run_SAM_to_BAM.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Imports"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "import sys\n",
    "import subprocess\n",
    "import shutil"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Main"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Setup"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "my_local_path = \"/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/\"\n",
    "samtools_root = ''.join([my_local_path, \"samtools/\" ])\n",
    "samtools_exe_path = ''.join([samtools_root, \"bin/samtools\" ])\n",
    "sam_files_path = ''.join([my_local_path, \"data/sam_files\" ])\n",
    "bam_files_path = ''.join([my_local_path, \"data/bam_files\" ])\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "#TODO - Make Install more pythonic\n",
    "if not os.path.exists(samtools_root):\n",
    "    !wget https://github.com/samtools/samtools/releases/download/1.15/samtools-1.15.tar.bz2\n",
    "    !tar xjf samtools-1.15.tar.bz2\n",
    "    !mkdir samtools\n",
    "    !cd /gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/samtools-1.15/ && ./configure --prefix=/gpfs/gpfs0/project/ds6011-sp22-wiki-data/dod/capstone/samtools && make && make install"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
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      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/hisat2_simulate_reads.py’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/hisat2_read_statistics.py’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/make_zm3_snp_tran_ercc.sh’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/make_grch37_tran.sh’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/make_rn6.sh’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/make_hg38_snp.sh’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/make_rnor6.sh’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/make_grch38_tran.sh’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/make_grch38_snp_rep.sh’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/make_grch37_snp_tran.sh’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/convert_quals.pl’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/make_canFam2.sh’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/make_grcm38_tran.sh’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/make_grch38_snp_tran.sh’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/make_wbcel235.sh’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/make_a_thaliana_tair.sh’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/make_grch37_snp_tran_ercc.sh’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/make_r64_tran.sh’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/make_hg19.sh’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/make_ce10.sh’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/make_hg38_allsnp.sh’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/make_grcm38.sh’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/make_wbcel235_tran.sh’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/make_b_taurus_UMD3.sh’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/make_mm10.sh’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/infer_fraglen.pl’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/make_grch38_snp_tran_ercc.sh’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/make_hg38_snp_tran.sh’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/make_grch38_snp.sh’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/make_hg38.sh’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/make_rnor6_tran.sh’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/make_grcm38_snp_tran.sh’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/make_rn4.sh’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/gen_2b_occ_lookup.pl’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/gen_occ_lookup.pl’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/make_bdgp6.sh’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/make_grch37.sh’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/make_mm9.sh’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/make_r64.sh’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/make_e_coli.sh’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/make_grch38.sh’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/make_bdgp6_tran.sh’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/make_dm6.sh’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/make_sc3.sh’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/make_grch38_rep.sh’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/make_grcm38_snp.sh’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/gen_solqual_lookup.pl’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/scripts/make_grch37_snp.sh’: Operation not permitted\n",
      "chmod: changing permissions of ‘/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1/hisat2-build-l’: Operation not permitted\n",
      "/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod\n"
     ]
    }
   ],
   "source": [
    "#TODO - Make Recursion more pythonic\n",
    "!chmod -R 755 /gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/samtools\n",
    "!chmod -R 755 /gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/hisat2-2.2.1\n",
    "%cd /gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'/gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/data/bam_files'"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "bam_files_path"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Reading SAMs for Project: PRJNA281708\n",
      "\tProject Path:  /gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/data/sam_files/PRJNA281708\n",
      "\tProcessing: SRR1982660.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR1982814.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR1982612.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR1982783.sam\n",
      "\tBam File Exists. Continuing\n",
      "\n",
      "Reading SAMs for Project: PRJNA634526\n",
      "\tProject Path:  /gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/data/sam_files/PRJNA634526\n",
      "\tProcessing: SRR14209589.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR14209634.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR14209590.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR14209614.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR14209603.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR14209651.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR14209708.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR14209655.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR14209591.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR14209588.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR14209592.sam\n",
      "\tBam File Exists. Continuing\n",
      "\n",
      "Reading SAMs for Project: PRJEB43291\n",
      "\tProject Path:  /gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/data/sam_files/PRJEB43291\n",
      "\tProcessing: ERR5354928.sam\n",
      "\tBam File Exists. Continuing\n",
      "\n",
