chip-seq_rna-seq_peak_collection.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "9de1b51e",
   "metadata": {},
   "source": [
    "# Program name: ChIP-seq peak collection of gene set from RNA-seq experiment\n",
    "\n",
    "- Version: 2023-02-20\n",
    "- Author: Vera Laub\n",
    "- Stage: complete\n",
    "- Input: .txt with RNA-Seq data (ENSEMBLE ID, Gene ID, Fold change), .txt files with ChIP-seq data (Gene ID, peak chr, peak start, peak stop, summit chr, summit start, summit stop)\n",
    "- Output: .bed files with ChIP-seq peaks of all genes defined in RNA-seq file (peak chr, peak start, peak stop, Gene ID); peaks for up/downregulated genes are saved in separate files; whole peaks and 200nt summit of peaks saved in separate files for subsequent analysis\n",
    "- Description: This program serves the purpose of assembling Genes from an RNA-seq file (1. Input) and collecting the respective ChIP-seq peaks (2. Input), i.e. PBX1 ChIP-seq peaks of genes that are differentially regulated in Pbx1 kd RNA-seq in aNS cells (but can be used on any kind of ChIP/RNA-seq, if necessary data is provided). Code meant to be flexible :)!"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "2702652c",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
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'ENSMUSG00000044647\\tCsrnp3\\t-0.39\\n', 'ENSMUSG00000019775\\tRgs17\\t-0.39\\n', 'ENSMUSG00000014329\\tBicc1\\t-0.40\\n', 'ENSMUSG00000023961\\tEnpp4\\t-0.40\\n', 'ENSMUSG00000007950\\tAbhd8\\t-0.40\\n', 'ENSMUSG00000036617\\tEtl4\\t-0.40\\n', 'ENSMUSG00000044365\\tCxxc4\\t-0.40\\n', 'ENSMUSG00000034758\\tTle6\\t-0.40\\n', 'ENSMUSG00000004127\\tTrmt10a\\t-0.40\\n', 'ENSMUSG00000059810\\tRgs3\\t-0.40\\n', 'ENSMUSG00000032194\\tKank2\\t-0.41\\n', 'ENSMUSG00000041261\\tCar8\\t-0.41\\n', 'ENSMUSG00000040488\\tLtbp4\\t-0.41\\n', 'ENSMUSG00000049470\\tAff4\\t-0.41\\n', 'ENSMUSG00000022664\\tSlc35a5\\t-0.41\\n', 'ENSMUSG00000028630\\tDyrk2\\t-0.41\\n', 'ENSMUSG00000017493\\tIgfbp4\\t-0.41\\n', 'ENSMUSG00000090125\\tPou3f1\\t-0.42\\n', 'ENSMUSG00000009356\\tLpo\\t-0.42\\n', 'ENSMUSG00000026211\\tObsl1\\t-0.42\\n', 'ENSMUSG00000021175\\tCdca7l\\t-0.42\\n', 'ENSMUSG00000027792\\tBche\\t-0.42\\n', 'ENSMUSG00000040102\\tKlhl42\\t-0.42\\n', 'ENSMUSG00000020728\\tCep112\\t-0.42\\n', 'ENSMUSG00000038319\\tKcnh2\\t-0.43\\n', 'ENSMUSG00000022899\\tSlc15a2\\t-0.43\\n', 'ENSMUSG00000032198\\tDock6\\t-0.43\\n', 'ENSMUSG00000025736\\tJmjd8\\t-0.43\\n', 'ENSMUSG00000023191\\tP3h3\\t-0.44\\n', 'ENSMUSG00000055053\\tNfic\\t-0.44\\n', 'ENSMUSG00000040690\\tCol16a1\\t-0.44\\n', 'ENSMUSG00000028527\\tAk4\\t-0.44\\n', 'ENSMUSG00000024940\\tLtbp3\\t-0.44\\n', 'ENSMUSG00000047216\\tCdh19\\t-0.45\\n', 'ENSMUSG00000029363\\tRfc5\\t-0.45\\n', 'ENSMUSG00000041308\\tSntb2\\t-0.45\\n', 'ENSMUSG00000028766\\tAlpl\\t-0.46\\n', 'ENSMUSG00000064043\\tTrerf1\\t-0.46\\n', 'ENSMUSG00000022389\\tTef\\t-0.46\\n', 'ENSMUSG00000001750\\tTcirg1\\t-0.46\\n', 