query_haplor_and_get_hg19_pos.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "library(haploR)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "snp_data <- read.table(\"/projects/pfenninggroup/machineLearningForComputationalBiology/eramamur_stuff/ad_variants_processing/snigdha_snp_list_unique.txt\",\n",
    "                       sep='\\t',\n",
    "                       header=TRUE)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "rsids <- as.vector(snp_data[[\"LD_RSID\"]])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "hg19_positions = c()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
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      "rs142277866 47464969 CTTTTCCTTTTCTT C[1] \"\"\n",
      "rs9395262 47465267 T C[1] \"\"\n",
      "rs7738044 47469273 A G[1] \"\"\n",
      "rs12214064 47473207 C T[1] \"\"\n",
      "rs9473122 47474962 C T[1] \"\"\n",
      "rs9473123 47475339 G A[1] \"\"\n",
      "rs9463335 47479136 G A[1] \"\"\n",
      "rs13211285 47479618 C T[1] \"\"\n",
      "rs4711880 47480676 A G[1] \"\"\n",
      "rs1872505 47480975 C G[1] \"\"\n",
      "rs9473126 47481833 C G[1] \"\"\n",
      "rs4715025 47483653 C G[1] \"\"\n",
      "rs7749271 47485002 T C[1] \"\"\n",
      "rs7767350 47485126 C T[1] \"\"\n",
      "rs67769713 47487097 TGTGATG T[1] \"\"\n",
      "rs10948363 47487762 A G[1] \"\"\n",
      "rs9296561 47488938 G A[1] \"\"\n",
      "rs6913202 47489104 A G[1] \"\"\n",
      "rs13201473 47489708 G A[1] \"\"\n",
      "rs7749167 47493940 G A[1] \"\"\n",
      "rs9296564 47494759 A G[1] \"\"\n",
      "rs7754282 47502024 G C[1] \"\"\n",
      "rs6904764 47503497 A T[1] \"\"\n",
      "rs9473128 47505010 C T[1] \"\"\n",
      "rs9349413 47511491 A G[1] \"\"\n",
      "rs74607583 47514246 T A[1] \"\"\n",
      "rs7774667 47514758 G A[1] \"\"\n",
      "rs2151974 47515630 G A[1] \"\"\n",
      "rs2151975 47515663 T C[1] \"\"\n",
      "rs2171089 47515811 A G[1] \"\"\n",
      "rs9367284 47516369 A G[1] \"\"\n",
      "rs6931011 47525202 G A[1] \"\"\n",
      "rs9381575 47528764 C G[1] \"\"\n",
      "rs34744382 47536444 C T[1] \"\"\n",
      "rs12193051 47541415 C G[1] \"\"\n",
      "rs9395279 47542864 C T[1] \"\"\n",
      "rs9357546 47549495 C T[1] \"\"\n",
      "rs67325630 47550529 TTG T[1] \"\"\n",
      "rs9395283 47551444 T C[1] \"\"\n",
      "rs9349415 47551861 T C[1] \"\"\n",
      "rs9349416 47551938 G A[1] \"\"\n",
      "rs9369716 47552180 A T[1] \"\"\n",
      "rs13193054 47552817 C A[1] \"\"\n",
      "rs9296567 47553402 G A[1] \"\"\n",
      "rs9395285 47554177 G A[1] \"\"\n",
      "rs9369717 47554468 T G[1] \"\"\n",
      "rs1485780 47556630 A C[1] \"\"\n",
      "rs9381578 47556634 C T[1] \"\"\n",
      "rs9381579 47556680 C T[1] \"\"\n",
      "rs10456570 47559451 A G[1] \"\"\n",
      "rs6903331 47562915 A G[1] \"\"\n",
      "rs2396825 47568696 A G[1] \"\"\n",
      "rs9395286 47575332 T C[1] \"\"\n",
      "rs13212790 47576367 T C[1] \"\"\n",
      "rs9349417 47580657 A G[1] \"\"\n",
      "rs9381581 47580695 G A[1] \"\"\n",
      "rs12195738 47583664 C T[1] \"\"\n",
      "rs9463342 47585106 A T[1] \"\"\n",
      "rs10948367 47585615 A G[1] \"\"\n",
      "rs1948047 47585912 T C[1] \"\"\n",
      "rs143419962 47587049 AACAT A[1] \"\"\n",
      "rs34945135 47587294 ACTT A[1] \"\"\n",
      "rs2171086 47590104 C T[1] \"\"\n",
      "rs7754971 47590476 C T[1] \"\"\n",
      "rs1476679 100004446 C T[1] \"\"\n",
      "rs34919929 100012334 G A[1] \"\"\n",
      "rs60738304 100012579 A C[1] \"\"\n",
      "rs6971558 100079857 A T[1] \"\"\n",
      "rs12539172 100091795 T C[1] \"\"\n",
      "rs7791765 143099107 T G[1] \"\"\n",
      "rs10808026 143099133 C A[1] \"\"\n",
