Mercurial > repos > saketkc > oncodrivefm
changeset 0:8447ba178b06
Init
| author | Saket Choudhary <saketkc@gmail.com> |
|---|---|
| date | Wed, 20 Nov 2013 01:15:34 +0530 |
| parents | |
| children | 386fa4776fde |
| files | tools/oncodrivefm_tool/README.rst tools/oncodrivefm_tool/oncodrivefm_tool.py tools/oncodrivefm_tool/oncodrivefm_tool.xml tools/oncodrivefm_tool/tool_dependencies.xml |
| diffstat | 4 files changed, 245 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/oncodrivefm_tool/README.rst Wed Nov 20 01:15:34 2013 +0530 @@ -0,0 +1,34 @@ +Galaxy wrapper for the CHASM webservice at CRAVAT(v2.0) +=================================================== + +This tool is copyright 2013 by Saket Choudhary, Indian Institute of Technology Bombay +All rights reserved. MIT licensed. + +Licence (MIT) +============= + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE. + +Citations +=========== + + +If you use this Galaxy tool in work leading to a scientific publication please cite: + + Gonzalez-Perez A and Lopez-Bigas N. 2012. Functional impact bias reveals cancer drivers. Nucleic Acids Res., 10.1093/nar/gks743.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/oncodrivefm_tool/oncodrivefm_tool.py Wed Nov 20 01:15:34 2013 +0530 @@ -0,0 +1,131 @@ +#!/usr/bin/python +import argparse +import sys +import os +import tempfile +import shutil +import subprocess +import ntpath + +""" + -h, --help show this help message and exit + -o PATH, --output-path PATH + Directory where output files will be written + -n NAME Analysis name + --output-format FORMAT + The FORMAT for the output file + -N NUMBER, --samplings NUMBER + Number of samplings to compute the FM bias pvalue + -e ESTIMATOR, --estimator ESTIMATOR + Test estimator for computation. + --gt THRESHOLD, --gene-threshold THRESHOLD + Minimum number of mutations per gene to compute the FM + bias + --pt THRESHOLD, --pathway-threshold THRESHOLD + Minimum number of mutations per pathway to compute the + FM bias + -s SLICES, --slices SLICES + Slices to process separated by commas + -m PATH, --mapping PATH + File with mappings between genes and pathways to be + analysed + --save-data The input data matrix will be saved + --save-analysis The analysis results will be saved + -j CORES, --cores CORES + Number of cores to use for calculations. Default is 0 + that means all the available cores + -D KEY=VALUE Define external parameters to be saved in the results + -L LEVEL, --log-level LEVEL + Define log level: debug, info, warn, error, critical, + notset +""" +def stop_err( msg ): + sys.stderr.write( '%s\n' % msg ) + sys.exit() +def main(params): + parser = argparse.ArgumentParser() + ##TAKEN directly from the source code + parser.add_argument("-N", "--samplings", dest="num_samplings", type=int, default=10000, metavar="NUMBER", + help="Number of samplings to compute the FM bias pvalue") + parser.add_argument("-e", "--estimator", dest="estimator", metavar="ESTIMATOR", + choices=["mean", "median"], default="mean", + help="Test estimator for computation.") + parser.add_argument("--gt", "--gene-threshold", dest="mut_gene_threshold", type=int, default=2, metavar="THRESHOLD", + help="Minimum number of mutations per gene to compute the FM bias") + parser.add_argument("--pt", "--pathway-threshold", dest="mut_pathway_threshold", type=int, default=10, metavar="THRESHOLD", + help="Minimum number of mutations per pathway to compute the FM bias") + parser.add_argument("-s", "--slices", dest="slices", metavar="SLICES", + help="Slices to process separated by commas") + parser.add_argument("-m", "--mapping", dest="mapping", metavar="PATH", + help="File with mappings between genes and pathways to be analysed") + parser.add_argument("-f", "--filter", dest="filter", metavar="PATH", + help="File containing the features to be filtered. By default labels are includes," + " labels preceded with - are excludes.") + #parser.add_argument("-o", "--output_path", type=str, required=True, help="Directory where output files will be written") + parser.add_argument("-o1", "--output1", type=str, dest="output1", required=True) + + parser.add_argument("-o2", "--output2", type=str, dest="output2", required=False) + parser.add_argument("-n", "--analysis_name", type=str, required=False, help="Analysis name") + #parser.add_argument("-e", "--estimator", type=str, required=False, choices=["mean-empirical","median-empirical","mean-zscore","median-zscore"], help="Test estimator for computation") + parser.add_argument("--output-format", dest="output_format", required=False, + metavar="FORMAT", + choices=["tsv", "tsv.gz", "tsv.bz2"], + default="tsv", + help="The FORMAT for the output file") + parser.add_argument("-j", "--cores", dest="num_cores", type=int, + metavar="CORES", + help="Number of cores to use for calculations.