'ENSMUSG00000010064\\tSlc38a3\\t-0.46\\n', 'ENSMUSG00000044646\\tZbtb7c\\t-0.47\\n', 'ENSMUSG00000059895\\tPtp4a3\\t-0.47\\n', 'ENSMUSG00000029338\\tAntxr2\\t-0.48\\n', 'ENSMUSG00000055817\\tMta3\\t-0.48\\n', 'ENSMUSG00000029238\\tClock\\t-0.49\\n', 'ENSMUSG00000022883\\tRobo1\\t-0.49\\n', 'ENSMUSG00000040818\\tDennd6a\\t-0.49\\n', 'ENSMUSG00000032265\\tTent5a\\t-0.49\\n', 'ENSMUSG00000042846\\tLrrtm3\\t-0.49\\n', 'ENSMUSG00000023367\\tTmem176a\\t-0.49\\n', 'ENSMUSG00000037010\\tApln\\t-0.50\\n', 'ENSMUSG00000042246\\tTmc7\\t-0.50\\n', 'ENSMUSG00000100252\\tMir124-2hg\\t-0.50\\n', 'ENSMUSG00000042284\\tItga1\\t-0.51\\n', 'ENSMUSG00000035847\\tIds\\t-0.52\\n', 'ENSMUSG00000000782\\tTcf7\\t-0.52\\n', 'ENSMUSG00000024191\\tBnip1\\t-0.53\\n', 'ENSMUSG00000026207\\tSpeg\\t-0.53\\n', 'ENSMUSG00000038305\\tSpats2l\\t-0.53\\n', 'ENSMUSG00000087370\\tTmem170b\\t-0.53\\n', 'ENSMUSG00000041688\\tAmot\\t-0.54\\n', 'ENSMUSG00000029185\\tFam114a1\\t-0.56\\n', 'ENSMUSG00000048794\\tCfap100\\t-0.56\\n', 'ENSMUSG00000022018\\tRgcc\\t-0.57\\n', 'ENSMUSG00000025572\\tTmc6\\t-0.57\\n', 'ENSMUSG00000010476\\tEbf3\\t-0.59\\n', 'ENSMUSG00000044966\\tFbxo48\\t-0.59\\n', 'ENSMUSG00000032238\\tRora\\t-0.60\\n', 'ENSMUSG00000106062\\tGm43820\\t-0.61\\n', 'ENSMUSG00000066687\\tZbtb16\\t-0.61\\n', 'ENSMUSG00000029086\\tProm1\\t-0.61\\n', 'ENSMUSG00000025597\\tKlhl4\\t-0.61\\n', 'ENSMUSG00000025582\\tNptx1\\t-0.62\\n', 'ENSMUSG00000015090\\tPtgds\\t-0.62\\n', 'ENSMUSG00000025511\\tTspan4\\t-0.62\\n', 'ENSMUSG00000022103\\tGfra2\\t-0.62\\n', 'ENSMUSG00000057176\\tCcdc189\\t-0.64\\n', 'ENSMUSG00000067215\\tUsp51\\t-0.65\\n', 'ENSMUSG00000047344\\tLancl3\\t-0.65\\n', 'ENSMUSG00000003949\\tHlf\\t-0.65\\n', 'ENSMUSG00000047497\\tAdamts12\\t-0.65\\n', 'ENSMUSG00000057751\\tMegf6\\t-0.66\\n', 'ENSMUSG00000023206\\tIl15ra\\t-0.66\\n', 'ENSMUSG00000020866\\tCacna1g\\t-0.67\\n', 'ENSMUSG00000059824\\tDbp\\t-0.67\\n', 'ENSMUSG00000038578\\tSusd1\\t-0.68\\n', 'ENSMUSG00000022324\\tMatn2\\t-0.68\\n', 'ENSMUSG00000030255\\tSspn\\t-0.68\\n', 'ENSMUSG00000028919\\tArhgef19\\t-0.69\\n', 'ENSMUSG00000068154\\tInsm1\\t-0.69\\n', 'ENSMUSG00000021775\\tNr1d2\\t-0.69\\n', 'ENSMUSG00000063060\\tSox7\\t-0.70\\n', 'ENSMUSG00000032377\\tPlscr4\\t-0.71\\n', 'ENSMUSG00000002147\\tStat6\\t-0.72\\n', 'ENSMUSG00000019718\\tL3hypdh\\t-0.73\\n', 'ENSMUSG00000032332\\tCol12a1\\t-0.75\\n', 'ENSMUSG00000087150\\tBC064078\\t-0.78\\n', 'ENSMUSG00000039037\\tSt6galnac5\\t-0.78\\n', 'ENSMUSG00000021991\\tCacna2d3\\t-0.78\\n', 'ENSMUSG00000033491\\tPrss35\\t-0.79\\n', 'ENSMUSG00000034796\\tCpne7\\t-0.80\\n', 'ENSMUSG00000021061\\tSptb\\t-0.80\\n', 'ENSMUSG00000037003\\tTns2\\t-0.82\\n', 'ENSMUSG00000029919\\tHpgds\\t-0.83\\n', 'ENSMUSG00000042532\\tGolga7b\\t-0.88\\n', 'ENSMUSG00000003849\\tNqo1\\t-0.91\\n', 'ENSMUSG00000036585\\tFgf1\\t-0.91\\n', 'ENSMUSG00000024235\\tMap3k8\\t-0.92\\n', 'ENSMUSG00000031636\\tPdlim3\\t-0.92\\n', 'ENSMUSG00000034853\\tAcot11\\t-0.95\\n', 'ENSMUSG00000027570\\tCol9a3\\t-0.96\\n', 'ENSMUSG00000070469\\tAdamtsl3\\t-1.01\\n', 'ENSMUSG00000028957\\tPer3\\t-1.04\\n', 'ENSMUSG00000037940\\tInpp4b\\t-1.08\\n', 'ENSMUSG00000016349\\tEef1a2\\t-1.15\\n', 'ENSMUSG00000022836\\tMylk\\t-1.19\\n', 'ENSMUSG00000024411\\tAqp4\\t-1.29\\n', 'ENSMUSG00000049511\\tHtr1b\\t-1.29\\n', 'ENSMUSG00000032269\\tHtr3a\\t-1.30\\n']\n"
