comparison COBRAxy/ras_generator.py @ 512:f32d3c9089fc draft

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511:0cb727788cae

    # read dataset and remove versioning from gene names
    dataset = read_dataset(ARGS.input, "dataset")
    orig_gene_list=dataset.index.copy()
    dataset.index =  [str(el.split(".")[0]) for el in dataset.index]  

    if any(dataset.index.duplicated(keep=False)):
        list_str=", ".join(orig_gene_list[dataset.index.duplicated(keep=False)])
        raise ValueError(f"ERROR: Duplicate entries in the gene dataset. The following genes are duplicated: "+list_str)       

    #load GPR rules
    rules = load_custom_rules()
    
    #create a list of all the gpr
    rules_total_string=""
    for id,rule in rules.items():
        rules_total_string+=rule.replace("(","").replace(")","") + " "
    rules_total_string=list(set(rules_total_string.split(" ")))

    #check if nan value must be ignored in the GPR 
    if ARGS.none:
    #    #e.g. (A or nan --> A)
        ignore_nan = True

512:f32d3c9089fc

    # read dataset and remove versioning from gene names
    dataset = read_dataset(ARGS.input, "dataset")
    orig_gene_list=dataset.index.copy()
    dataset.index =  [str(el.split(".")[0]) for el in dataset.index]  

    #load GPR rules
    rules = load_custom_rules()
    
    #create a list of all the gpr
    rules_total_string=""
    for id,rule in rules.items():
        rules_total_string+=rule.replace("(","").replace(")","") + " "
    rules_total_string=list(set(rules_total_string.split(" ")))

    if any(dataset.index.duplicated(keep=False)):
        genes_duplicates=orig_gene_list[dataset.index.duplicated(keep=False)]
        genes_duplicates_in_model=[elem for elem in genes_duplicates if elem in rules_total_string]
        if len(genes_duplicates_in_model)>0:#metabolic genes have duplicated entries in the dataset
            list_str=", ".join(genes_duplicates_in_model)
            raise ValueError(f"ERROR: Duplicate entries in the gene dataset present in one or more GPR. The following metabolic genes are duplicated: "+list_str)       

    #check if nan value must be ignored in the GPR 
    if ARGS.none:
    #    #e.g. (A or nan --> A)
        ignore_nan = True