      "rs56402156 143103481 G A[1] \"\"\n",
      "rs12703526 143107588 G T[1] \"\"\n",
      "rs11762262 143107876 C T[1] \"\"\n",
      "rs7810606 143108158 T C[1] \"\"\n",
      "rs11763230 143108841 C T[1] \"\"\n",
      "rs11767557 143109139 T C[1] \"\"\n",
      "rs75045569 143109208 T G[1] \"\"\n",
      "rs114360492 145950029 C T[1] \"\"\n",
      "rs7384878 99932049 C T[1] \"\"\n",
      "rs2405442 99971313 T C[1] \"\"\n",
      "rs1859788 99971834 A G[1] \"\"\n",
      "rs2906657 99984089 T C[1] \"\"\n",
      "rs34995835 99990364 T G[1] \"\"\n",
      "rs28834970 27195121 T C[1] \"\"\n",
      "rs57735330 27205046 AG A[1] \"\"\n",
      "rs6987305 27208126 G A[1] \"\"\n",
      "rs2322599 27211910 G A[1] \"\"\n",
      "rs73223431 27219987 C T[1] \"\"\n",
      "rs17057043 27220310 G A[1] \"\"\n",
      "rs755951 27226790 A C[1] \"\"\n",
      "rs112754919 27227453 C T[1] \"\"\n",
      "rs17057051 27227554 A G[1] \"\"\n",
      "rs7013346 27228666 C A[1] \"\"\n",
      "rs17447007 27230637 A G[1] \"\"\n",
      "rs12679874 27230819 A G[1] \"\"\n",
      "rs6557994 27232018 T C[1] \"\"\n",
      "rs2279590 27456253 T C[1] \"\"\n",
      "rs7982 27462481 A C,G[1] \"\"\n",
      "rs7982 27462481 A C,G[1] \"\"\n",
      "rs11136000 27464519 T C[1] \"\"\n",
      "rs4236673 27464929 A G[1] \"\"\n",
      "rs11787077 27465312 T C[1] \"\"\n",
      "rs1532276 27466157 T C[1] \"\"\n",
      "rs1532277 27466181 T C[1] \"\"\n",
      "rs1532278 27466315 T C[1] \"\"\n",
      "rs9331896 27467686 C T[1] \"\"\n",
      "rs2070926 27467821 C G[1] \"\"\n",
      "rs867230 27468503 C A[1] \"\"\n"
     ]
    }
   ],
   "source": [
    "for (rsid in rsids) {\n",
    "    extended_data <- getExtendedView(snp=rsid)\n",
    "    hg19_pos <- as.integer(as.character(extended_data[[1]]$`Sequence facts`$`pos hg19`))\n",
    "    hg19_positions <- c(hg19_positions, hg19_pos)\n",
    "    reference <- as.character(extended_data[[1]]$`Sequence facts`$`Reference`)\n",
    "    alternate <- as.character(extended_data[[1]]$`Sequence facts`$`Alternate`)\n",
    "    #cat(snp_data[row,\"REF\"])\n",
    "    cat(rsid)\n",
    "    cat(\" \")\n",
    "    cat(hg19_pos)\n",
    "    cat(\" \")\n",
    "    cat(reference)\n",
    "    cat(\" \")\n",
    "    #cat(snp_data[row,\"ALT\"])\n",
    "    cat(alternate)\n",
    "    print(\"\")\n",
    "}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
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7465267</li><li>47469273</li><li>47473207</li><li>47474962</li><li>47475339</li><li>47479136</li><li>47479618</li><li>47480676</li><li>47480975</li><li>47481833</li><li>47483653</li><li>47485002</li><li>47485126</li><li>47487097</li><li>47487762</li><li>47488938</li><li>47489104</li><li>47489708</li><li>47493940</li><li>47494759</li><li>47502024</li><li>47503497</li><li>47505010</li><li>47511491</li><li>47514246</li><li>47514758</li><li>47515630</li><li>47515663</li><li>47515811</li><li>47516369</li><li>47525202</li><li>47528764</li><li>47536444</li><li>47541415</li><li>47542864</li><li>47549495</li><li>47550529</li><li>47551444</li><li>47551861</li><li>47551938</li><li>47552180</li><li>47552817</li><li>47553402</li><li>47554177</li><li>47554468</li><li>47556630</li><li>47556634</li><li>47556680</li><li>47559451</li><li>47562915</li><li>47568696</li><li>47575332</li><li>47576367</li><li>47580657</li><li>47580695</li><li>47583664</li><li>47585106</li><li>47585615</li><li>47585912</li><li>47587049</li><li>47587294</li><li>47590104</li><li>47590476</li><li>100004446</li><li>100012334</li><li>100012579</li><li>100079857</li><li>100091795</li><li>143099107</li><li>143099133</li><li>143103481</li><li>143107588</li><li>143107876</li><li>143108158</li><li>143108