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Created September 26, 2015 17:57
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IPython notebook that downloads the code and data needed to reproduce figure 1 for this publication: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004105
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DeBoever_fig1_data.ipynb
{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"This notebook generates the directory structure and downloads the data necessary for reproducing the first figure of the paper [Transcriptome Sequencing Reveals Potential Mechanism of Cryptic 3’ Splice Site Selection in SF3B1-mutated Cancers](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004105). \n",
"\n",
"* The IPython notebooks for reproducing the whole paper is [here](https://github.com/cdeboever3/deboever-sf3b1-2015/tree/master/notebooks)\n",
"* The particlular IPython notebook that these data are necessary for reproduction is [here](https://github.com/cdeboever3/deboever-sf3b1-2015/blob/master/notebooks/figure01.ipynb)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"First get some essential functions from pypedia for the setup"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"import pypedia\n",
"from pypedia import run_setup_script, git_download, download, mkdir_p"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Get the cdeboever3/deboever-sf3b1-2015 repository."
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Could not determine file size\n",
"Downloading: https://github.com/cdeboever3/deboever-sf3b1-2015/archive/master.zip Bytes: None\n"
]
}
],
"source": [
"git_download('https://github.com/cdeboever3/deboever-sf3b1-2015.git', './')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"This package contains a setup.py script which is not in the default location. Let's run it."
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"running install\n",
"running bdist_egg\n",
"running egg_info\n",
"creating ds2014.egg-info\n",
"writing ds2014.egg-info/PKG-INFO\n",
"writing top-level names to ds2014.egg-info/top_level.txt\n",
"writing dependency_links to ds2014.egg-info/dependency_links.txt\n",
"writing manifest file 'ds2014.egg-info/SOURCES.txt'\n",
"reading manifest file 'ds2014.egg-info/SOURCES.txt'\n",
"writing manifest file 'ds2014.egg-info/SOURCES.txt'\n",
"installing library code to build/bdist.macosx-10.5-x86_64/egg\n",
"running install_lib\n",
"running build_py\n",
"creating build\n",
"creating build/lib\n",
"creating build/lib/ds2014\n",
"copying ds2014/__init__.py -> build/lib/ds2014\n",
"copying ds2014/fig.py -> build/lib/ds2014\n",
"creating build/bdist.macosx-10.5-x86_64\n",
"creating build/bdist.macosx-10.5-x86_64/egg\n",
"creating build/bdist.macosx-10.5-x86_64/egg/ds2014\n",
"copying build/lib/ds2014/__init__.py -> build/bdist.macosx-10.5-x86_64/egg/ds2014\n",
"copying build/lib/ds2014/fig.py -> build/bdist.macosx-10.5-x86_64/egg/ds2014\n",
"byte-compiling build/bdist.macosx-10.5-x86_64/egg/ds2014/__init__.py to __init__.pyc\n",
"byte-compiling build/bdist.macosx-10.5-x86_64/egg/ds2014/fig.py to fig.pyc\n",
"creating build/bdist.macosx-10.5-x86_64/egg/EGG-INFO\n",
"copying ds2014.egg-info/PKG-INFO -> build/bdist.macosx-10.5-x86_64/egg/EGG-INFO\n",
"copying ds2014.egg-info/SOURCES.txt -> build/bdist.macosx-10.5-x86_64/egg/EGG-INFO\n",
"copying ds2014.egg-info/dependency_links.txt -> build/bdist.macosx-10.5-x86_64/egg/EGG-INFO\n",
"copying ds2014.egg-info/top_level.txt -> build/bdist.macosx-10.5-x86_64/egg/EGG-INFO\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"zip_safe flag not set; analyzing archive contents...\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"creating dist\n",
"creating 'dist/ds2014-0.0.1-py2.7.egg' and adding 'build/bdist.macosx-10.5-x86_64/egg' to it\n",
"removing 'build/bdist.macosx-10.5-x86_64/egg' (and everything under it)\n",
"Processing ds2014-0.0.1-py2.7.egg\n",
"Removing /Users/alexandroskanterakis/anaconda/lib/python2.7/site-packages/ds2014-0.0.1-py2.7.egg\n",
"Copying ds2014-0.0.1-py2.7.egg to /Users/alexandroskanterakis/anaconda/lib/python2.7/site-packages\n",
"ds2014 0.0.1 is already the active version in easy-install.pth\n",
"\n",
"Installed /Users/alexandroskanterakis/anaconda/lib/python2.7/site-packages/ds2014-0.0.1-py2.7.egg\n",
"Processing dependencies for ds2014==0.0.1\n",
"Finished processing dependencies for ds2014==0.0.1\n"
]
}
],
"source": [
"run_setup_script('deboever-sf3b1-2015/ds2014/setup.py')"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"directories = [\n",
" 'deboever-sf3b1-2015/data',\n",
" 'deboever-sf3b1-2015/output',\n",
" 'deboever-sf3b1-2015/output/dexseq/',\n",
" 'deboever-sf3b1-2015/output/gencode_sjout_express_processing',\n",
"]\n",
"files = [\n",
" ('deboever-sf3b1-2015/output/dexseq/brca_cll_um_size_factors.tsv', 'http://files.figshare.com/1614201/brca_cll_um_size_factors.tsv'),\n",
" ('deboever-sf3b1-2015/output/dexseq/brca_cll_um_dexseq_results.tsv', 'http://files.figshare.com/1612888/brca_cll_um_dexseq_results.tsv'),\n",
" ('deboever-sf3b1-2015/output/gencode_sjout_express_processing/brca_cll_um_sj_counts.tsv', 'http://files.figshare.com/1614167/brca_cll_um_sj_counts.tsv'),\n",
" ('deboever-sf3b1-2015/output/gencode_sjout_express_processing/gene_fpkm.tsv', 'http://files.figshare.com/1612936/gene_fpkm.tsv'),\n",
" ('deboever-sf3b1-2015/data/cosmic_sf3b1.tsv', 'http://files.figshare.com/1612739/cosmic_sf3b1.tsv'),\n",
" ('deboever-sf3b1-2015/data/metadata.tsv', 'http://files.figshare.com/1612581/metadata.tsv'),\n",
" ('deboever-sf3b1-2015/data/sf3b1_mut_info.tsv', 'http://files.figshare.com/1612769/sf3b1_mut_info.tsv'),\n",
"]"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Create directory structure"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"for directory in directories:\n",
" mkdir_p(directory)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Download data"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Downloading: http://files.figshare.com/1614201/brca_cll_um_size_factors.tsv Bytes: 2415\n",
"2415 [100.00%]\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\n",
"Downloading: http://files.figshare.com/1612888/brca_cll_um_dexseq_results.tsv Bytes: 80978742\n",
"811008 [1.00%]\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\n",
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]
}
],
"source": [
"for filename, url in files:\n",
" download(url, filename)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Done"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 2",
"language": "python",
"name": "python2"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 2
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython2",
"version": "2.7.10"
}
},
"nbformat": 4,
"nbformat_minor": 0
}
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