Simple script to separate MaxQuant experiments

maxquant_separate_experiments.py

"""
Simple script to separate MaxQuant experiments
"""
import os
import sys
import numpy as np
import pandas as pd

def main(f):
    df = pd.read_table(f)
    cols = df.filter(like='LFQ intensity').columns
    for col in cols:
        subdf = df.copy()

        name = col.split('LFQ intensity ')[1]

        subdf['PrecursorArea'] = df[col]
        subdf.loc[ subdf['Identification type ' + name] == 'By matching', 'IonScore' ] = np.nan
        subdf.loc[ subdf['Identification type ' + name] == 'By matching', 'PEP' ] = np.nan

        x = os.path.splitext(f)
        outname = '{}_{}{}'.format(x[0], name, x[1])
        print('Writing', outname)

        subdf.to_csv(outname, sep='\t', index=False)



if __name__ == '__main__':
    main(sys.argv[1])