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comparison Marea/ras_generator.py @ 77:3b0e71e28c0b draft

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Fix custom rules not in xml
author bimib
date Sun, 03 Jan 2021 21:45:12 +0000
parents 3af9d394367c
children
comparison
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76:3f144565551f 77:3b0e71e28c0b
428 warnings.simplefilter('ignore') 428 warnings.simplefilter('ignore')
429 recon = cb.io.read_sbml_model(data) 429 recon = cb.io.read_sbml_model(data)
430 react = recon.reactions 430 react = recon.reactions
431 rules = [react[i].gene_reaction_rule for i in range(len(react))] 431 rules = [react[i].gene_reaction_rule for i in range(len(react))]
432 ids = [react[i].id for i in range(len(react))] 432 ids = [react[i].id for i in range(len(react))]
433 except cb.io.sbml3.CobraSBMLError: 433 except:
434 try: 434 try:
435 data = (pd.read_csv(data, sep = '\t', dtype = str, engine='python')).fillna('') 435 data = (pd.read_csv(data, sep = '\t', dtype = str, engine='python')).fillna('')
436 if len(data.columns) < 2: 436 if len(data.columns) < 2:
437 sys.exit('Execution aborted: wrong format of '+ 437 sys.exit('Execution aborted: wrong format of '+
438 'custom datarules\n') 438 'custom datarules\n')