys].source + ")")
591 #endregion 591 #endregion
592 592
593 #region output parsed mlst information 593 #region output parsed mlst information
594 print("formatting mlst outputs") 594 print("formatting mlst outputs")