Mercurial > repos > saketkc > chasm_web
changeset 0:aea1a2363a94
Initial commit
| author | Saket Choudhary <saketkc@gmail.com> |
|---|---|
| date | Fri, 01 Nov 2013 02:05:02 +0530 |
| parents | |
| children | 8eaaa7f6b619 |
| files | chasm/README.rst chasm/chasm_web.py chasm/chasm_web.xml |
| diffstat | 3 files changed, 354 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/chasm/README.rst Fri Nov 01 02:05:02 2013 +0530 @@ -0,0 +1,38 @@ +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: + +Carter, Hannah, et al. "Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations." +Cancer research 69.16 (2009): 6660-6667. + +Wong, Wing Chung, et al. "CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer." +Bioinformatics 27.15 (2011): 2147-2148.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/chasm/chasm_web.py Fri Nov 01 02:05:02 2013 +0530 @@ -0,0 +1,222 @@ +#!/usr/bin/python +""" +The MIT License (MIT) + +Copyright (c) 2013 Saket Choudhary, <saketkc@gmail.com> + +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. + +""" +import requests +import argparse +import sys +import time +from functools import wraps +import simplejson as json +import zipfile +import tempfile, ntpath, shutil +import xlrd +import csv +import os +sheet_map = {0:"Variant_Analysis.csv",1:"Amino_Acid_Level_Analysis.csv",2:"Gene_Level_Analysis.csv"} +def retry(ExceptionToCheck, tries=4, delay=3, backoff=2, logger=None): + """Retry calling the decorated function using an exponential backoff. + + http://www.saltycrane.com/blog/2009/11/trying-out-retry-decorator-python/ + original from: http://wiki.python.org/moin/PythonDecoratorLibrary#Retry + + :param ExceptionToCheck: the exception to check. may be a tuple of + exceptions to check + :type ExceptionToCheck: Exception or tuple + :param tries: number of times to try (not retry) before giving up + :type tries: int + :param delay: initial delay between retries in seconds + :type delay: int + :param backoff: backoff multiplier e.g. value of 2 will double the delay + each retry + :type backoff: int + :param logger: logger to use. If None, print + :type logger: logging.Logger instance + """ + def deco_retry(f): + + @wraps(f) + def f_retry(*args, **kwargs): + mtries, mdelay = tries, delay + while mtries > 1: + try: + return f(*args, **kwargs) + except ExceptionToCheck, e: + #msg = "%s, Retrying in %d seconds..." % (str(e), mdelay) + msg = "Retrying in %d seconds..." % (mdelay) + if logger: + logger.warning(msg) + else: + print msg + time.sleep(mdelay) + mtries -= 1 + mdelay *= backoff + return f(*args, **kwargs) + + return f_retry # true decorator + + return deco_retry +CANCERTYPES =["Bladder","Blood-Lymphocyte","Blood-Myeloid","Brain-Cerebellum","Brain-Glioblastoma_Multiforme","Brain-Lower_Grade_Glioma","Breast","Cervix","Colon","Head_and_Neck","Kidney-Chromophobe","Kidney-Clear_Cell","Kidney-Papiallary_Cell","Liver-Nonviral","Liver-Viral","Lung-Adenocarcinoma","Lung-Squamous_Cell","Melanoma","Other","Ovary","Pancreas","Prostate-Adenocarcinoma","Rectum","Skin","Stomach","Thyroid","Uterus"] +URL="http://www.cravat.us/ClassifierSelect1" +def stop_err( msg ): + sys.stderr.write( '%s\n' % msg ) + sys.exit() + +class CHASMWeb: + def __init__( self, mutationbox=None, filepath=None,is_hg_18=None, analysis_type=None, analysis_program=None, chosendb=None, cancer_type=None, email=None, annotate_genes=None, text_reports=None, mupit_out=None ): + self.mutationbox = mutationbox + self.filepath = filepath + self.is_hg_18 = is_hg_18 + self.analysis_type = analysis_type + self.analysis_program = analysis_program + self.chosendb = chosendb + self.email = email + self.annotate_genes = annotate_genes + self.cancer_type = cancer_type + self.email = email + self.annotate_genes = annotate_genes + self.text_reports=text_reports + self.mupit_input= mupit_out + def make_request( self ): + data = { + "mutationbox":self.mutationbox, + "hg18": self.is_hg_18, + "analysistype": self.analysis_type, + "chosendb": self.analysis_program, + "cancertype": self.cancer_type, + "geneannotcheckbox": self.annotate_genes, + "emailbox": self.email, + "tsvreport": self.text_reports, + "mupitinput": self.mupit_input, + } + stripped_data = {} + + for key,value in data.iteritems(): + if value==True: + value="on" + if value!=None and value!