update_cnv_ids.py

import pandas as pd
import argparse
import numpy as np


parser = argparse.ArgumentParser(description='Arguments for Running CNV Pipeline.')    
parser.add_argument('--dosagefile', type=str, default='Nope.', help='dosages in. sample ids in first column, each subsequent column is a gene. values are dosages')
parser.add_argument('--key', type=str, default='Nope.', help='key containing sample ids and phenotypes')
parser.add_argument('--out_path', type=str, default='Nope.', help='Path to prefix for output files.')
parser.add_argument('--pheno_out', type=str, default='Nope.', help='Path to phenotype outfile.')
args = parser.parse_args()

dosagefile = args.dosagefile
key_path = args.key
key = pd.read_csv(key_path)
dosagefile_out = args.out_path
pheno_out = args.pheno_out

dosage = pd.read_csv(dosagefile)
dosage_merge = dosage.merge(key[['GP2sampleID','filename']], left_on='sampleid', right_on='filename')
dosage_out = dosage_merge.drop(columns=['sampleid','filename']).set_index('GP2sampleID').reset_index().rename(columns={'GP2sampleID':'sampleid'})

dosage_pheno = dosage_out.merge(key.loc[:,['GP2sampleID','pheno_for_qc']], left_on='sampleid', right_on='GP2sampleID', how='left')
dosage_pheno2 = dosage_pheno.drop(columns=["GP2sampleID"])
dosage_pheno_out = dosage_pheno2.loc[dosage_pheno2['pheno_for_qc'] != -9]
dosage_pheno_out.loc[:,'pheno'] = np.where(dosage_pheno_out['pheno_for_qc'] == 1, 0, 1)
dosage_pheno_out[['sampleid','pheno']].to_csv(pheno_out, sep='\t', header=True, index=False)

dosage_final = dosage_out.loc[dosage_out.sampleid.isin(dosage_pheno_out.sampleid)]
dosage_final.to_csv(dosagefile_out, header=True, index=False)