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Added iPython Notebook to Count SNPs/Gene #1

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Aug 17, 2015
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Added iPython Notebook to Count SNPs/Gene #1

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cc27544
added initial snp notebook
cgreene Aug 17, 2015
fb1a153
make changes to calculate overlap b/w snp panels and entrez genes
cgreene Aug 17, 2015
6f60bae
Add files that required manual interaction with UCSC browser
cgreene Aug 17, 2015
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147 changes: 147 additions & 0 deletions SNP-to-Gene.ipynb
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{
"metadata": {
"name": "",
"signature": "sha256:8b80827953d8aced53bbdd46a64733cad875a09e2849075aa6ee01ede4f78485"
},
"nbformat": 3,
"nbformat_minor": 0,
"worksheets": [
{
"cells": [
{
"cell_type": "code",
"collapsed": false,
"input": [
"#download illumina chip files\n",
"url = 'http://www.ebi.ac.uk/arrayexpress/files/A-GEOD-8882/A-GEOD-8882.adf.txt'\n",
"! wget --no-verbose --timestamping --directory-prefix download {url}\n",
"url = 'http://www.ebi.ac.uk/arrayexpress/files/A-GEOD-6434/A-GEOD-6434.adf.txt'\n",
"! wget --no-verbose --timestamping --directory-prefix download {url}"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"2015-08-17 08:17:56 URL:http://www.ebi.ac.uk/arrayexpress/files/A-GEOD-8882/A-GEOD-8882.adf.txt [24316605/24316605] -> \"download/A-GEOD-8882.adf.txt\" [1]\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"2015-08-17 08:18:15 URL:http://www.ebi.ac.uk/arrayexpress/files/A-GEOD-6434/A-GEOD-6434.adf.txt [24862681/24862681] -> \"download/A-GEOD-6434.adf.txt\" [1]\r\n"
]
}
],
"prompt_number": 2
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"humanhap550 = set([])\n",
"hh550_fh = open(\"download/A-GEOD-6434.adf.txt\")\n",
"for line in hh550_fh:\n",
" if line.startswith('rs'):\n",
" toks = line.strip().split('\\t')\n",
" humanhap550.add(toks[1])\n",
"\n",
"print(str(len(humanhap550)) + \" SNPs with rs#s on HH550\")\n",
"o_fh = open(\"data/hh550-snp-for-bed.txt\", 'w')\n",
"o_fh.write('\\n'.join(humanhap550))\n",
"o_fh.close()"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"561303 SNPs with rs#s on HH550\n"
]
}
],
"prompt_number": 11
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"humanomni1 = set([])\n",
"omni1_fh = open(\"download/A-GEOD-8882.adf.txt\")\n",
"for line in omni1_fh:\n",
" if line.startswith('rs'):\n",
" toks = line.strip().split('\\t')\n",
" humanomni1.add(toks[1])\n",
"\n",
"print(str(len(humanomni1)) + \" SNPs with rs#s on HOmni1\")\n",
"o_fh = open(\"data/ho1-snp-for-bed.txt\", 'w')\n",
"o_fh.write('\\n'.join(humanomni1))\n",
"o_fh.close()"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"970342 SNPs with rs#s on HOmni1\n"
]
}
],
"prompt_number": 12
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Follow instructions at http://www.gettinggeneticsdone.com/2011/06/mapping-snps-to-genes-for-gwas.html to get a BED file. Use GRCh37/hg19 and dbSNP Common SNPs(142). Name the downloaded files bed-hh550.bed and bed-ho1.bed. Move both of these files to \"data/\""
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"#Download Entrez mappings.\n",
"url = 'http://files.figshare.com/230645/entrez.txt'\n",
"! wget --no-verbose --timestamping --directory-prefix download {url}\n",
"\n",
"# add chr to the front to match the UCSC files\n",
"! sed 's/^/chr/' download/entrez.txt > download/chr_entrez.txt"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 15
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"# Count the overlaps\n",
"! windowBed -w 10000 -c -a download/chr_entrez.txt -b data/bed-hh550.bed > data/hh550-entrez.bed\n",
"! windowBed -w 10000 -c -a download/chr_entrez.txt -b data/bed-ho1.bed > data/ho1-entrez.bed\n"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 16
},
{
"cell_type": "code",
"collapsed": false,
"input": [],
"language": "python",
"metadata": {},
"outputs": []
}
],
"metadata": {}
}
]
}
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