import max_quant as MQ # Process the MaxQuant results of the cdc55 delta experiment if __name__ == '__main__': root = '../' table_dir = os.path.join(root, 'tables') fasta_path = os.path.join(root, 'yeast_cont_20140324.fasta') mq_txt_folder = 'MQ_txt_cdc55D' evidence_path = os.path.join(root, 'MaxQuant', mq_txt_folder, 'evidence.txt') experiments_toreverse = [ '01_cdc55', '04_cdc55', '07_cdc55', 'B_cdc55', 'D_cdc55', 'E_cdc55', 'G_cdc55', 'J_cdc55' ] setup = 'cdc55D' # Import Evidence evidence, normalization_data = MQ.process_evidence(evidence_path, fasta_path) evidence['Setup'] = setup MQ.reverse_ratios(evidence, experiments_toreverse) # Generate output files evidence_outpath = os.path.join(table_dir, 'evidence_' + setup + '.tsv') phosphosite_outpath = os.path.join(table_dir, 'phospho_' + setup + '.tsv') protein_outpath = os.path.join(table_dir, 'protein_' + setup + '.tsv') MQ.write_evidence_table(evidence, evidence_outpath) MQ.write_phosphosite_table(evidence, phosphosite_outpath, prob_cutoff=0.7) MQ.write_protein_table(evidence, protein_outpath)
for exp in ['01_hog1as_5min', '02_hog1as_5min']: exp_to_setup[exp] = 'SR-hog1as' for exp in [ '01_nacl_5min', '02_nacl_5min', '03_nacl_5min', '04_nacl_5min', '05_nacl_5min', '06_nacl_5min' ]: exp_to_setup[exp] = 'SR' # Import Evidence evidence, normalization_data = MQ.process_evidence(evidence_path, fasta_path) evidence['Setup'] = [exp_to_setup[exp] for exp in evidence['Experiment']] evidence = evidence[(evidence['Setup'] != 'exclude')] MQ.reverse_ratios(evidence, experiments_toreverse) # Generate output files for setup in setups: ev_setup = evidence[(evidence['Setup'] == setup)] evidence_outpath = os.path.join(table_dir, 'evidence_' + setup + '.tsv') phosphosite_outpath = os.path.join(table_dir, 'phospho_' + setup + '.tsv') protein_outpath = os.path.join(table_dir, 'protein_' + setup + '.tsv') MQ.write_evidence_table(ev_setup, evidence_outpath) MQ.write_phosphosite_table(ev_setup, phosphosite_outpath, prob_cutoff=0.7) MQ.write_protein_table(ev_setup, protein_outpath)