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sift_web/.DS_Store sift_web/._.DS_Store sift_web/README.rst sift_web/sift_web.py sift_web/sift_web.xml sift_web/tool_dependencies.xml |
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| diff -r d54007492bc4 -r 19590303d460 sift_web/README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sift_web/README.rst Thu Sep 04 17:45:46 2014 -0400 |
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| @@ -0,0 +1,42 @@ +Galaxy wrapper for the SIFT webservice +=================================================== + +This tool is copyright 2014 by Saket Choudhary<saketkc@gmail.com>, 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: + +Kumar P, Henikoff S, Ng PC. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc. 2009;4(7):1073-81. + +Ng PC, Henikoff S. Predicting the Effects of Amino Acid Substitutions on Protein Function Annu Rev Genomics Hum Genet. 2006;7:61-80. + +Ng PC, Henikoff S. SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res. 2003 Jul 1;31(13):3812-4. + +Ng PC, Henikoff S. Accounting for Human Polymorphisms Predicted to Affect Protein Function. Genome Res. 2002 Mar;12(3):436-46. + +Ng PC, Henikoff S. Predicting Deleterious Amino Acid Substitutions. Genome Res. 2001 May;11(5):863-74. |
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| diff -r d54007492bc4 -r 19590303d460 sift_web/sift_web.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sift_web/sift_web.py Thu Sep 04 17:45:46 2014 -0400 |
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| @@ -0,0 +1,128 @@ +#!/usr/bin/env python +import requests +import argparse +import sys +from functools import wraps +import time +from bs4 import BeautifulSoup + +__url__ = 'http://provean.jcvi.org/genome_prg_2.php' + + +def stop_err(msg, err=1): + sys.stderr.write('%s\n' % msg) + sys.exit(err) + + +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 SIFTWeb: + + def __init__(self): + self.full_download_url = 'http://provean.jcvi.org/serve_file.php?VAR=g%s/%s.result.tsv' + self.condensed_download_url = 'http://provean.jcvi.org/serve_file.php?VAR=g%s/%s.result.one.tsv' + self.summary_download_url = 'http://provean.jcvi.org/serve_file.php?VAR=g%s/%s.result.summary.tsv' + self.url_dict = {'full': self.full_download_url, + 'condensed': self.condensed_download_url, + 'summary': self.summary_download_url} + + def upload(self, inputpath): + payload = {'table': 'human37_66'} + in_txt = open(inputpath, 'rb').read() + payload['CHR'] = in_txt + request = requests.post( __url__, data=payload)#, files={'CHR_file': open(path)}) + return request.text + + @retry(requests.exceptions.HTTPError) + def get_full_data(self, job_id, full_output): + r = requests.request( + 'GET', (self.full_download_url) % (job_id, job_id)) + if r.text != 'No file exists': + with open(full_output, 'wb') as f: + f.write(r.text) + else: + return requests.HTTPError() + + @retry(requests.exceptions.HTTPError) + def get_condensed_data(self, job_id, condensed_output): + r = requests.request( + 'GET', (self.condensed_download_url) % (job_id, job_id)) + if r.text != 'No file exists': + with open(condensed_output, 'wb') as f: + f.write(r.text) + else: + raise(requests.HTTPError()) + + @retry(requests.exceptions.HTTPError) + def get_summary_data(self, job_id, summary_output): + r = requests.request( + 'GET', (self.summary_download_url) % (job_id, job_id)) + if r.text != 'No file exists': + with open(summary_output, 'wb') as f: + f.write(r.text) + else: + raise(requests.HTTPError()) + + +def main(params): + parser = argparse.ArgumentParser() + parser.add_argument('--input', type=str, required=True) + parser.add_argument('--output1', type=str, required=True) + parser.add_argument('--output2', type=str, required=True) + parser.add_argument('--output3', type=str, required=True) + args = parser.parse_args(params) + sift_web = SIFTWeb() + content = sift_web.upload(args.input) + soup = BeautifulSoup(content) + p = soup.findAll('p') + job_id = p[1].string.split(':')[-1].replace(' ', '').replace(').', '') + sift_web.get_full_data(job_id, args.output1) + sift_web.get_condensed_data(job_id, args.output2) + sift_web.get_summary_data(job_id, args.output3) + + +if __name__ == '__main__': + main(sys.argv[1:]) |
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| diff -r d54007492bc4 -r 19590303d460 sift_web/sift_web.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sift_web/sift_web.xml Thu Sep 04 17:45:46 2014 -0400 |
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| @@ -0,0 +1,21 @@ +<tool id="sift_web" name="SIFTWeb"> + <description>SIFT/Provean web service</description> + <requirements> + <requirement type="package" version="2.2.1">requests</requirement> + <requirement type="package" version="4.1.0">beautifulsoup4</requirement> + <requirement type="python-module">requests</requirement> + <requirement type="python-package">bs4</requirement> + </requirements> + <command interpreter="python"> + sift_web.py --input $input --output1 $output1 --output2 $output2 --output3 $output3 + </command> + <inputs> + <param name="input" format="txt" type="data" label="Input Variants"/> + </inputs> + <outputs> + <data name="output1" format="tabular"/> + <data name="output2" format="tabular"/> + <data name="output3" format="tabular"/> + </outputs> +</tool> + |
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| diff -r d54007492bc4 -r 19590303d460 sift_web/tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sift_web/tool_dependencies.xml Thu Sep 04 17:45:46 2014 -0400 |
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| @@ -0,0 +1,9 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="beautifulsoup4" version="4.1.0"> + <repository changeset_revision="4890592e10f8" name="package_beautifulsoup4_4_1_0" owner="saket-choudhary" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <package name="requests" version="2.2.1"> + <repository changeset_revision="04c9eef6c14b" name="package_requests_2_2_1" owner="saket-choudhary" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |