Mercurial > repos > miller-lab > genome_diversity
annotate mkpthwpng.py @ 28:184d14e4270d
Update to Miller Lab devshed revision 4ede22dd5500
| author | Richard Burhans <burhans@bx.psu.edu> |
|---|---|
| date | Wed, 17 Jul 2013 12:46:46 -0400 |
| parents | 66a183c44dd5 |
| children |
| rev | line source |
|---|---|
| 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 | |
|
23
66a183c44dd5
bugfix for Pathway Image tool
Richard Burhans <burhans@bx.psu.edu>
parents:
0
diff
changeset
|
33 form["org"]=sppPrefx |
| 0 | 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() |