RNAseq/generateReferences.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "import pandas as pd\n",
    "from tqdm import tqdm"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "faBaseDirs='/cellar/users/btsui/Data/ensembl/release/cdna/'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "inRefNames=pd.Series(os.listdir(faBaseDirs))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "selectedFas=inRefNames#[inRefNames.str.contains(\"|\".join(inSpecieList),case=False)]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "144"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(selectedFas)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  1%|          | 1/144 [01:34<3:45:00, 94.41s/it]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0\n"
     ]
    }
   ],
   "source": [
    "for fname in tqdm(selectedFas):\n",
    "    reference=faBaseDirs+fname\n",
    "    specie=fname.split('.')[0]\n",
    "    myCmd='/cellar/users/btsui/Program/kallisto index -i /cellar/users/btsui/Data/kalisto_ref/'+specie+' '+reference\n",
    "    print( os.system(myCmd))\n",
    "    "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#specie"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# scratch"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "asdasd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "!gunzip -c  /cellar/users/btsui/Data/ensembl/release/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz | head"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "reference='/cellar/users/btsui/Data/SAILFISH_TRANSCRIPTOME_INDEX_renamed/Homo_sapiens/Homo_sapiens.GRCh38.cdna.all.fa'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "'/cellar/users/btsui/Program/kallisto index -i /cellar/users/btsui/Data/kalisto_ref/Homo_sapiens '+reference"
   ]
  }
 ],
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