      "Reading SAMs for Project: PRJNA694172\n",
      "\tProject Path:  /gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/data/sam_files/PRJNA694172\n",
      "\tProcessing: SRR13510369.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR13510375.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR13510373.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR13510372.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR13510368.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR13510374.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR13510371.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR13510367.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR13510370.sam\n",
      "\tBam File Exists. Continuing\n",
      "\n",
      "Reading SAMs for Project: PRJEB35615\n",
      "\tProject Path:  /gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/data/sam_files/PRJEB35615\n",
      "\tProcessing: ERR3698053.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: ERR3698054.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: ERR3698079.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: ERR3698058.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: ERR3698060.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: ERR3698056.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: ERR3698080.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: ERR3698061.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: ERR3698086.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: ERR3698055.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: ERR3698089.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: ERR3698082.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: ERR3698091.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: ERR3698096.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: ERR3698084.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: ERR3698057.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: ERR3698081.sam\n",
      "\tBam File Exists. Continuing\n",
      "\n",
      "Reading SAMs for Project: PRJNA277616\n",
      "\tProject Path:  /gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/data/sam_files/PRJNA277616\n",
      "\tProcessing: SRR1926133.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR1909613.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR1909639.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR1926134.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR1867792.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR1926136.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR1926135.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR1926132.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR1909638.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR1909637.sam\n",
      "\tBam File Exists. Continuing\n",
      "\n",
      "Reading SAMs for Project: PRJNA784038\n",
      "\tProject Path:  /gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/data/sam_files/PRJNA784038\n",
      "\tProcessing: SRR17051753.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR17051755.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR17051757.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR17051752.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR17051754.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR17051756.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR17051758.sam\n",
      "\tBam File Exists. Continuing\n",
      "\n",
      "Reading SAMs for Project: PRJNA41223\n",
      "\tProject Path:  /gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/data/sam_files/PRJNA41223\n",
      "\tProcessing: ERR013145.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: ERR015879.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: ERR013159.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: ERR015526.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: ERR015530.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: ERR013151.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: ERR013144.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: ERR016004.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: ERR016160.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: ERR015969.sam\n",
      "\tBam File Exists. Continuing\n",
      "\n",
      "Reading SAMs for Project: PRJNA475246\n",
      "\tProject Path:  /gpfs/gpfs0/project/ds6011-sp22-wiki-data/ds6011-sp22-dod/data/sam_files/PRJNA475246\n",
      "\tProcessing: SRR7280796.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR7280798.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR7280800.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR7280793.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR7280792.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR7280799.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR7280794.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR7280797.sam\n",
      "\tBam File Exists. Continuing\n",
      "\tProcessing: SRR7280791.sam\n",
      "\tBam File Exists. Continuing\n",
      "\n"
     ]
    }
   ],
   "source": [
    "directories = os.listdir(sam_files_path)\n",
    "#directories = [\"PRJNA475246\"] # Process Single Project\n",
    "for directory in directories:\n",
    "    if not directory.startswith(\"PRJ\"):\n",
    "        continue\n",
    "    print(\"Reading SAMs for Project: {}\".format(directory))\n",
    "    project = '/'.join([sam_files_path, directory])\n",
    "    print(\"\\tProject Path: \",project)\n",
    "    #print()\n",
    "    for sam in os.listdir(project):\n",
    "        print(\"\\tProcessing:\", sam)\n",
    "        samfile = '/'.join([project, sam])\n",
    "        bamfile = '/'.join([bam_files_path, project.split(\"/\")[-1],sam[:-4]]) + \".bam\"\n",
    "        if not os.path.exists(project.replace(\"sam\",\"bam\")):\n",
    "            os.makedirs(project.replace(\"sam\",\"bam\"))\n",
    "        if os.path.exists(bamfile):\n",
    "            print(\"\\tBam File Exists. Continuing\")\n",
    "            continue\n",
    "        cmd = [\n",
    "            samtools_exe_path,\n",
    "            \"view\", \"-bS\",\n",
    "            samfile       \n",
    "            ]\n",
    "        print(\"\\tRunning Command: \", \" \".join(cmd))\n",
    "        with open(bamfile, \"w\") as outfile:\n",
    "            subprocess.run(cmd, stdout=outfile)  \n",
    "        cmd = [\n",
    "            samtools_exe_path,\n",
    "            \"sort\",\n",
    "            bamfile,\n",
    "            \"-o\",\n",
    "            bamfile[:-4] + \"_sorted.bam\"       \n",
    "            ]\n",
    "        print()\n",
    "        print(\"\\tRunning Command: \", \" \".join(cmd))\n",
    "        subprocess.run(cmd)\n",
    "        print(\"Sorted Path: \", str(bamfile[:-4] + \"_sorted.bam\"))\n",
    "        if os.path.exists(str(bamfile[:-4]) + \"_sorted.bam\"):\n",
    "            os.remove(bamfile)\n",
    "            shutil.move( str(bamfile[:-4]) + \"_sorted.bam\" , bamfile)\n",
    "    print()"
   ]
  },
  {
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