comparison SAINT_preprocessing_mq_pep.py @ 35:26cc583a4ae4 draft

Uploaded

34:05c5844e037b

    if prey == 'true':
        make_prey(MaxQuant_input)
        no_error_inter(MaxQuant_input)
        os.rename('prey.txt', sys.argv[5])
    elif prey == 'false':
        if os.path.isfile('error proteins.txt') == True:
            no_error_inter(MaxQuant_input)
        pass
    elif prey != 'true' or 'false':
        sys.exit("Invalid Prey Argument: Y or N")
    os.rename('inter.txt', sys.argv[4])
    os.rename("bait.txt", sys.argv[7])


def get_info(uniprot_accession_in): 
    # Get aa lengths and gene name.
    error = open('error proteins.txt', 'a+')
    data = open(fasta_db, 'r')
    data_lines = data.readlines()
    db_len = len(data_lines)
    seqlength = 0
    count = 0

    output_file.close()


def no_error_inter(MaxQuant_input):
    # Remake inter file without protein errors from Uniprot.
    err = readtab("error proteins.txt")
    bait = readtab(baitfile)
    data = read_MaxQuant(MaxQuant_input).data
    header = read_MaxQuant(MaxQuant_input).header
    header = [MQ_var.replace(r"\"", "") for MQ_var in header]
    header = [MQ_var.replace(r"Intensity.", r"") for MQ_var in header]

35:26cc583a4ae4

    if prey == 'true':
        make_prey(MaxQuant_input)
        no_error_inter(MaxQuant_input)
        os.rename('prey.txt', sys.argv[5])
    elif prey == 'false':
        if os.path.isfile('./error_proteins.txt') == True:
            no_error_inter(MaxQuant_input)
        pass
    elif prey != 'true' or 'false':
        sys.exit("Invalid Prey Argument: Y or N")
    os.rename('inter.txt', sys.argv[4])
    os.rename("bait.txt", sys.argv[7])


def get_info(uniprot_accession_in): 
    # Get aa lengths and gene name.
    error = open('./error_proteins.txt', 'a+')
    data = open(fasta_db, 'r')
    data_lines = data.readlines()
    db_len = len(data_lines)
    seqlength = 0
    count = 0

    output_file.close()


def no_error_inter(MaxQuant_input):
    # Remake inter file without protein errors from Uniprot.
    err = readtab("./error_proteins.txt")
    bait = readtab(baitfile)
    data = read_MaxQuant(MaxQuant_input).data
    header = read_MaxQuant(MaxQuant_input).header
    header = [MQ_var.replace(r"\"", "") for MQ_var in header]
    header = [MQ_var.replace(r"Intensity.", r"") for MQ_var in header]