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#!/usr/bin/env python3
"""
#v_1.00
"""
import sys, os, time, re
import urllib, urllib2, cookielib
from optparse import OptionParser
# print current time and information on screen
def Info(infoStr):
print "[%s] %s" %(time.strftime('%H:%M:%S'), infoStr)
def prepare_optparser():
"""Prepare optparser object. New options will be added in this
function first.
"""
usage = "usage: %prog <-f STRING -s STRING> [options]"
description = "Transcription factors binds to two DNAs: SNPs and\or site-directed mutations."
optparser = OptionParser(version="%prog v1.02", 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("-f", "--snpf1",dest="firstSeq",type="string",
help="Select a nucleotide sequence of the SNP variant #1.")
optparser.add_option("-s", "--snpf2",dest="secondSeq",type="string",
help="Select a nucleotide sequence of the SNP variant #2.")
optparser.add_option("--snpdm1",dest="snpdm1",type="int",
help="""Select How the unknown binds to DNA#1.\n
Enter integer from 0 to 5\n
default:1""", default=1)
optparser.add_option("--snpdm2",dest="snpdm2",type="int",
help="""Select How the unknown binds to DNA#2.\n
Enter integer from 0 to 5\n
default:2""", default=2)
optparser.add_option("--sign",dest="significance",type="int",
help="Select significance. Enter integer from 0 to 15", default=10)
return optparser
def opt_validate(optparser):
"""Validate options from a OptParser object.
Return: Validated options object.
"""
(options,args) = optparser.parse_args()
if options.firstSeq and '"' in options.firstSeq:
options.firstSeq = options.firstSeq.replace('"','')
if options.secondSeq and '"' in options.secondSeq:
options.secondSeq = options.secondSeq.replace('"','')
if not options.firstSeq and not options.secondSeq:
optparser.print_help()
sys.exit(1)
if not 0 <= options.snpdm1 <= 5 and 0 <= options.snpdm2 <= 5:
Info('Wanring: snpdm values must be in range from 0 to 5.')
sys.exit(1)
if not 0 <= options.significance <= 16:
Info('Wanring: Significance value must be in range from 0 to 16.')
sys.exit(1)
print
return options
class RSNP:
def __init__(self, options):
self.firstSeq = options.firstSeq
self.secondSeq = options.secondSeq
self.snpdm1 = options.snpdm1
self.snpdm2 = options.snpdm2
self.significance = options.significance
self.opts_string = "# Argument List:\n" +\
"# first sequence = %s\n" %options.firstSeq +\
"# second sequence = %s\n" %options.secondSeq +\
"# Unknown binds to DNA#1 = %d\n" %options.snpdm1 +\
"# Unknown binds to DNA#2 = %d\n" %options.snpdm2 +\
"# Significance = %d\n" %options.significance
self.firstSeqFromFile = ""
self.secondSeqFromFile = ""
self.absentSides = []
self.presentSides = []
self.noIdeaSides = []
def sendQuery(self):
cookie_jar = cookielib.CookieJar()
opener = urllib2.build_opener(urllib2.HTTPCookieProcessor(cookie_jar))
urllib2.install_opener(opener)
# do POST
url = 'http://samurai.bionet.nsc.ru/cgi-bin/03/programs/rsnp_lin/rsnpd.pl'
req = urllib2.Request(url, "b1=Calculate&snpf1={0}&snpf2={1}&SNPDM_0={2}&SNPDM_1={3}&DSL={4}".format(self.firstSeq, self.secondSeq, self.snpdm1, self.snpdm2, self.significance))
rsp = urllib2.urlopen(req)
content = rsp.read()
res = content.find('PRESENT:</b> ')
if res == -1:
print "Result is empty"
else:
content = content[res+18:]
res = content.find('<P align')
content = content[:res]
out = content.split()
for item in out:
if item:
print("PRESENT:"+item)
def main():
opts=opt_validate(prepare_optparser())
g = RSNP(opts)
g.sendQuery()
if __name__ == "__main__":
main()
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