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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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{ | |
"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", | |
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"155648 [73.71%]\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\n", | |
"163840 [77.59%]\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\n", | |
"172032 [81.47%]\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\n", | |
"180224 [85.35%]\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\n", | |
"188416 [89.23%]\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\n", | |
"196608 [93.11%]\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\n", | |
"204800 [96.99%]\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\n", | |
"211163 [100.00%]\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\n" | |
] | |
} | |
], | |
"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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