{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "outMaskedFastaDir='/cellar/users/btsui/Data/ensembl/snp_masked/'\n",
    "specie='Mus_musculus'\n",
    "outMaskedFDir=outMaskedFastaDir+specie+'.fa'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [],
   "source": [
    "testChrom='MT'\n",
    "startI=152185369"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1\n",
      "2\n",
      "3\n",
      "4\n",
      "5\n",
      "6\n",
      "7\n",
      "8\n",
      "9\n",
      "10\n",
      "11\n",
      "12\n",
      "13\n",
      "14\n",
      "15\n",
      "16\n",
      "17\n",
      "18\n",
      "19\n",
      "X\n",
      "Y\n",
      "MT\n"
     ]
    }
   ],
   "source": [
    "from Bio import SeqIO\n",
    "import gzip\n",
    "maskedFasta=outMaskedFDir+'.gz'\n",
    "#unmaskedFasta='/cellar/users/btsui/Data/ensembl/release/fasta/Homo_sapiens.GRCh38.dna_rm.toplevel.fa'\n",
    "with gzip.open(maskedFasta, \"rb\") as handle:\n",
    "    for record in SeqIO.parse(handle=handle, format=\"fasta\") :\n",
    "        print(record.id)\n",
    "        if record.id==testChrom:\n",
    "                break\n",
    "\n",
    "        "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [],
   "source": [
    "#record[]\n",
    "#152184370\t152186370\n",
    "\n",
    "#str((record[11546:13546]).seq)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
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   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython2",
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