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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
#id mapping
def getPDBIdandChain(uniprotID):
#data from http://www.bioinf.org.uk/pdbsws/
dirPath = os.path.dirname(sys.argv[0])
fileName ='pdb_uniprot_chain_map.lst.2'
if len(dirPath) != 0:
fileName = dirPath + "/pdb_uniprot_chain_map.lst.2"
fileName = fileName.replace('\\', '/')
f = open (fileName, 'r')
pdbId = ''
chain = ''
while(1):
line = f.readline()
if not line:
break
line = line.rstrip('\n')
columns = line.split()
if len(columns) != 3:
continue
if columns[2] == uniprotID:
pdbId = columns[0]
chain = columns[1]
f.close()
return pdbId, chain
# 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 <-i STRING -c STRING -p INT -t STRING> [options]"
description = "Script for protStability3D 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("-i","--protid",dest="protId",type="string",
help="Enter a protein (uniprot) ID.")
optparser.add_option("-c", "--chain", dest="chain",type="string",
help="Enter chain.")
optparser.add_option("-p", "--pos", dest="mutPos",type="int",
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.chain and options.protId and options.mutPos and options.aminoType):
optparser.print_help()
sys.exit(1)
id, chain = getPDBIdandChain(options.protId)
if not (id and chain):
print "NO PDB ID"
sys.exit(1)
options.chain = chain
options.protId = id
return options
class Protstability3d:
def __init__(self, options):
self.protId = options.protId
self.mutPos = options.mutPos
self.chain = options.chain
self.aminoType = options.aminoType
self.url = 'http://www-bionet.sscc.ru/psd2/rest.php?tool=protstability3d'
def sendQuery(self):
opener = urllib2.build_opener(NoRedirectHandler())
urllib2.install_opener(opener)
# do POST
params = urllib.urlencode({'pdb': self.protId, 'chain': self.chain, '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=protstability3d&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_3D' ':' + str(itemlist[0].firstChild.nodeValue)
print res
def main():
opts=opt_validate(prepare_optparser())
g = Protstability3d(opts)
g.sendQuery()
if __name__ == "__main__":
main()
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