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1 #!/usr/bin/env python
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2 # -*- coding: utf-8 -*-
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3 #
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4 # calclenchange.py
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5 #
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6 # Copyright 2011 Oscar Bedoya-Reina <oscar@niska.bx.psu.edu>
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7 #
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8 # This program is free software; you can redistribute it and/or modify
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9 # it under the terms of the GNU General Public License as published by
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10 # the Free Software Foundation; either version 2 of the License, or
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11 # (at your option) any later version.
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12 #
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13 # This program is distributed in the hope that it will be useful,
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14 # but WITHOUT ANY WARRANTY; without even the implied warranty of
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15 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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16 # GNU General Public License for more details.
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17 #
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18 # You should have received a copy of the GNU General Public License
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19 # along with this program; if not, write to the Free Software
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20 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
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21 # MA 02110-1301, USA.
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22
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23 import argparse,os,sys
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24
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25
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26 def main():
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27 parser = argparse.ArgumentParser(description='Adds the fields KEGG gene codes and KEGG pathways to an input table of ENSEMBL transcript codes.')
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28 parser.add_argument('--loc_file',metavar='correlational database',type=str,help='correlational database')
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29 parser.add_argument('--species',metavar='species name',type=str,help='the species of interest in loc_file')
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30 parser.add_argument('--output',metavar='output TXT file',type=str,help='the output file with the table in txt format. The output will have two more fields: KEGG gene codes and KEGG pathways of each ENSEMBL code' )
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31 parser.add_argument('--posENSEMBLclmn',metavar='column number',type=int,help='the column with the ENSEMBLE transcript code')
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32 parser.add_argument('--input',metavar='input TXT file',type=str,help='the input file with the table in txt format')
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33 #~
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34 #~Open arguments
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35 class C(object):
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36 pass
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37 fulargs=C()
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38 parser.parse_args(sys.argv[1:],namespace=fulargs)
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39 #test input vars
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40 inputf,loc_file,species,output,posENSEMBLclmn=fulargs.input,fulargs.loc_file,fulargs.species,fulargs.output,fulargs.posENSEMBLclmn
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41 posENSEMBLclmn-=1#correct pos
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42 #~ Get the extra variables
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43 crDB=[x.split() for x in open(loc_file).read().splitlines() if x.split()[0]==species][0]
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44 sppPrefx,dinput=crDB[0],crDB[1]#X should be replaced by the position in which the Conversion Dictionary File (CDF) is placed
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45 #make a dictionary of the input CDF
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46 dKEGGcPthws=dict([(x.split('\t')[0],'\t'.join(x.split('\t')[1:])) for x in open(dinput).read().splitlines() if x.strip()])
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47 #~ add the two new columns
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48 sall=[]
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49 #lENSEMBLTc=[x.split('\t') for x in open(inputf).read().splitlines() if x.strip()]
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50 lENSEMBLTc = []
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51 with open(inputf) as fh:
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52 for line in fh:
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53 if line.startswith('#'):
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54 continue
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55 lENSEMBLTc.append(line.rstrip('\r\n').split('\t'))
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56 nLines=len(lENSEMBLTc)
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57 cLines=0
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58 sall=[]#the output list for with additional fields
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59 #~
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60 while cLines<nLines:
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61 cLines+=1
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62 lENSEMBLTcKEGGgKEGGpth=lENSEMBLTc.pop(0)
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63 ENSEMBLTc=lENSEMBLTcKEGGgKEGGpth[posENSEMBLclmn]
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64 try:
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65 KEGGgKEGGpth=dKEGGcPthws[ENSEMBLTc]
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66 except:
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67 KEGGgKEGGpth='\t'.join(['U','N'])
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68 sall.append('\t'.join(['\t'.join(lENSEMBLTcKEGGgKEGGpth),KEGGgKEGGpth]))
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69 #~
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70 salef=open(output,'w')
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71 salef.write('\n'.join(sall))
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72 salef.close()
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73 return 0
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74
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75
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76 if __name__ == '__main__':
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77 main()
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78
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