     ]
    }
   ],
   "source": [
    "# Set up list of genes used for collection of peaks\n",
    "\n",
    "# Retrieve RNA-seq peaks file\n",
    "file = open(\"pbx1_chip_rna_pbx1kd/rna-seq_aNS_pbx1_kd.txt\", \"r\")\n",
    "rna_seq_genes = file.readlines()\n",
    "file.close()\n",
    "\n",
    "#print(rna_seq_genes)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "58d8cf6f",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Upregulated genes used for peak collection: ['Ifi203', 'Miat', 'Wnt2', 'Gna14', 'Crabp1', 'Mab21l3', 'Acta2', 'Shh', 'Cidea', 'Muc15']\n",
      "Downregulated genes used for peak collection: ['Ccnd2', 'Atad2', 'Trak1', 'Xiap', 'Add3', 'Zfp652', 'Ptar1', 'Klf12', 'Bbx', 'Dcp2']\n"
     ]
    }
   ],
   "source": [
    "# Iterate over RNA-seq file and store information of genes in list, process data to remove whitepsace    \n",
    "for n in range(0, len(rna_seq_genes)):\n",
    "    rna_seq_genes[n] = rna_seq_genes[n].strip()\n",
    "    rna_seq_genes[n] = rna_seq_genes[n].split()\n",
    "    rna_seq_genes[n][2] = float(rna_seq_genes[n][2])\n",
    "    \n",
    "\n",
    "# Initiate 2 separate list of up-/ downregulated genes\n",
    "genes_id_up = []\n",
    "genes_id_down = []\n",
    "j = 0\n",
    "\n",
    "for line in range(0, len(rna_seq_genes)):\n",
    "    if rna_seq_genes[j][2] > 0:\n",
    "        genes_id_up.append(rna_seq_genes[j][1])\n",
    "        j += 1\n",
    "    elif rna_seq_genes[j][2] < 0:\n",
    "        genes_id_down.append(rna_seq_genes[j][1])\n",
    "        j += 1\n",
    "\n",
    "\n",
    "print(\"Upregulated genes used for peak collection:\", genes_id_up[:10])\n",
    "print(\"Downregulated genes used for peak collection:\", genes_id_down[:10])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "7c667dcc",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['Gm10655\\tchr9\\t61368487\\t61372608\\tchr9\\t61370468\\t61370668\\n', 'Xpo1\\tchr11\\t23255159\\t23256311\\tchr11\\t23255740\\t23255940\\n', 'D930016D06Rik\\tchr5\\t104570442\\t104572056\\tchr5\\t104571465\\t104571665\\n', 'Slc39a3\\tchr10\\t81036891\\t81037851\\tchr10\\t81037299\\t81037499\\n', 'Sp2\\tchr11\\t96975685\\t96978462\\tchr11\\t96977668\\t96977868\\n', 'Actr2\\tchr11\\t20112098\\t20113457\\tchr11\\t20112899\\t20113099\\n', 'Dcaf4\\tchr12\\t83520026\\t83520919\\tchr12\\t83520367\\t83520567\\n', 'Acap2\\tchr16\\t31199390\\t31201701\\tchr16\\t31201137\\t31201337\\n', 'Nek7\\tchr1\\t138617295\\t138618621\\tchr1\\t138618062\\t138618262\\n', 'Fbxl19\\tchr7\\t127768548\\t127770250\\tchr7\\t127768904\\t127769104\\n']\n"
