6-filterGenesByTFs.py

# -*- coding: utf-8 -*-
import pandas as pd
import numpy as np

def main():
    filteredBedIntersectPath = "../results/bedIntersectWaWbTFBSinGenesFiltered.tsv"
    tfByGenesAndTissuesPath = "../results/tfByGenesAndTissues.tsv"
    tissueNames = ["adipose_tissue", "adrenal_gland", "brain", "breast", "colon",
                   "heart", "kidney", "leukocyte", "liver", "lung", "lymph_node", "ovary",
                   "prostate", "skeletal_muscle", "testis", "thyriod"]

    print("<Reading input data>")
    filteredBedIntersect = pd.read_csv(filteredBedIntersectPath, sep="\t")

    #start dict with 0 values for the frequencies
    tfbsByTF = dict()
    for tfName in filteredBedIntersect['tfName'].unique():
        tfbsByTF[tfName] = dict()
        for tissueName in tissueNames:
            tfbsByTF[tfName][tissueName] = 0

    #read tf frequency on tissues from lists
    for tissue in tissueNames:
        tissueTFsPath = "../results/TFsPerTissue/" + tissue + "_tfs.txt"
        tissueTFs = pd.read_csv(tissueTFsPath, sep='\t')
        for index, row in tissueTFs.iterrows():
            tfbsByTF[row['tfName']][tissue] += row['frequency']

    #create rows for new df
    tfRows = []
    for tfName in filteredBedIntersect['tfName'].unique():
        newRow = dict()
        newRow['tfName'] = tfName
        for tissueName in tissueNames:
            newRow[tissueName] = tfbsByTF[tfName][tissueName]
        tfRows.append(newRow)

    tfDf = pd.DataFrame(tfRows, columns=(['tfName'] + tissueNames))
    tfDf['allTissues'] = tfDf[np.array(list(tissueNames))].sum(axis=1)
    filteredBedIntersect = filteredBedIntersect.groupby(filteredBedIntersect.columns.tolist()).size().reset_index().rename(columns={0:'count'})
    filteredBedIntersect = filteredBedIntersect['tfName'].value_counts().to_dict()
    allGenes = []
    for date, row in tfDf.T.iteritems():
        allGenes.append(filteredBedIntersect[row[0]])
    tfDf['allGenes'] = allGenes
    tfDf.to_csv(tfByGenesAndTissuesPath, sep="\t", index=False)
    print("</Dataframe saved at " + tfByGenesAndTissuesPath + ">")

if __name__ == "__main__":
    main()