|
0
|
1 #!/usr/bin/env python
|
|
|
2 # -*- coding: utf-8 -*-
|
|
|
3 #
|
|
|
4 # mkpthwpng.py
|
|
|
5 #
|
|
|
6 # Copyright 2011 Oscar Bedoya-Reina <oscar@niska.bx.psu.edu>
|
|
|
7 #
|
|
|
8 # This program is free software; you can redistribute it and/or modify
|
|
|
9 # it under the terms of the GNU General Public License as published by
|
|
|
10 # the Free Software Foundation; either version 2 of the License, or
|
|
|
11 # (at your option) any later version.
|
|
|
12 #
|
|
|
13 # This program is distributed in the hope that it will be useful,
|
|
|
14 # but WITHOUT ANY WARRANTY; without even the implied warranty of
|
|
|
15 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
|
|
16 # GNU General Public License for more details.
|
|
|
17 #
|
|
|
18 # You should have received a copy of the GNU General Public License
|
|
|
19 # along with this program; if not, write to the Free Software
|
|
|
20 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
|
|
|
21 # MA 02110-1301, USA.
|
|
|
22
|
|
|
23 import argparse,mechanize,os,sys
|
|
|
24
|
|
|
25 #this return an image made up from a list of genes and pathway code
|
|
|
26 def rtnHTMLformat(tmpddGenrcgenPresent,sppPrefx,pthwcod,ouPthwpng):
|
|
|
27 inpx='\n'.join(tmpddGenrcgenPresent)#inpx="ALDH2 color \nALDH3A1 color"
|
|
|
28 request=mechanize.Request("http://www.genome.jp/kegg/tool/map_pathway2.html")
|
|
|
29 response = mechanize.urlopen(request)
|
|
|
30 forms = mechanize.ParseResponse(response, backwards_compat=False)
|
|
|
31 form=forms[0]
|
|
|
32 form["unclassified"]=inpx
|
|
|
33 form["org_name"]=[sppPrefx]
|
|
|
34 request2 = form.click()
|
|
|
35 response2 = mechanize.urlopen(request2)
|
|
|
36 a=str(response2.read()).split('href="/kegg-bin/show_pathway?')[1]
|
|
|
37 code=a.split('/')[0]#response2.read()
|
|
|
38 request=mechanize.Request("http://www.genome.jp/kegg-bin/show_pathway?%s/%s.args"%(code,pthwcod))#request=mechanize.Request("http://www.genome.jp/kegg-bin/show_pathway?%s/%s.args"%('13171478854246','hsa00410'))
|
|
|
39 response = mechanize.urlopen(request)
|
|
|
40 forms = mechanize.ParseResponse(response, backwards_compat=False)
|
|
|
41 form=forms[1]
|
|
|
42 status=' NOT '
|
|
|
43 try:
|
|
|
44 imgf=str(forms[1]).split('/mark_pathway')[1].split('/')[0]
|
|
|
45 os.system("wget --quiet http://www.genome.jp/tmp/mark_pathway%s/%s.png -O %s"%(imgf,pthwcod,ouPthwpng))
|
|
|
46 status=' '
|
|
|
47 except:
|
|
|
48 pass
|
|
|
49 return 'A pathway image was%ssuccefully produced...'%status
|
|
|
50
|
|
|
51
|
|
|
52 def main():
|
|
|
53 parser = argparse.ArgumentParser(description='Obtain KEGG images from a list of genes.')
|
|
|
54 parser.add_argument('--input',metavar='input TXT file',type=str,help='the input file with the table in txt format')
|
|
|
55 parser.add_argument('--output',metavar='output PNG image',type=str,help='the output image file in png format')
|
|
|
56 parser.add_argument('--KEGGpath',metavar='KEGG pathway code (i.e. cfa00230)',type=str,help='the code of the pathway of interest')
|
|
|
57 parser.add_argument('--posKEGGclmn',metavar='column number',type=int,help='the column with the KEGG pathway code/name')
|
|
|
58 parser.add_argument('--KEGGgeneposcolmn',metavar='column number',type=int,help='column with the KEGG gene code')
|
|
|
59 #~Open arguments
|
|
|
60 class C(object):
|
|
|
61 pass
|
|
|
62 fulargs=C()
|
|
|
63 parser.parse_args(sys.argv[1:],namespace=fulargs)
|
|
|
64 #test input vars
|
|
|
65 inputf,outputf,KEGGpathw,posKEGGclmn,Kgeneposcolmn=fulargs.input,fulargs.output,fulargs.KEGGpath,fulargs.posKEGGclmn,fulargs.KEGGgeneposcolmn
|
|
|
66 # make posKEGGclmn, Kgeneposcolmn 0-based
|
|
|
67 sppPrefx= KEGGpathw[:3]
|
|
|
68 posKEGGclmn -= 1
|
|
|
69 Kgeneposcolmn -= 1
|
|
|
70 #make a dictionary of valid genes
|
|
|
71 dKEGGcPthws=dict([(x.split('\t')[Kgeneposcolmn],set([y.split('=')[0] for y in x.split('\t')[posKEGGclmn].split('.')])) for x in open(inputf).read().splitlines()[1:] if x.strip()])
|
|
|
72 for mt1gene in [x for x in dKEGGcPthws.keys() if x.find('.')>-1]:#to crrect names with more than one gene
|
|
|
73 pthwsAssotd=dKEGGcPthws.pop(mt1gene)
|
|
|
74 for eachg in mt1gene.split('.'):
|
|
|
75 dKEGGcPthws[eachg]=pthwsAssotd
|
|
|
76 tmpddGenrcgenPresent=set()
|
|
|
77 sKEGGc=dKEGGcPthws.keys()
|
|
|
78 lsKEGGc=len(sKEGGc)
|
|
|
79 ctPthw=0
|
|
|
80 while ctPthw < lsKEGGc:#to save memory
|
|
|
81 eachK=sKEGGc.pop()
|
|
|
82 alPthws=dKEGGcPthws[eachK]
|
|
|
83 if KEGGpathw in alPthws:
|
|
|
84 tmpddGenrcgenPresent.add('\t'.join([eachK,'red']))
|
|
|
85 ctPthw+=1
|
|
|
86 #run the program
|
|
|
87 rtnHTMLformat(tmpddGenrcgenPresent,sppPrefx,KEGGpathw,outputf)
|
|
|
88 return 0
|
|
|
89
|
|
|
90
|
|
|
91 if __name__ == '__main__':
|
|
|
92 main()
|
