hannes-brt
2/1/2013 - 12:44 AM
Readbase API example
Readbase API example
{
"metadata": {
"name": "Map Bodymap STAR"
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"input": [
"import urllib2\n",
"import subprocess\n",
"import os\n",
"import json"
],
"language": "python",
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"prompt_number": 16
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"source": [
"Query the database for Bodymap 2.0 files (`study_id=ERP000546`) that are single end (`library_layout=single`)\n",
"Read all of the results (`.read()`), and split on newlines (the results are returned one uid by line)"
]
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"input": [
"uids = urllib2.urlopen('http://128.100.241.98/readbase/query?study_id=ERP000546&library_layout=single').read().split('\\n')"
],
"language": "python",
"metadata": {},
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"prompt_number": 6
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"source": [
"Now request the JSON metadata for all the experiments. The uids are given as a comma-separated list in the URL and the result is automatically parsed by the JSON module."
]
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"cell_type": "code",
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"input": [
"metadata_json = json.load(urllib2.urlopen('http://128.100.241.98/readbase/get-json?uid=' + ','.join(uids)))"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 19
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{
"cell_type": "markdown",
"metadata": {},
"source": [
"Here I extract the run ids for all runs and all experiments (an experiment can have more than one run, so we need to iterate over all runs for the experiment)."
]
},
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"cell_type": "code",
"collapsed": false,
"input": [
"run_ids = [run['run_id'] for experiment in metadata_json for run in experiment['runs']]"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 29
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Load the genome into shared memory for the STAR mapping algorithm."
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"subprocess.check_output(['/home/hannes/usr/bin/STAR', '--genomeDir', '/data/hg19/', '--genomeLoad', 'LoadAndExit'])"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "pyout",
"prompt_number": 33,
"text": [
"'Jan 31 17:14:32 ..... Started STAR run\\n'"
]
}
],
"prompt_number": 33
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"input": [
"# Parameter for STAR\n",
"star_parameters = [\n",
" '--genomeDir', '/data/hg19',\n",
" '--runThreadN', '32']"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 36
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"cell_type": "code",
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"input": [
"# Run STAR for each file in a new directory\n",
"for run_id in run_ids:\n",
" os.chdir('/data/Bodymap/STAR_maps/')\n",
" if not os.path.exists(run_id): os.mkdir(run_id)\n",
" os.chdir(run_id)\n",
" print run_id\n",
" path = '/data/Bodymap/ERP000546_fastq/' + run_id + '.fastq'\n",
" subprocess.check_output(['/home/hannes/usr/bin/STAR'] + star_parameters + ['--readFilesIn'] + [path])"
],
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"cell_type": "code",
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"input": [
"# Remove the index from the shared memory\n",
"os.chdir('/data/Bodymap/STAR_maps/')\n",
"subprocess.check_output(['/home/hannes/usr/bin/STAR', '--genomeDir', '/data/hg19/', '--genomeLoad', 'Remove'])"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "pyout",
"prompt_number": 35,
"text": [
"'Jan 31 19:12:47 ..... Started STAR run\\n'"
]
}
],
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