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)