{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Initialize Variables and Make Directories"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "source bioinf_intro_config.sh\n",
    "mkdir -p $TRIMMED $MYINFO $GENOME_DIR $STAR_OUT"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Make adapter file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "echo \">Adapter\n",
    "AGATCGGAAGAGCACACGTCTGAACTCCAGTCA\n",
    ">AdapterRead2\n",
    "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT\n",
    ">Adapter_rc\n",
    "TGACTGGAGTTCAGACGTGTGCTCTTCCGATCT\n",
    ">AdapterRead2_rc\n",
    "ACACTCTTTCCCTACACGACGCTCTTCCGATCT\" >  $MYINFO/neb_e7600_adapters.fasta"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Download and Index Genome"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "SHARED_URL=\"ftp://ftp.ensemblgenomes.org/pub/release-39/fungi\"\n",
    "FASTA=${GENOME_DIR}/Cryptococcus_neoformans_var_grubii_h99.CNA3.dna.toplevel.fa\n",
    "GTF=${GENOME_DIR}/Cryptococcus_neoformans_var_grubii_h99.CNA3.39.gtf"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "2018-07-24 13:27:47 URL: ftp://ftp.ensemblgenomes.org/pub/release-39/fungi/gtf/fungi_basidiomycota1_collection/cryptococcus_neoformans_var_grubii_h99/Cryptococcus_neoformans_var_grubii_h99.CNA3.39.gtf.gz [1796344] -> \"/home/jovyan/work/scratch/bioinf_intro/genome/Cryptococcus_neoformans_var_grubii_h99.CNA3.39.gtf.gz.1\" [1]\n",
      "2018-07-24 13:27:49 URL: ftp://ftp.ensemblgenomes.org/pub/release-39/fungi/fasta/fungi_basidiomycota1_collection/cryptococcus_neoformans_var_grubii_h99/dna/Cryptococcus_neoformans_var_grubii_h99.CNA3.dna.toplevel.fa.gz [5922212] -> \"/home/jovyan/work/scratch/bioinf_intro/genome/Cryptococcus_neoformans_var_grubii_h99.CNA3.dna.toplevel.fa.gz.1\" [1]\n",
      "gzip: /home/jovyan/work/scratch/bioinf_intro/genome/Cryptococcus_neoformans_var_grubii_h99.CNA3.dna.toplevel.fa already exists; do you wish to overwrite (y or n)? \n"
     ]
    }
   ],
   "source": [
    "wget --no-verbose --directory-prefix ${GENOME_DIR} \"${SHARED_URL}/gtf/fungi_basidiomycota1_collection/cryptococcus_neoformans_var_grubii_h99/$(basename $GTF).gz\"\n",
    "wget --no-verbose --directory-prefix ${GENOME_DIR} \"${SHARED_URL}/fasta/fungi_basidiomycota1_collection/cryptococcus_neoformans_var_grubii_h99/dna/$(basename $FASTA).gz\"\n",
    "\n",
    "gunzip -f ${FASTA}.gz\n",
    "gunzip -f ${GTF}.gz"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Jul 24 13:32:28 ..... started STAR run\n",
      "Jul 24 13:32:28 ... starting to generate Genome files\n",
      "Jul 24 13:32:29 ... starting to sort Suffix Array. This may take a long time...\n",
      "Jul 24 13:32:29 ... sorting Suffix Array chunks and saving them to disk...\n",
      "Jul 24 13:32:52 ... loading chunks from disk, packing SA...\n",
      "Jul 24 13:32:52 ... finished generating suffix array\n",
      "Jul 24 13:32:52 ... generating Suffix Array index\n",
      "Jul 24 13:32:54 ... completed Suffix Array index\n",
      "Jul 24 13:32:54 ..... processing annotations GTF\n",
      "Jul 24 13:32:55 ..... inserting junctions into the genome indices\n",
      "Jul 24 13:33:38 ... writing Genome to disk ...\n",
      "Jul 24 13:33:38 ... writing Suffix Array to disk ...\n",
      "Jul 24 13:33:39 ... writing SAindex to disk\n",
      "Jul 24 13:33:39 ..... finished successfully\n"
     ]
    }
   ],
   "source": [
    "STAR \\\n",
    "    --runMode genomeGenerate \\\n",
    "    --genomeDir $GENOME_DIR \\\n",
    "    --genomeFastaFiles ${FASTA} \\\n",
    "    --sjdbGTFfile ${GTF} \\\n",
    "    --outFileNamePrefix ${STAR_OUT}/genome_ \\\n",
    "    --genomeSAindexNbases 11\n",
    "# --genomeSAindexNbases 6"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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