841</li><li>143109139</li><li>143109208</li><li>145950029</li><li>99932049</li><li>99971313</li><li>99971834</li><li>99984089</li><li>99990364</li><li>27195121</li><li>27205046</li><li>27208126</li><li>27211910</li><li>27219987</li><li>27220310</li><li>27226790</li><li>27227453</li><li>27227554</li><li>27228666</li><li>27230637</li><li>27230819</li><li>27232018</li><li>27456253</li><li>27462481</li><li>27462481</li><li>27464519</li><li>27464929</li><li>27465312</li><li>27466157</li><li>27466181</li><li>27466315</li><li>27467686</li><li>27467821</li><li>27468503</li></ol>\n"
      ],
      "text/latex": [
       "\\begin{enumerate*}\n",
       "\\item 11707563\n",
       "\\item 11707915\n",
       "\\item 11714507\n",
       "\\item 11714686\n",
       "\\item 11717397\n",
       "\\item 11718331\n",
       "\\item 11718713\n",
       "\\item 11719074\n",
       "\\item 11720308\n",
       "\\item 11720620\n",
       "\\item 11723257\n",
       "\\item 121433926\n",
       "\\item 121435587\n",
       "\\item 121436004\n",
       "\\item 47380340\n",
       "\\item 59856028\n",
       "\\item 59857581\n",
       "\\item 59858036\n",
       "\\item 59858497\n",
       "\\item 59858712\n",
       "\\item 59859576\n",
       "\\item 59859609\n",
       "\\item 59860178\n",
       "\\item 59861814\n",
       "\\item 59861983\n",
       "\\item 59862261\n",
       "\\item 59865671\n",
       "\\item 59866175\n",
       "\\item 59866309\n",
       "\\item 59867379\n",
       "\\item 59867913\n",
       "\\item 59869090\n",
       "\\item 59869119\n",
       "\\item 59870196\n",
       "\\item 59870788\n",
       "\\item 59871604\n",
       "\\item 59872498\n",
       "\\item 59873448\n",
       "\\item 59874475\n",
       "\\item 59874817\n",
       "\\item 59875585\n",
       "\\item 59876036\n",
       "\\item 59877143\n",
       "\\item 59877394\n",
       "\\item 59877697\n",
       "\\item 59877967\n",
       "\\item 59878001\n",
       "\\item 59880038\n",
       "\\item 59881524\n",
       "\\item 59881561\n",
       "\\item 59882306\n",
       "\\item 59885120\n",
       "\\item 59885493\n",
       "\\item 59885888\n",
       "\\item 59890674\n",
       "\\item 59896901\n",
       "\\item 59899911\n",
       "\\item 59900106\n",
       "\\item 59900575\n",
       "\\item 59902799\n",
       "\\item 59903287\n",
       "\\item 59903793\n",
       "\\item 59904959\n",
       "\\item 59906476\n",
       "\\item 59906792\n",
       "\\item 59906972\n",
       "\\item 59907097\n",
       "\\item 59907399\n",
       "\\item 59909610\n",
       "\\item 59909647\n",
       "\\item 59911161\n",
       "\\item 59913806\n",
       "\\item 59914267\n",
       "\\item 59914726\n",
       "\\item 59915129\n",
       "\\item 59916087\n",
       "\\item 59916253\n",
       "\\item 59916749\n",
       "\\item 59916905\n",
       "\\item 59918162\n",
       "\\item 59918505\n",
       "\\item 59918613\n",
       "\\item 59918612\n",
       "\\item 59918837\n",
       "\\item 59919165\n",
       "\\item 59920231\n",
       "\\item 59920505\n",
       "\\item 59921596\n",
       "\\item 59922320\n",
       "\\item 59923081\n",
       "\\item 59923194\n",
       "\\item 59923508\n",
       "\\item 59923991\n",
       "\\item 59924422\n",
       "\\item 59924959\n",
       "\\item 59926256\n",
       "\\item 59927039\n",
       "\\item 59927484\n",
       "\\item 59928672\n",
       "\\item 59932023\n",
       "\\item 59932024\n",
       "\\item 59932579\n",
       "\\item 59933492\n",
       "\\item 59936757\n",
       "\\item 59936926\n",
       "\\item 59936979\n",
       "\\item 59939307\n",
       "\\item 59940599\n",
       "\\item 59942081\n",
       "\\item 59942757\n",
