comparison COBRAxy/rps_generator.py @ 402:ccccb731c953 draft

Uploaded

401:6c7ddf68381a

        Namespace: An object containing parsed arguments.
    """
    parser = argparse.ArgumentParser(usage = '%(prog)s [options]',
                                     description = 'process some value\'s'+
                                     ' abundances and reactions to create RPS scores.')
    parser.add_argument('-rc', '--reaction_choice', 
                        type = str,
                        default = 'default',
                        choices = ['default','custom'], 
                        help = 'chose which type of reaction dataset you want use')
    parser.add_argument('-cm', '--custom',
                        type = str,
                        help='your dataset if you want custom reactions')
    parser.add_argument('-td', '--tool_dir',
                        type = str,
                        required = True,
                        help = 'your tool directory')
    parser.add_argument('-ol', '--out_log', 

    """

    cell_lines = dataset[0][1:]
    abundances_dict = {}

    translationIsApplied = ARGS.reaction_choice == "default"
    for row in dataset[1:]:
        id = get_metabolite_id(row[0], syn_dict) #if translationIsApplied else row[0]
        if id: 
            abundances_dict[id] = list(map(utils.Float(), row[1:]))

    with open(ARGS.tool_dir + '/local/pickle files/synonyms.pickle', 'rb') as sd:
        syn_dict = pk.load(sd)

    dataset = utils.readCsv(utils.FilePath.fromStrPath(ARGS.input), '\t', skipHeader = False)
    tmp_dict = None
    if ARGS.reaction_choice == 'default':
        reactions = pk.load(open(ARGS.tool_dir + '/local/pickle files/reactions.pickle', 'rb'))
        substrateFreqTable = pk.load(open(ARGS.tool_dir + '/local/pickle files/substrate_frequencies.pickle', 'rb'))
    
    elif ARGS.reaction_choice == 'custom':
        reactions = reactionUtils.parse_custom_reactions(ARGS.custom)
        for r, s in reactions.items():
            tmp_list = list(s.keys())
            for k in tmp_list:
                if k[-2] == '_':
                    s[k[:-2]] = s.pop(k)
        substrateFreqTable = {}
        for _, substrates in reactions.items():
            for substrateName, _ in substrates.items():
                if substrateName not in substrateFreqTable: substrateFreqTable[substrateName] = 0
                substrateFreqTable[substrateName] += 1

        print(f"Reactions: {reactions}")
        print(f"Substrate Frequencies: {substrateFreqTable}")
        print(f"Synonyms: {syn_dict}")
        tmp_dict = {}

402:ccccb731c953

        Namespace: An object containing parsed arguments.
    """
    parser = argparse.ArgumentParser(usage = '%(prog)s [options]',
                                     description = 'process some value\'s'+
                                     ' abundances and reactions to create RPS scores.')
    
    parser.add_argument("-rl", "--model_upload", type = str,
        help = "path to input file containing the reactions")

    # model_upload custom
    parser.add_argument('-td', '--tool_dir',
                        type = str,
                        required = True,
                        help = 'your tool directory')
    parser.add_argument('-ol', '--out_log', 

    """

    cell_lines = dataset[0][1:]
    abundances_dict = {}

    for row in dataset[1:]:
        id = get_metabolite_id(row[0], syn_dict) #if translationIsApplied else row[0]
        if id: 
            abundances_dict[id] = list(map(utils.Float(), row[1:]))

    with open(ARGS.tool_dir + '/local/pickle files/synonyms.pickle', 'rb') as sd:
        syn_dict = pk.load(sd)

    dataset = utils.readCsv(utils.FilePath.fromStrPath(ARGS.input), '\t', skipHeader = False)
    tmp_dict = None
    #if ARGS.reaction_choice == 'default':
    #    reactions = pk.load(open(ARGS.tool_dir + '/local/pickle files/reactions.pickle', 'rb'))
    #    substrateFreqTable = pk.load(open(ARGS.tool_dir + '/local/pickle files/substrate_frequencies.pickle', 'rb'))
    
    #elif ARGS.reaction_choice == 'custom':
    reactions = reactionUtils.parse_custom_reactions(ARGS.model_upload)
    for r, s in reactions.items():
        tmp_list = list(s.keys())
        for k in tmp_list:
            if k[-2] == '_':
                s[k[:-2]] = s.pop(k)
    substrateFreqTable = {}
    for _, substrates in reactions.items():
        for substrateName, _ in substrates.items():
            if substrateName not in substrateFreqTable: substrateFreqTable[substrateName] = 0
            substrateFreqTable[substrateName] += 1

        print(f"Reactions: {reactions}")
        print(f"Substrate Frequencies: {substrateFreqTable}")
        print(f"Synonyms: {syn_dict}")
        tmp_dict = {}