=False: + stripped_data[key]=value + #print stripped_data + if not self.mutationbox: + file_payload={"inputfile":open(self.filepath)} + request = requests.post(URL, data=stripped_data, files=file_payload) + else: + request = requests.post(URL, data=stripped_data, files=dict(foo='bar')) + job_id = json.loads(request.text)["jobId"] + return job_id + @retry(requests.exceptions.HTTPError) + def zip_exists(self,job_id ): + url="http://www.cravat.us/results/%s/%s.zip" %(job_id,job_id) + zip_download_request = requests.request("GET", url) + if zip_download_request.status_code==404: + raise requests.HTTPError() + else: + return url + def download_zip( self, url, job_id): + self.tmp_dir = tempfile.mkdtemp() + r = requests.get( url, stream=True ) + if r.status_code == 200: + self.path = os.path.join( self.tmp_dir,job_id+".zip" ) + with open(self.path, 'wb') as f: + for chunk in r.iter_content(128): + f.write(chunk) + else: + self.path = None + return self.path + + def move_files( self, file_map ): + fh = open(self.path,"rb") + zip_files = zipfile.ZipFile(fh) + for name in zip_files.namelist(): + filename = ntpath.basename(name) + extension = ntpath.splitext(filename)[-1] + source_file = zip_files.open(name) + if extension==".txt": + target_file = open(file_map["error.txt"],"wb") + elif filename!="SnvGet Feature Description.xls" and extension!=".xls": + target_file = open(file_map[filename],"wbb")#file(os.path.join(output_dir,filename),"wb") + else: + target_file=None + if target_file: + with source_file,target_file: + shutil.copyfileobj(source_file,target_file) + if filename=="SnvGet Feature Description.xls": + with xlrd.open_workbook(source_file) as wb: + sheet_names = wb.sheet_names() + for name in sheet_names: + sh=wb.sheet_by_name(name) + name_shortened= name.replace(" ").strip()+".csv" + with open(name_shortened,'wb') as f: + c = csv.writer(f) + for r in range(sh.nrows): + c.writerow(sh.row_values(r)) + shutil.rmtree(self.tmp_dir) + fh.close() +def main(params): + + parser = argparse.ArgumentParser() + parser.add_argument("-i","--input", type=str, dest="mutationbox", help="Input variants") + parser.add_argument("--path",type=str,dest="input_file_location", help="Input file location") + parser.add_argument("--hg18", dest="hg18", action="store_true") + parser.add_argument("--analysis_type",dest="analysis_type",type=str,choices=["driver","functional","geneannotationonly"], default="driver") + parser.add_argument("--chosendb",dest="chosendb",type=str,nargs="*",choices=["CHASM","SnvGet"], default="CHASM") + parser.add_argument("--cancertype", dest="cancer_type", type=str, choices=CANCERTYPES, required=True) + parser.add_argument("--email", dest="email", required=True, type=str) + parser.add_argument("--annotate", dest="annotate", action="store_true", default=None ) + parser.add_argument("--tsv_report", dest="tsv_report", action="store_true", default=None ) + parser.add_argument("--mupit_out", dest="mupit_out", action="store_true", default=None ) + parser.add_argument("--gene_analysis_out", dest="gene_analysis_out", type=str, required=True) + parser.add_argument("--variant_analysis_out", dest="variant_analysis_out", type=str, required=True) + parser.add_argument("--amino_acid_level_analysis_out", dest="amino_acid_level_analysis_out", type=str, required=True,) + parser.add_argument("--error_file", dest="error_file_out", type=str, required=True) + parser.add_argument("--snv_box_out", dest="snv_box_out", type=str, required=False) + parser.add_argument("--snv_features", dest="snv_features_out", type=str, required=False) + args = (parser.parse_args(params)) + chasm_web = CHASMWeb(mutationbox=args.mutationbox, + filepath=args.input_file_location, + is_hg_18 = args.hg18, + analysis_type=args.analysis_type, + chosendb = args.chosendb, + cancer_type = args.cancer_type, + email=args.email, + annotate_genes=args.annotate, + text_reports=args.tsv_report, + mupit_out=args.mupit_out) + job_id=chasm_web.make_request() + file_map = {"Amino_Acid_Level_Analysis.tsv":args.amino_acid_level_analysis_out, + "SNVBox.tsv":args.snv_box_out, + "Variant_Analysis.tsv":args.variant_analysis_out, + "Gene_Level_Analysis.tsv":args.gene_analysis_out, + "SnvGet Feature Description.xls":args.snv_features_out, + "error.txt":args.error_file_out + } + url = chasm_web.zip_exists(job_id) + download = chasm_web.download_zip(url,job_id) + if download: + move = chasm_web.move_files(file_map=file_map) + else: + stop_err("Unable to download from the server") + +if __name__=="__main__": + main(sys.argv[1:])
