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#v 1.0
import sys, os, time, re
import urllib, urllib2
from optparse import OptionParser
from HTMLParser import HTMLParser
from xml.dom.minidom import parseString
# Define a function for the thread
class NoRedirectHandler(urllib2.HTTPRedirectHandler):
def http_error_302(self, req, fp, code, msg, headers):
infourl = urllib.addinfourl(fp, headers, req.get_full_url())
infourl.status = code
infourl.code = code
return infourl
http_error_300 = http_error_302
http_error_301 = http_error_302
http_error_303 = http_error_302
http_error_307 = http_error_302
def prepare_optparser():
"""Prepare optparser object. New options will be added in this
function first.
"""
usage = "usage: %prog <-s FASTA_SEQ -p POSITION -t AMINO_TYPE> [options]"
description = "Script for protStability1D tool."
optparser = OptionParser(version="%prog v1.0", description=description, usage=usage, add_help_option=False)
optparser.add_option("-h","--help",action="help",help="Show this help message and exit.")
optparser.add_option("-s","--seq",dest="fastaSeq",type="string",
help="Enter a fasta sequence.")
optparser.add_option("-p", "--pos", dest="mutPos",type="string",
help="Enter mutation position.")
optparser.add_option("-t", "--type", dest="aminoType",type="string",
help="Enter amino acid type.")
return optparser
def opt_validate(optparser):
"""Validate options from a OptParser object.
Return: Validated options object.
"""
(options,args) = optparser.parse_args()
if not (options.fastaSeq and options.mutPos and options.aminoType):
optparser.print_help()
sys.exit(1)
if '"' in options.fastaSeq:
options.fastaSeq = options.fastaSeq.replace('"','')
print
return options
class Protstability1d:
def __init__(self, options):
self.fastaSeq = options.fastaSeq
if not options.mutPos:
options.mutPos = ""
self.mutPos = options.mutPos
if not options.aminoType:
options.aminoType = ""
self.aminoType = options.aminoType
self.url = 'http://www-bionet.sscc.ru/psd2/rest.php?tool=protstability1d'
def sendQuery(self):
opener = urllib2.build_opener(NoRedirectHandler())
urllib2.install_opener(opener)
# do POST
params = urllib.urlencode({'seq': self.fastaSeq, 'pos_mut': self.mutPos, 'mutation': self.aminoType})
req = urllib2.Request(self.url, params)
rsp = urllib2.urlopen(req)
content = rsp.read()
res = content.find('qid=')
content = content[res+5:]
res = content.find('"')
content = content[:res]
self.url = "http://www-bionet.sscc.ru/psd2/rest.php?tool=protstability1d&q=%s" %content
self.getResult()
def getResult(self):
opener = urllib2.build_opener(NoRedirectHandler())
urllib2.install_opener(opener)
content = "working"
while content.find('working') >= 0:
req = urllib2.Request(self.url)
rsp = urllib2.urlopen(req)
content = rsp.read()
time.sleep(0.1)
self.parseOutput(content)
def parseOutput(self, content):
xmldoc = parseString(content)
itemlist = xmldoc.getElementsByTagName('stability')
if itemlist.length <= 0:
print "Result is empty"
sys.exit(1)
res = "STABILITY_1D" ':' + str(itemlist[0].firstChild.nodeValue)
print res
def main():
opts=opt_validate(prepare_optparser())
g = Protstability1d(opts)
g.sendQuery()
if __name__ == "__main__":
main()
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