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#v 1.0
import sys, os
import urllib, urllib2
from optparse import OptionParser
import csv
from xml.dom.minidom import parseString
import StringIO
def prepare_optparser():
"""Prepare optparser object. New options will be added in this
function first.
"""
usage = "usage: %prog <-i STRING> [options]"
description = "SNPChIPTools."
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","--id",dest="id",type="string",
help="Enter ID.")
optparser.add_option("--ug", dest="ug",type="string",
help="Enter UG('true' or 'false'). Default: 'true'")
return optparser
def opt_validate(optparser):
"""Validate options from a OptParser object.
Return: Validated options object.
"""
(options,args) = optparser.parse_args()
if not (options.id):
optparser.print_help()
sys.exit(1)
return options
class Snp2pdbsite:
def __init__(self, options):
self.id = options.id
if not options.ug:
options.ug = "true"
self.ug = options.ug
self.url = 'http://lungry1.bionet.nsc.ru/cgi-bin/SNPProject/SNPChIPTools.cgi'
def sendQuery(self):
opener = urllib2.build_opener()
urllib2.install_opener(opener)
# do POST
params = urllib.urlencode({'id_SNP': self.id, 'UG': self.ug})
req = urllib2.Request(self.url, params)
rsp = urllib2.urlopen(req)
content = rsp.read()
self.parseOutput(content)
def parseOutput(self, content):
sidx = content.find('checked onclick="submit()"> ')
eidx = content.find('></td></tr></table></form>')
if eidx > sidx and eidx != -1 and sidx != -1:
content = content[sidx:eidx]
csv_dict = csv.DictReader(StringIO.StringIO(content), delimiter='\t', quotechar='|')
id_score = {}
for row in csv_dict:
score = row[" score"]
if score is None:
continue
score = score.strip()
id = row[" \xd2\xd4 "]
if id is None:
continue
id = id.strip()
if not (score is None):
id_score[id] = score
#print("SNP_CHIP:{0}[{1}];".format(id, score))
if len(id_score) != 0:
out_str = 'SNP_CHIP:'
for id in id_score:
out_str = out_str + str(id) + '[' + str(id_score[id]) + '];'
print out_str
def main():
opts=opt_validate(prepare_optparser())
g = Snp2pdbsite(opts)
g.sendQuery()
if __name__ == "__main__":
main()
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