# HG changeset patch # User Saket Choudhary # Date 1384888710 -19800 # Node ID 742c7ee37f8b00eab264169482137a3ba5236223 push diff -r 000000000000 -r 742c7ee37f8b tools/condel/README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/condel/README.rst Wed Nov 20 00:48:30 2013 +0530 @@ -0,0 +1,36 @@ +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: + +Improving the Assessment of the Outcome of Nonsynonymous SNVs with a Consensus Deleteriousness Score, +Condel (2011) Abel González-Pérez and Nuria López-Bigas, American Journal of Human Genetics 10.1016/j.ajhg.2011.03.004 + diff -r 000000000000 -r 742c7ee37f8b tools/condel/condel_web.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/condel/condel_web.py Wed Nov 20 00:48:30 2013 +0530 @@ -0,0 +1,140 @@ +import sys +sys.path.insert(0, '/home/saket/requests-new-urllib3-api/requests/packages/') +sys.path.insert(0, '/home/saket/requests-new-urllib3-api') + + +import requests +import pycurl +import os +from os.path import getsize +import argparse +import sys +import cStringIO +from functools import wraps +import tempfile, shutil,time + +__url__="http://bg.upf.edu/condel/taskService" +def stop_err( msg ): + sys.stderr.write( '%s\n' % msg ) + sys.exit() + +def retry(ExceptionToCheck, tries=10, 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 + pass + time.sleep(mdelay) + mtries -= 1 + mdelay *= backoff + return f(*args, **kwargs) + + return f_retry # true decorator + + return deco_retry + +class TransficUploader: + def __init__(self): + + self.c = pycurl.Curl() + self.c.setopt(pycurl.URL, __url__) + self.c.setopt(pycurl.UPLOAD, 1) + #c.setopt(pycurl.USERPWD, 'saket.kumar:whatsinaname.') + self.c.setopt(pycurl.PROXY, 'http://saket.kumar:whatsinaname.@netmon.iitb.ac.in:80/') + #c.setopt(pycurl.PROXYPORT, 80) + #c.setopt(pycurl.PROXYTYPE_HTTP,1) + #self.c.setopt(pycurl.VERBOSE, 1) + self.c.setopt(pycurl.HTTPHEADER, ['Expect:']) + #c.setopt(pycurl.HTTPPROXYTUNNEL, 1) + self.c.setopt(pycurl.UPLOAD, 1) + #c.perform() + self.c.setopt(pycurl.NOPROGRESS, 1); + #curl_easy_setopt(hnd, CURLOPT_UPLOAD, 1L); + self.c.setopt(pycurl.USERAGENT, "curl/7.27.0"); + #curl_easy_setopt(hnd, CURLOPT_HTTPHEADER, slist1); + #curl_easy_setopt(hnd, CURLOPT_MAXREDIRS, 50L); + self.c.setopt(pycurl.SSL_VERIFYPEER, 1); + self.c.setopt(pycurl.CUSTOMREQUEST, "PUT") + #curl_easy_setopt(hnd, CURLOPT_VERBOSE, 1L); + self.c.setopt(pycurl.TCP_NODELAY, 1); + self.buf = cStringIO.StringIO() + self.c.setopt(self.c.WRITEFUNCTION, self.buf.write) + + + def upload_file(self,filepath): + f = open(filepath) + self.c.setopt(pycurl.INFILE, f) + self.c.setopt(pycurl.INFILESIZE, getsize(filepath)) + + def run(self): + self.c.perform() + + def get_url(self): + return self.buf.getvalue().strip() + + @retry(requests.exceptions.HTTPError) + def result_exists(self,url ): + #url="http://www.cravat.us/results/%s/%s.zip" %(job_id,job_id) + download_request = requests.request("GET", url) + if download_request.status_code==404 or download_request==500: + raise requests.HTTPError() + else: + return url + @retry(requests.exceptions.HTTPError) + def download_result(self, url,outpath): + tmp_dir = tempfile.mkdtemp() + r = requests.get( url, stream=True ) + if r.status_code == 500: + raise requests.HTTPError() + else: + path = os.path.join( tmp_dir,"results.csv") + with open(path, 'wb') as f: + for chunk in r.iter_content(128): + f.write(chunk) + shutil.move(path,outpath) + shutil.rmtree(tmp_dir) + + + +def main(params): + parser = argparse.ArgumentParser() + parser.add_argument("--input",type=str,required=True) + parser.add_argument("--output",type=str,required=True) + args = parser.parse_args(params) + uploader = TransficUploader(); + uploader.upload_file(args.input) + uploader.run() + url = uploader.get_url() + url = uploader.result_exists(url) + download = uploader.download_result(url,args.output) +if __name__=="__main__": + main(sys.argv[1:]) diff -r 000000000000 -r 742c7ee37f8b tools/condel/condel_web.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/condel/condel_web.xml Wed Nov 20 00:48:30 2013 +0530 @@ -0,0 +1,35 @@ + + Condel web service + + condel_web.py --input $input --output $output + + + + + + + + + **What it does** + Condel stands for CONsensus DELeteriousness score of non-synonymous single nucleotide variants (SNVs). + The idea behind it is to integrate the output of computational tools aimed at assessing the impact of non synonymous + SNVs on protein function. To do this, it computes a weighted average of the scores (WAS) of these tools. + Condel was developed to integrate the outputs of five tools: SIFT, Polyphen2, MAPP, LogR Pfam E-value + (implemented ad hoc following the instructions at Clifford RJ, Edmonson MN, Nguyen C, and Buetow KH (2004) + Large-scale analysis of non-synonymous coding region single nucleotide polymorphisms. Bioinformatics 20, 1006-1014) and MutationAssessor + + + The scores of different methods are weighted using the complementary cumulative distributions produced by the five + methods on a dataset of approximately 20000 missense SNPs, both deleterious and neutral. + The probability that a predicted deleterious mutation is not a false positive of the method and the probability that a + predicted neutral mutation is not a false negative are employed as weights + + **Citation** + + If you use this Galaxy tool in work leading to a scientific publication please cite: + + Improving the Assessment of the Outcome of Nonsynonymous SNVs with a Consensus Deleteriousness Score, + Condel (2011) Abel González-Pérez and Nuria López-Bigas, American Journal of Human Genetics 10.1016/j.ajhg.2011.03.004 + + + diff -r 000000000000 -r 742c7ee37f8b tools/condel/tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/condel/tool_dependencies.xml Wed Nov 20 00:48:30 2013 +0530 @@ -0,0 +1,7 @@ + + + + + + +