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/chasm/chasm_web.xml Fri Nov 01 02:05:02 2013 +0530 @@ -0,0 +1,94 @@ +<tool id="chasm_webservice" name="CHASM Webservice" version="1.0.0" hidden="false"> + <requirements> + <requirement type="python-module">requests</requirement> + <requirement type="python-module">xlrd</requirement> + </requirements> + <description>CHASM score using CRAVAT webservice</description> + <command interpreter="python"> + chasm_web.py --path $input --analysis_type $analysis_type --cancertype $tissue_type --email $__user_email__ --gene_analysis_out $gene_analysis_out --variant_analysis_out $variant_analysis_out --amino_acid_level_analysis_out $amino_acid_level_analysis_out --error_file $error_file + </command> + <inputs> + <param format="txt" name="input" type="data" label="Variants File" /> + <param name="analysis_type" type="select" label="Choose analysis type" help=" + Cancer driver analysis predicts whether\ + the submitted variants are cancer drivers.\ + Functional effect analysis predicts whether\ + the submitted variants will have any\ + functional effect on their translated proteins.\ + Annotation only provides\ + GeneCard and PubMed information on\ + the genes containing the submitted variants."> + <option value="driver">Cancer driver analysis</option> + <option value="functional">Functional effect analysis</option> + <option value="geneannotationonly">Annotation only</option> + </param> + + <param name="gene_annotation" type="select" label="Include Gene annotation"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + + <param name="tissue_type" type="select" label="Tissue Type"> + <option value="Bladder">Bladder</option> + <option value="Blood-Lymphocyte">Blood-Lymphocyte</option> + <option value="Blood-Myeloid">Blood-Myeloid</option> + <option value="Brain-Cerebellum">Brain-Cerebellum</option> + <option value="Brain-Glioblastoma_Multiforme">Brain-Glioblastoma_Multiforme</option> + <option value="Brain-Lower_Grade_Glioma">Brain-Lower_Grade_Glioma</option> + <option value="Breast">Breast</option> + <option value="Cervix">Cervix</option> + <option value="Colon">Colon</option> + <option value="Head_and_Neck">Head_and_Neck</option> + <option value="Kidney-Chromophobe">Kidney-Chromophobe</option> + <option value="Kidney-Clear_Cell">Kidney-Clear_Cell</option> + <option value="Kidney-Papiallary_Cell">Kidney-Papiallary_Cell</option> + <option value="Liver-Nonviral">Liver-Nonviral</option> + <option value="Liver-Viral">Liver-Viral</option> + <option value="Lung-Adenocarcinoma">Lung-Adenocarcinoma</option> + <option value="Lung-Squamous_Cell">Lung-Squamous_Cell</option> + <option value="Melanoma">Melanoma</option> + <option value="Other">Other</option> + <option value="Ovary">Ovary</option> + <option value="Pancreas">Pancreas</option> + <option value="Prostate-Adenocarcinoma">Prostate-Adenocarcinoma</option> + <option value="Rectum">Rectum</option> + <option value="Skin">Skin</option> + <option value="Stomach">Stomach</option> + <option value="Thyroid">Thyroid</option> + <option value="Uterus">Uterus</option> + </param> + </inputs> + <outputs> + <data format="tabular" name="gene_analysis_out"/> + <data format="tabular" name="variant_analysis_out" /> + <data format="tabular" name="amino_acid_level_analysis_out" /> + <data format="tabular" name="error_file"/> + </outputs> + <help> + **What it does** + * CHASM (Cancer-specific High-throughput Annotation of Somatic Mutations) is a method that predicts the functional significance of somatic missense variants + observed in the genomes of cancer cells, allowing variants to be prioritized in subsequent functional studies, based on the probability that they confer + increased fitness to a cancer cell. CHASM uses a machine learning method called Random Forest to distinguish between driver and passenger somatic missense variation. + The Random Forest is trained on a positive class of drivers curated from the COSMIC database and a negative class of passengers, generated in silico, + according to passenger base substitution frequencies estimated for a specific tumor type. Each variant is represented by a list of features, + including amino acid substitution properties, alignment-based estimates of conservation at the variant position, predicted local structure and annotations from + the UniProt Knowledgebase. Only missense mutations are analyzed by CHASM. For more information on CHASM, please visit http://wiki.chasmsoftware.org + + * SNVGet retrieves selected predictive features for a variant. Features can be broadly categorized into 3 types: + - Amino Acid Substitution features + - Protein-based position-specific features + - Exon-specific features + Only missense mutations are analyzed by SNVGet. For more information on SNVBox (database made with SNVGet), please visit http://wiki.chasmsoftware.org + * VEST is a method that predicts the functional effect of a variant. + + + + **Citation** + If you use this Galaxy tool in work leading to a scientific publication please cite: + + Carter, Hannah, et al. "Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations." + Cancer research 69.16 (2009): 6660-6667. + + Wong, Wing Chung, et al. "CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer." + Bioinformatics 27.15 (2011): 2147-2148. +</tool>