     ]
    }
   ],
   "source": [
    "# Set up list of ChIP-seq peaks to collect from\n",
    "\n",
    "# Retrieve ChIP-seq peaks file\n",
    "file = open(\"pbx1_chip_rna_pbx1kd/chip_seq_pbx1_aNS.txt\", \"r\")\n",
    "chip_seq_peaks = file.readlines()\n",
    "file.close()\n",
    "\n",
    "print(chip_seq_peaks[:10])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "08d91fa6",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[['Gm10655', 'chr9', '61368487', '61372608', 'chr9', '61370468', '61370668'], ['Xpo1', 'chr11', '23255159', '23256311', 'chr11', '23255740', '23255940'], ['D930016D06Rik', 'chr5', '104570442', '104572056', 'chr5', '104571465', '104571665'], ['Slc39a3', 'chr10', '81036891', '81037851', 'chr10', '81037299', '81037499'], ['Sp2', 'chr11', '96975685', '96978462', 'chr11', '96977668', '96977868'], ['Actr2', 'chr11', '20112098', '20113457', 'chr11', '20112899', '20113099'], ['Dcaf4', 'chr12', '83520026', '83520919', 'chr12', '83520367', '83520567'], ['Acap2', 'chr16', '31199390', '31201701', 'chr16', '31201137', '31201337'], ['Nek7', 'chr1', '138617295', '138618621', 'chr1', '138618062', '138618262'], ['Fbxl19', 'chr7', '127768548', '127770250', 'chr7', '127768904', '127769104']]\n"
     ]
    }
   ],
   "source": [
    "# Iterate over ChIP-seq file and store information of peaks in list, process data to remove whitepsace    \n",
    "for n in range(0, len(chip_seq_peaks)):\n",
    "    chip_seq_peaks[n] = chip_seq_peaks[n].strip()\n",
    "    chip_seq_peaks[n] = chip_seq_peaks[n].split()\n",
    "    \n",
    "print(chip_seq_peaks[:10])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "id": "29623ee3",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Function to retrieve ChIP-seq peak information of defined gene set\n",
    "# something is wrong with counters!\n",
    "\n",
    "\n",
    "def construct_peak_collection(genes, chip_peaks, output_list):\n",
    "    k = 0\n",
    "    for line in range(len(genes)):\n",
    "        i = 0\n",
    "        for line in range(len(chip_peaks)):\n",
    "            if genes[k] == chip_peaks[i][0]:\n",
    "                output_list.append([chip_peaks[i][1], chip_peaks[i][2], chip_peaks[i][3], chip_peaks[i][0]])\n",
    "            i += 1\n",
    "        k += 1\n",
    "    return output_list"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "id": "8408549b",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Create list for ChIP-seq (whole) peaks with : Gene ID, chr, peak start, peak stop\n",
    "j = 0\n",
    "chip_seq_whole_peaks = []\n",
    "\n",
    "for n in range(0, len(chip_seq_peaks)):\n",
    "    chip_seq_whole_peaks.append([chip_seq_peaks[j][0], chip_seq_peaks[j][1], chip_seq_peaks[j][2], chip_seq_peaks[j][3]])\n",
    "    j += 1\n",
    "    \n",
    "#print(chip_seq_whole_peaks[:10])\n",
    "\n",
    "\n",
    "# Store information of ChIP-seq (whole) peaks of upregulated genes in two different lists\n",
