tin_hist.py

#!/usr/bin/env python3

import argparse
import pandas as pd
import numpy as np
import warnings
warnings.simplefilter(action='ignore', category=FutureWarning)


def get_args():
    parser = argparse.ArgumentParser()
    parser.add_argument(
        '-r', '--repRID', help="The replicate RID.", required=True)
    args = parser.parse_args()
    return args


def main():
    args = get_args()
    tin = pd.read_csv(args.repRID + '_sorted.deduped.tin.xls',
                      sep="\t", header=0)

    hist = pd.cut(tin['TIN'], bins=pd.interval_range(
        start=0, freq=10, end=100, closed='right')).value_counts(sort=False)
    labels = ["{0} - {1}".format(i, i + 9) for i in range(1, 100, 10)]
    #labels[0] = '0 - 10'
    binned = tin.assign(Bins=lambda x: pd.cut(tin['TIN'], range(
        0, 105, 10), labels=labels, include_lowest=False, right=True))
    binned['chrom'] = binned['chrom'] = binned['chrom'].replace(
        'chr1', 'chr01')
    binned['chrom'] = binned['chrom'].replace('chr2', 'chr02')
    binned['chrom'] = binned['chrom'].replace('chr3', 'chr03')
    binned['chrom'] = binned['chrom'].replace('chr4', 'chr04')
    binned['chrom'] = binned['chrom'].replace('chr5', 'chr05')
    binned['chrom'] = binned['chrom'].replace('chr6', 'chr06')
    binned['chrom'] = binned['chrom'].replace('chr7', 'chr07')
    binned['chrom'] = binned['chrom'].replace('chr8', 'chr08')
    binned['chrom'] = binned['chrom'].replace('chr9', 'chr09')
    hist = pd.pivot_table(binned, values='geneID',
                          index='Bins', columns='chrom', aggfunc=np.size)
    hist['TOTAL'] = hist.sum(axis=1)
    hist = hist[['TOTAL'] + [i for i in hist.columns if i != 'TOTAL']]
    hist = hist.T.fillna(0.0).astype(int)
    #hist = hist.apply(lambda x: x/x.sum()*100, axis=1)
    hist.to_csv(args.repRID + '_tin.hist.tsv', sep='\t')
    medFile = open(args.repRID + '_tin.med.csv', "w")
    medFile.write(str(round(tin['TIN'][(tin['TIN'] != 0)].median(), 2)))
    medFile.close()


if __name__ == '__main__':
    main()