Mercurial > repos > miller-lab > genome_diversity

comparison calctfreq.py @ 0:2c498d40ecde

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author miller-lab
date Mon, 09 Apr 2012 12:03:06 -0400
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1 #!/usr/bin/env python
2 # -*- coding: utf-8 -*-
3 #
4 # calcfreq.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,os,sys
24 from decimal import Decimal,getcontext
25 from LocationFile import LocationFile
26
27 #method to rank the the pthways by mut. freq.
28 def rankd(ltfreqs):
29 ordvals=sorted(ltfreqs)#sort and reverse freqs.
30 #~
31 outrnk=[]
32 tmpFreq0,tmpCount,tmpPthw=ordvals.pop()#the highest possible value
33 crank=1
34 outrnk.append('\t'.join([str(tmpCount),str(tmpFreq0),str(crank),tmpPthw]))
35 totalnvals=len(ordvals)
36 cnt=0
37 while totalnvals>cnt:
38 cnt+=1
39 tmpFreq,tmpCount,tmpPthw=ordvals.pop()
40 if tmpFreq!=tmpFreq0:
41 crank=len(outrnk)+1
42 tmpFreq0=tmpFreq
43 outrnk.append('\t'.join([str(tmpCount),str(tmpFreq),str(crank),tmpPthw]))
44 return outrnk
45
46
47 def main():
48 parser = argparse.ArgumentParser(description='Obtain KEGG images from a list of genes.')
49 parser.add_argument('--input',metavar='input TXT file',type=str,help='the input file with the table in txt format')
50 parser.add_argument('--output',metavar='output TXT file',type=str,help='the output file with the table in txt format. Column 1 is the count of genes in the list, Column 2 is the percentage of the pathway genes present on the list. Column 3 is the rank based on column 2')
51 parser.add_argument('--posKEGGclmn',metavar='column number',type=int,help='the column with the KEGG pathway code/name')
52 parser.add_argument('--KEGGgeneposcolmn',metavar='column number',type=int,help='column with the KEGG gene code')
53 parser.add_argument('--loc_file',metavar='location file',type=str,help='location file')
54 parser.add_argument('--species',metavar='species',type=str,help='species')
55 #~Open arguments
56 class C(object):
57 pass
58 fulargs=C()
59 parser.parse_args(sys.argv[1:],namespace=fulargs)
60 #test input vars
61 inputf,outputf,posKEGGclmn,Kgeneposcolmn=fulargs.input,fulargs.output,fulargs.posKEGGclmn,fulargs.KEGGgeneposcolmn
62 locf,species=fulargs.loc_file,fulargs.species
63 #make a dictionary of valid genes
64 posKEGGclmn-=1
65 Kgeneposcolmn-=1
66 dKEGGcPthws=dict([(x.split('\t')[Kgeneposcolmn],set(x.split('\t')[posKEGGclmn].split('.'))) for x in open(inputf).read().splitlines()[1:] if x.strip()])
67 sdGenes=set([x for x in dKEGGcPthws.keys() if x.find('.')>-1])
68 while True:#to correct names with more than one gene
69 try:
70 mgenes=sdGenes.pop()
71 pthwsAssotd=dKEGGcPthws.pop(mgenes)
72 mgenes=mgenes.split('.')
73 for eachg in mgenes:
74 dKEGGcPthws[eachg]=pthwsAssotd
75 except:
76 break
77 #~ Count genes
78 getcontext().prec=2#set 2 decimal places
79
80 location_file = LocationFile(locf)
81 prefix, kxml_dir_path, dict_file = location_file.get_values(species)
82 dPthContsTotls = {}
83 try:
84 with open(dict_file) as fh:
85 for line in fh:
86 line = line.rstrip('\r\n')
87 value, key = line.split('\t')
88 dPthContsTotls[key] = int(value)
89 except IOError, err:
90 print >> sys.stderr, 'Error opening dict file {0}: {1}'.format(dict_file, err.strerror)
91 sys.exit(1)
92
93 dPthContsTmp=dict([(x,0) for x in dPthContsTotls.keys()])#create a list of genes
94 sdGenes=set([x for x in dKEGGcPthws.keys()])#list of all genes
95 cntGens=0
96 ltGens=len(sdGenes)
97 while cntGens<ltGens:
98 cGen=sdGenes.pop()
99 sKEGGcPthws=dKEGGcPthws.pop(cGen)
100 for eachP in sKEGGcPthws:
101 if eachP!='N':
102 dPthContsTmp[eachP]+=1
103 cntGens+=1
104 #~ Calculate Freqs.
105 ltfreqs=[((Decimal(dPthContsTmp[x])/Decimal(dPthContsTotls[x])),Decimal(dPthContsTmp[x]),x) for x in dPthContsTotls]
106 tabllfreqs='\n'.join(rankd(ltfreqs))
107 salef=open(outputf,'w')
108 salef.write(tabllfreqs)
109 salef.close()
110 return 0
111
112
113 if __name__ == '__main__':
114 main()