    "chip_seq_peaks_Pbx1kd_up = []\n",
    "chip_seq_peaks_Pbx1kd_up = construct_peak_collection(genes_id_up, chip_seq_whole_peaks, chip_seq_peaks_Pbx1kd_up)\n",
    "#print(chip_seq_peaks_Pbx1kd_up[:10])\n",
    "\n",
    "\n",
    "# Save information on (whole) peaks of upregulated genes in output file\n",
    "chip_seq_peaks_Pbx1kd_up_output = open(\"pbx1_chip_rna_pbx1kd/chip_seq_whole_peaks_Pbx1kd_up.bed\", \"w\")\n",
    "\n",
    "def reconstruct_peak_file(chr_peaks_kd_targets):\n",
    "    k = 0\n",
    "    for line in range(len(chr_peaks_kd_targets)):\n",
    "        chip_seq_peaks_Pbx1kd_up_output.write(chr_peaks_kd_targets[k][0] + \"\\t\" + chr_peaks_kd_targets[k][1] + \"\\t\" + chr_peaks_kd_targets[k][2]  + \"\\t\" + chr_peaks_kd_targets[k][3] + \"\\n\")\n",
    "        k += 1\n",
    "    return chip_seq_peaks_Pbx1kd_up_output\n",
    "\n",
    "reconstruct_peak_file(chip_seq_peaks_Pbx1kd_up)\n",
    "chip_seq_peaks_Pbx1kd_up_output.close()\n",
    "\n",
    "\n",
    "\n",
    "# Store information of ChIP-seq (whole) peaks of downregulated genes in two different lists\n",
    "chip_seq_peaks_Pbx1kd_down = []\n",
    "chip_seq_peaks_Pbx1kd_down = construct_peak_collection(genes_id_down, chip_seq_whole_peaks, chip_seq_peaks_Pbx1kd_down)\n",
    "\n",
    "\n",
    "\n",
    "# Save information on (whole) peaks of downregulated genes in output file\n",
    "chip_seq_peaks_Pbx1kd_down_output = open(\"pbx1_chip_rna_pbx1kd/chip_seq_whole_peaks_Pbx1kd_down.bed\", \"w\")\n",
    "\n",
    "def reconstruct_peak_file(chr_peaks_kd_targets):\n",
    "    k = 0\n",
    "    for line in range(len(chr_peaks_kd_targets)):\n",
    "        chip_seq_peaks_Pbx1kd_down_output.write(chr_peaks_kd_targets[k][0] + \"\\t\" + chr_peaks_kd_targets[k][1] + \"\\t\" + chr_peaks_kd_targets[k][2]  + \"\\t\" + chr_peaks_kd_targets[k][3] + \"\\n\")\n",
    "        k += 1\n",
    "    return chip_seq_peaks_Pbx1kd_down_output\n",
    "\n",
    "reconstruct_peak_file(chip_seq_peaks_Pbx1kd_down)\n",
    "chip_seq_peaks_Pbx1kd_down_output.close()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 44,
   "id": "a9861eb1",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[['Gm10655', 'chr9', '61370468', '61370668'], ['Xpo1', 'chr11', '23255740', '23255940'], ['D930016D06Rik', 'chr5', '104571465', '104571665'], ['Slc39a3', 'chr10', '81037299', '81037499'], ['Sp2', 'chr11', '96977668', '96977868'], ['Actr2', 'chr11', '20112899', '20113099'], ['Dcaf4', 'chr12', '83520367', '83520567'], ['Acap2', 'chr16', '31201137', '31201337'], ['Nek7', 'chr1', '138618062', '138618262'], ['Fbxl19', 'chr7', '127768904', '127769104']]\n",
      "[['chr1', '173942666', '173942866', 'Ifi203'], ['chr6', '17968913', '17969113', 'Wnt2'], ['chr6', '18029846', '18030046', 'Wnt2'], ['chr6', '18031674', '18031874', 'Wnt2'], ['chr19', '16593447', '16593647', 'Gna14'], ['chr19', '16484858', '16485058', 'Gna14'], ['chr19', '16540895', '16541095', 'Gna14'], ['chr19', '16598958', '16599158', 'Gna14'], ['chr19', '16442097', '16442297', 'Gna14'], ['chr19', '16529349', '16529549', 'Gna14']]\n"