       "\\item 59942815\n",
       "\\item 59943109\n",
       "\\item 59944580\n",
       "\\item 59944810\n",
       "\\item 59944898\n",
       "\\item 59945065\n",
       "\\item 59945745\n",
       "\\item 59947252\n",
       "\\item 59948374\n",
       "\\item 59951433\n",
       "\\item 59953313\n",
       "\\item 59955357\n",
       "\\item 59956938\n",
       "\\item 59957092\n",
       "\\item 59957513\n",
       "\\item 59958380\n",
       "\\item 59958687\n",
       "\\item 59959843\n",
       "\\item 59959969\n",
       "\\item 59961427\n",
       "\\item 59961486\n",
       "\\item 59961786\n",
       "\\item 59962166\n",
       "\\item 59962189\n",
       "\\item 59964992\n",
       "\\item 59965725\n",
       "\\item 59965789\n",
       "\\item 59966295\n",
       "\\item 59967526\n",
       "\\item 59967807\n",
       "\\item 59967831\n",
       "\\item 59968382\n",
       "\\item 59968741\n",
       "\\item 59973929\n",
       "\\item 59975078\n",
       "\\item 59975165\n",
       "\\item 59976111\n",
       "\\item 59978255\n",
       "\\item 59980315\n",
       "\\item 59981218\n",
       "\\item 59981801\n",
       "\\item 59982470\n",
       "\\item 59984676\n",
       "\\item 59986333\n",
       "\\item 59986399\n",
       "\\item 59986817\n",
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       "\\item 100004446\n",
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       "\\item 27467686\n",
       "\\item 27467821\n",
       "\\item 27468503\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
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       "\n",
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      ],
      "text/plain": [
       "   [1]  11707563  11707915  11714507  11714686  11717397  11718331  11718713\n",
       "   [8]  11719074  11720308  11720620  11723257 121433926 121435587 121436004\n",
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       "[1149]  47556680  47559451  47562915  47568696  47575332  47576367  47580657\n",
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       "[1163]  47590104  47590476 100004446 100012334 100012579 100079857 100091795\n",
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       "[1177] 143109139 143109208 145950029  99932049  99971313  99971834  99984089\n",
       "[1184]  99990364  27195121  27205046  27208126  27211910  27219987  27220310\n",
       "[1191]  27226790  27227453  27227554  27228666  27230637  27230819  27232018\n",
       "[1198]  27456253  27462481  27462481  27464519  27464929  27465312  27466157\n",
       "[1205]  27466181  27466315  27467686  27467821  27468503"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "hg19_positions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "snp_data[\"haploreg_hg19_pos\"] <- hg19_positions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "snp_data_relevant_columns <- subset(snp_data, select = c(\"CHR\",\"haploreg_hg19_pos\",\"LD_RSID\",\"REF\",\"ALT\") )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "write.table(snp_data_relevant_columns,\n",
    "            file = \"/projects/pfenninggroup/machineLearningForComputationalBiology/eramamur_stuff/ad_variants_processing/snigdha_snp_list_unique_haploreg_hg19_positions.txt\",\n",
    "            sep = \"\\t\",\n",
    "            quote = FALSE,\n",
    "            row.names=FALSE)"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "R [conda env:r-3.6]",
   "language": "R",
   "name": "conda-env-r-3.6-r"
  },
  "language_info": {
   "codemirror_mode": "r",
   "file_extension": ".r",
   "mimetype": "text/x-r-source",
   "name": "R",
   "pygments_lexer": "r",
   "version": "3.6.3"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}