comparison COBRAxy/ras_generator.py @ 398:09064ce8f095 draft

Uploaded

397:de4a373e338b

    """
    parser = argparse.ArgumentParser(
        usage = '%(prog)s [options]',
        description = "process some value's genes to create a comparison's map.")
    
    parser.add_argument(
        '-rs', '--rules_selector', 
        type = utils.Model, default = utils.Model.ENGRO2, choices = list(utils.Model),
        help = 'chose which type of dataset you want use')
    
    parser.add_argument("-rl", "--rule_list", type = str,
        help = "path to input file with custom rules, if provided")

    parser.add_argument("-rn", "--rules_name", type = str, help = "custom rules name")
    # ^ I need this because galaxy converts my files into .dat but I need to know what extension they were in
    
    parser.add_argument(
        '-n', '--none',
        type = utils.Bool("none"), default = True,

    performed, significantly impacting the runtime.

    Returns:
        Dict[str, ruleUtils.OpList] : dict mapping reaction IDs to rules.
    """
    datFilePath = utils.FilePath.fromStrPath(ARGS.rule_list) # actual file, stored in galaxy as a .dat
    
    try: filenamePath = utils.FilePath.fromStrPath(ARGS.rules_name) # file's name in input, to determine its original ext
    except utils.PathErr as err:
        raise utils.PathErr(filenamePath, f"Please make sure your file's name is a valid file path, {err.msg}")
     
    if filenamePath.ext is utils.FileFormat.PICKLE: return utils.readPickle(datFilePath)

    dataset.iloc[:, 0] = (dataset.iloc[:, 0]).astype(str)

    # remove versioning from gene names
    dataset.iloc[:, 0] = dataset.iloc[:, 0].str.split('.').str[0]

    # handle custom models
    model :utils.Model = ARGS.rules_selector

    if model is utils.Model.Custom:
        rules = load_custom_rules()
        reactions = list(rules.keys())

        save_as_tsv(ras_for_cell_lines(dataset, rules), reactions)
        if ERRORS: utils.logWarning(
            f"The following genes are mentioned in the rules but don't appear in the dataset: {ERRORS}",
            ARGS.out_log)
        
        return
    
    # This is the standard flow of the ras_generator program, for non-custom models.
    name = "RAS Dataset"
    type_gene = gene_type(dataset.iloc[0, 0], name)

    rules      = model.getRules(ARGS.tool_dir)
    genes      = data_gene(dataset, type_gene, name, None)
    ids, rules = load_id_rules(rules.get(type_gene))

    resolve_rules, err = resolve(genes, rules, ids, ARGS.none, name)
    create_ras(resolve_rules, name, rules, ids, ARGS.ras_output)
    
    if err: utils.logWarning(
        f"Warning: gene(s) {err} not found in class \"{name}\", " +
        "the expression level for this gene will be considered NaN",
        ARGS.out_log)
    
    print("Execution succeded")

###############################################################################
if __name__ == "__main__":

398:09064ce8f095

    """
    parser = argparse.ArgumentParser(
        usage = '%(prog)s [options]',
        description = "process some value's genes to create a comparison's map.")
    
    parser.add_argument("-rl", "--model_upload", type = str,
        help = "path to input file with custom rules, if provided")

    parser.add_argument("-rn", "--model_upload_name", type = str, help = "custom rules name")
    # ^ I need this because galaxy converts my files into .dat but I need to know what extension they were in
    
    parser.add_argument(
        '-n', '--none',
        type = utils.Bool("none"), default = True,

    performed, significantly impacting the runtime.

    Returns:
        Dict[str, ruleUtils.OpList] : dict mapping reaction IDs to rules.
    """
    datFilePath = utils.FilePath.fromStrPath(ARGS.model_upload) # actual file, stored in galaxy as a .dat

    try: filenamePath = utils.FilePath.fromStrPath(ARGS.model_upload_name) # file's name in input, to determine its original ext
    except utils.PathErr as err:
        raise utils.PathErr(filenamePath, f"Please make sure your file's name is a valid file path, {err.msg}")
     
    if filenamePath.ext is utils.FileFormat.PICKLE: return utils.readPickle(datFilePath)

    dataset.iloc[:, 0] = (dataset.iloc[:, 0]).astype(str)

    # remove versioning from gene names
    dataset.iloc[:, 0] = dataset.iloc[:, 0].str.split('.').str[0]

    rules = load_custom_rules()
    reactions = list(rules.keys())

    save_as_tsv(ras_for_cell_lines(dataset, rules), reactions)
    if ERRORS: utils.logWarning(
        f"The following genes are mentioned in the rules but don't appear in the dataset: {ERRORS}",
        ARGS.out_log)  


    ############

    # handle custom models
    #model :utils.Model = ARGS.rules_selector

    #if model is utils.Model.Custom:
    #    rules = load_custom_rules()
    #    reactions = list(rules.keys())

    #    save_as_tsv(ras_for_cell_lines(dataset, rules), reactions)
    #    if ERRORS: utils.logWarning(
    #        f"The following genes are mentioned in the rules but don't appear in the dataset: {ERRORS}",
    #        ARGS.out_log)
        
    #    return
    
    # This is the standard flow of the ras_generator program, for non-custom models.
    #name = "RAS Dataset"
    #type_gene = gene_type(dataset.iloc[0, 0], name)

    #rules      = model.getRules(ARGS.tool_dir)
    #genes      = data_gene(dataset, type_gene, name, None)
    #ids, rules = load_id_rules(rules.get(type_gene))

    #resolve_rules, err = resolve(genes, rules, ids, ARGS.none, name)
    #create_ras(resolve_rules, name, rules, ids, ARGS.ras_output)
    
    #if err: utils.logWarning(
    #    f"Warning: gene(s) {err} not found in class \"{name}\", " +
    #    "the expression level for this gene will be considered NaN",
    #    ARGS.out_log)
    
    print("Execution succeded")

###############################################################################
if __name__ == "__main__":