     ]
    }
   ],
   "source": [
    "# Create list for ChIP-seq (200nt summit) peaks with : Gene ID, chr, peak start, peak stop\n",
    "j = 0\n",
    "chip_seq_200nt_peaks = []\n",
    "\n",
    "for n in range(0, len(chip_seq_peaks)):\n",
    "    chip_seq_200nt_peaks.append([chip_seq_peaks[j][0], chip_seq_peaks[j][4], chip_seq_peaks[j][5], chip_seq_peaks[j][6]])\n",
    "    j += 1\n",
    "    \n",
    "print(chip_seq_200nt_peaks[:10])\n",
    "\n",
    "\n",
    "# Store information of ChIP-seq (200nt summit) peaks of upregulated genes in two different lists\n",
    "chip_seq_peaks_200nt_Pbx1kd_up = []\n",
    "chip_seq_peaks_200nt_Pbx1kd_up = construct_peak_collection(genes_id_up, chip_seq_200nt_peaks, chip_seq_peaks_200nt_Pbx1kd_up)\n",
    "print(chip_seq_peaks_200nt_Pbx1kd_up[:10])\n",
    "\n",
    "\n",
    "# Save information on 200nt summit peaks of upregulated genes in output file\n",
    "chip_seq_peaks_200nt_Pbx1kd_up_output = open(\"pbx1_chip_rna_pbx1kd/chip_seq_200nt_peaks_Pbx1kd_up.bed\", \"w\")\n",
    "\n",
    "def reconstruct_peak_file(chr_peaks_kd_targets):\n",
    "    k = 0\n",
    "    for line in range(len(chr_peaks_kd_targets)):\n",
    "        chip_seq_peaks_200nt_Pbx1kd_up_output.write(chr_peaks_kd_targets[k][0] + \"\\t\" + chr_peaks_kd_targets[k][1] + \"\\t\" + chr_peaks_kd_targets[k][2]  + \"\\t\" + chr_peaks_kd_targets[k][3] + \"\\n\")\n",
    "        k += 1\n",
    "    return chip_seq_peaks_200nt_Pbx1kd_up_output\n",
    "\n",
    "reconstruct_peak_file(chip_seq_peaks_200nt_Pbx1kd_up)\n",
    "chip_seq_peaks_200nt_Pbx1kd_up_output.close()\n",
    "\n",
    "\n",
    "# Store information of ChIP-seq (200nt summit) peaks of downregulated genes in two different lists\n",
    "chip_seq_peaks_200nt_Pbx1kd_down = []\n",
    "chip_seq_peaks_200nt_Pbx1kd_down = construct_peak_collection(genes_id_down, chip_seq_200nt_peaks, chip_seq_peaks_200nt_Pbx1kd_down)\n",
    "\n",
    "\n",
    "\n",
    "# Save information on 200nt summit peaks of downregulated genes in output file\n",
    "chip_seq_peaks_200nt_Pbx1kd_down_output = open(\"pbx1_chip_rna_pbx1kd/chip_seq_200nt_peaks_Pbx1kd_down.bed\", \"w\")\n",
    "\n",
    "def reconstruct_peak_file(chr_peaks_kd_targets):\n",
    "    k = 0\n",
    "    for line in range(len(chr_peaks_kd_targets)):\n",
    "        chip_seq_peaks_200nt_Pbx1kd_down_output.write(chr_peaks_kd_targets[k][0] + \"\\t\" + chr_peaks_kd_targets[k][1] + \"\\t\" + chr_peaks_kd_targets[k][2]  + \"\\t\" + chr_peaks_kd_targets[k][3] + \"\\n\")\n",
    "        k += 1\n",
    "    return chip_seq_peaks_200nt_Pbx1kd_down_output\n",
    "\n",
    "reconstruct_peak_file(chip_seq_peaks_200nt_Pbx1kd_down)\n",
    "chip_seq_peaks_200nt_Pbx1kd_down_output.close()"
   ]
  }
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