Mercurial > repos > saketkc > chasm_web
changeset 2:57d45e85852f
Move files to tools
| author | Saket Choudhary <saketkc@gmail.com> |
|---|---|
| date | Fri, 01 Nov 2013 02:08:16 +0530 |
| parents | 8eaaa7f6b619 |
| children | 89407d4da3ca |
| files | chasm/README.rst chasm/chasm_web.py chasm/chasm_web.xml |
| diffstat | 3 files changed, 0 insertions(+), 354 deletions(-) [+] |
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--- a/chasm/README.rst Fri Nov 01 02:07:53 2013 +0530 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,38 +0,0 @@ -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.
--- a/chasm/chasm_web.py Fri Nov 01 02:07:53 2013 +0530 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,222 +0,0 @@ -#!/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:])
--- a/chasm/chasm_web.xml Fri Nov 01 02:07:53 2013 +0530 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,94 +0,0 @@ -<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>