Mercurial > repos > saket-choudhary > sift_web

changeset 3:5717f4376968 draft

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author saket-choudhary
date Thu, 04 Sep 2014 17:46:05 -0400
parents 19590303d460
children 5cc3210369ac
files 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
diffstat 6 files changed, 0 insertions(+), 200 deletions(-) [+]
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--- a/sift_web/README.rst	Thu Sep 04 17:45:46 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,42 +0,0 @@
-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.  
--- a/sift_web/sift_web.py	Thu Sep 04 17:45:46 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,128 +0,0 @@
-#!/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:])
--- a/sift_web/sift_web.xml	Thu Sep 04 17:45:46 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,21 +0,0 @@
-<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>
-
--- a/sift_web/tool_dependencies.xml	Thu Sep 04 17:45:46 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-<?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>