comparison Marea/marea.py @ 53:7b57a93ac594 draft

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52:88b7180d7b79

            split_rules.append([])
    if err_rules:
        warning('Warning: wrong format rule in ' + str(err_rules) + '\n')
    return (split_rules, list(set(tmp_gene_in_rule)))

def make_recon(data):
    try:
        import cobra as cb
        import warnings
        with warnings.catch_warnings():
            warnings.simplefilter('ignore')
            recon = cb.io.read_sbml_model(data)
        react = recon.reactions
        rules = [react[i].gene_reaction_rule for i in range(len(react))]
        ids = [react[i].id for i in range(len(react))]
    except cb.io.sbml.CobraSBMLError:
        try:
            data = (pd.read_csv(data, sep = '\t', dtype = str, engine='python')).fillna('')
            if len(data.columns) < 2:
                sys.exit('Execution aborted: wrong format of '+
                         'custom datarules\n')
            if not len(data.columns) == 2:
                warning('Warning: more than 2 columns in custom datarules.\n' +
                        'Extra columns have been disregarded\n')
            ids = list(data.iloc[:, 0])
            rules = list(data.iloc[:, 1])
        except pd.errors.EmptyDataError:
            sys.exit('Execution aborted: wrong format of custom datarules\n')
        except pd.errors.ParserError:
            sys.exit('Execution aborted: wrong format of custom datarules\n')            
    split_rules, tmp_genes = do_rules(rules)
    gene_in_rule = {}
    for i in tmp_genes:
        gene_in_rule[i] = 'ok'
    return (ids, split_rules, gene_in_rule)

############################ gene #############################################

def data_gene(gene, type_gene, name, gene_custom):
    args = process_args(sys.argv)    

    create_svg = check_bool(args.generate_svg)
    create_pdf = check_bool(args.generate_pdf)

    if os.path.isdir('result') == False:
        os.makedirs('result')
        
    if args.custom_rules == 'true':
        ids, rules, gene_in_rule = make_recon(args.custom_rule)

    class_pat = {}
    
    if args.option == 'datasets':
        num = 1

53:7b57a93ac594

            split_rules.append([])
    if err_rules:
        warning('Warning: wrong format rule in ' + str(err_rules) + '\n')
    return (split_rules, list(set(tmp_gene_in_rule)))


############################ gene #############################################

def data_gene(gene, type_gene, name, gene_custom):
    args = process_args(sys.argv)    

    create_svg = check_bool(args.generate_svg)
    create_pdf = check_bool(args.generate_pdf)

    if os.path.isdir('result') == False:
        os.makedirs('result')

    class_pat = {}
    
    if args.option == 'datasets':
        num = 1