\ + Default is 0 that means all the available cores") + parser.add_argument("-D", dest="defines", metavar="KEY=VALUE", action="append", help="Define external parameters to be saved in the results") + parser.add_argument("-L", "--log-level", dest="log_level", metavar="LEVEL", default=None, + choices=["debug", "info", "warn", "error", "critical", "notset"], + help="Define log level: debug, info, warn, error, critical, notset") + parser.add_argument("-i", "--input", dest="input_path", required=True, type=str, help="Path to input file") + args = vars(parser.parse_args(params)) + try: + mapping_path = args["mapping_path"] + except KeyError: + mapping_path = "no_mapping_path" + #if mapping_path=="no_mapping_path": + #params.remove(mapping_path) + #params.remove("-m") + output_dir = tempfile.mkdtemp() + params.append("-o") + params.append(output_dir) + params.append(args["input_path"]) + cmd = "oncodrivefm " + i=0 + while i<len(params): + p=params[i] + if p=="-i" or p=="-o1" or p=="-o2": + i+=2 + else: + i+=1 + cmd += " "+p + cmd += " 2>&1 " + #tmp = tempfile.NamedTemporaryFile( dir=output_dir ).name + #tmp_stderr = open( tmp, 'wb' ) + print cmd + proc = subprocess.Popen(args=cmd, shell=True) + returncode = proc.wait() + #tmp_stderr.close() + + if args['analysis_name'] is not None: + prefix = args["analysis_name"] + else: + ##refer: http://stackoverflow.com/a/8384788/756986 + prefix = ntpath.basename(args["input_path"]).split(".")[0] + if args["mapping"] is not None: + pathway_file = prefix+"-pathways" + else: + pathway_file = None + output_format = args["output_format"] + genes_output_file_name = os.path.join(output_dir, prefix+"-genes."+output_format) + shutil.move(genes_output_file_name,args["output1"]) + if pathway_file: + pathway_output_file_name = os.path.join(output_dir, pathway_file+"."+output_format) + shutil.move(pathway_output_file_name,args["output2"]) + if os.path.exists( output_dir ): + shutil.rmtree( output_dir ) +if __name__=="__main__": + main(sys.argv[1:])
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/oncodrivefm_tool/oncodrivefm_tool.xml Wed Nov 20 01:15:34 2013 +0530 @@ -0,0 +1,73 @@ +<tool id="oncodrivefm_tool" name="OncodriveFM"> + <description>OncodriveFM </description> + <tool_dependency> + <package name="oncodrivefm"> + <install version="0.6-dev"> + <actions> + <action type="setup_virtualenv">distribute</action> + <action type="setup_virtualenv">python-dateutil==2.1</action> + <action type="setup_virtualenv">pytz==2013b</action> + <action type="setup_virtualenv">numpy==1.7.1</action> + <action type="setup_virtualenv">scipy==0.12.0</action> + <action type="setup_virtualenv">pandas==0.12.0</action> + <action type="setup_virtualenv">statsmodels==0.4.3</action> + <action type="setup_virtualenv">https://bitbucket.org/bbglab/oncodrivefm/get/master.tar.gz</action> + </actions> + </install> + <readme>OncodriveFm avalable at https://bitbucket.org/bbglab/oncodrivefm/</readme> + </package> + </tool_dependency> + + <command interpreter="python"> + #if $mappingpathcondition.hasmapfile=="yes" + oncodrivefm_tool.py -N $samplings -e $estimator --gt $gene_threshold --pt $pathway_threshold -s $slices -m $mapping_path -o1 $output1 -o2 $output2 -i $input + #else + oncodrivefm_tool.py -N $samplings -e $estimator --gt $gene_threshold --pt $pathway_threshold -s $slices -o1 $output1 -o2 $output2 -i $input + #end if + </command> + <inputs> + <param name="input" format="tabular" type="data" label="Input" /> + <param name="samplings" type="integer" label="Samplings" help="Number of samplings to compute the FM bias pvalue" optional="true" value="10000"/> + + <param name="estimator" type="select" label="Estimator" help="Test estimator for computation" optional="true"> + <option value="median">Median</option> + <option value="mean">Mean</option> + </param> + + + <param name="gene_threshold" type="integer" label="Gene Threshold" help="Minimum number of mutations per gene to compute the FM bias" optional="true" value="2"/> + <param name="pathway_threshold" type="integer" label="Pathway Threshold" help="Minimum number of mutations per pathway to compute the FM bias" optional="true" value="10" /> + <param name="slices" type="text" label="Slices" help="Slices to process separated by commas(slices=SIFT,PPH2,MA)" optional="true" value="SIFT,PPH2,MA"/> + <conditional name="mappingpathcondition"> + <param name="hasmapfile" type="select" label="Have a mapping gene file"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="yes"> + <param name="mapping_path" type="data" format="tabular" label=" File with mappings between genes and pathways to be analysed"/> + </when> + </conditional> + </inputs> + <outputs> + + <data format="tabular" name="output1"/> + <data format="tabular" name="output2" > + <filter>mappingpathcondition["hasmapfile"]=="yes"</filter> + </data> + </outputs> + <help> + **What it does** + Oncodrive-fm is an approach to uncover driver genes or gene modules. + It computes a metric of functional impact using three well-known methods (SIFT, PolyPhen2 and MutationAssessor) + and assesses how the functional impact of variants found in a gene across several tumor samples deviates from + a null distribution. It is thus based on the assumption that any bias towards the accumulation of variants + with high functional impact is an indication of positive selection and can thus be used to detect candidate + driver genes or gene modules. + + **Citation** + If you use this Galaxy tool in work leading to a scientific publication please cite: + + Gonzalez-Perez A and Lopez-Bigas N. 2012. Functional impact bias reveals cancer drivers. Nucleic Acids Res., 10.1093/nar/gks743. + +</tool> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/oncodrivefm_tool/tool_dependencies.xml Wed Nov 20 01:15:34 2013 +0530 @@ -0,0 +1,7 @@ +<?xml version='1.0' encoding='utf-8'?> +<tool_dependency> + <package name="requests" version="2.0.1"> + <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="package_requests_2_0" owner="saketkc"/> + </package> +</tool_dependency> +