1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
|
#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 <-p STRING -c STRING -m STRING> [options]"
description = "SNP2PDBSite."
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("-p","--protId",dest="protId",type="string",
help="Enter protein (uniprot) ID.")
optparser.add_option("-c", "--chain", dest="chain",type="string",
help="Enter chain.")
optparser.add_option("-m", "--mut", dest="mutation",type="string",
help="Enter mutation.")
return optparser
def opt_validate(optparser):
"""Validate options from a OptParser object.
Return: Validated options object.
"""
(options,args) = optparser.parse_args()
if not (options.protId and options.chain and options.mutation):
optparser.print_help()
sys.exit(1)
if '"' in options.protId:
options.protId = options.protId.replace('"','')
if '"' in options.mutation:
options.mutation = options.mutation.replace('"','')
id, chain = getPDBIdandChain(options.protId)
if not (id and chain):
sys.exit(1)
options.chain = chain
options.protId = id
mutList = list(options.mutation)
mutList[0] = chain
options.mutation = "".join(mutList)
return options
class Snp2pdbsite:
def __init__(self, options):
self.protId = options.protId
if not options.chain:
options.chain = ""
self.chain = options.chain
if not options.mutation:
options.mutation = ""
self.mutation = options.mutation
self.url = 'http://www-bionet.sscc.ru/psd2/rest.php?tool=snp2pdbsite'
def sendQuery(self):
opener = urllib2.build_opener(NoRedirectHandler())
urllib2.install_opener(opener)
# do POST
params = urllib.urlencode({'pdb': self.protId, 'chain': self.chain, 'mut': self.mutation})
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=snp2pdbsite&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):
if len(content) == 0:
print "Result is empty"
sys.exit(1)
xmldoc = parseString(content)
itemlist = xmldoc.getElementsByTagName('aa')
if itemlist.length <= 0:
print "Result is empty"
sys.exit(1)
for item in itemlist:
print "PDB_SITE" + ':' + item.getAttribute("pos") + item.getAttribute("aa") + ';'
def main():
opts=opt_validate(prepare_optparser())
g = Snp2pdbsite(opts)
g.sendQuery()
if __name__ == "__main__":
main()
|
