python/export_param.py

   1 #!/usr/bin/env python
   2 # -*- coding: utf-8 -*-
   3
   4 ###########################################################
   5 #
   6 ###########################################################
   7
   8 import bz2
   9
  10 def writeStruct(fid,plif):
  11    fid.write('%s_limits=%s\n'%(plif.name,str(plif.limits)))
  12    fid.write('%s_penalties=%s\n'%(plif.name,str(plif.penalties)))
  13    fid.write('%s_bins=%d\n'%(plif.name,len(plif.limits)))
  14
  15    if plif.name == 'intron':
  16       fid.write('%s_len_limits=%s\n'%(plif.name,str(plif.limits)))
  17       fid.write('%s_len_penalties=%s\n'%(plif.name,str(plif.penalties)))
  18       fid.write('%s_len_bins=%d\n'%(plif.name,len(plif.limits)))
  19       fid.write('%s_len_min=%d\n'%(plif.name,plif.min_len))
  20       fid.write('%s_len_max=%d\n'%(plif.name,plif.max_len))
  21       fid.write('%s_len_transform=%s\n'%(plif.name,plif.transform))
  22
  23 def export_param(filename,h,d,a,mmatrix):
  24
  25    # Exports a bz2 file with the trained PALMA. Assumes splice sites and intron length used.
  26    h.name = 'intron'
  27    d.name = 'donor'
  28    a.name = 'acceptor'
  29
  30    fid = bz2.BZ2File(filename+'.bz2','w')
  31
  32    fid.write('%palma definition file version: 1.0\n\n')
  33    fid.write('%penalties\n');
  34
  35    writeStruct(fid, h);
  36    writeStruct(fid, a);
  37    writeStruct(fid, d);
  38
  39    # substitution matrix
  40    mmatrix = mmatrix.reshape(6,6)
  41    fid.write('substitution_matrix=[')
  42    for row in range(6):
  43       if row == 5:
  44          fid.write('%f, %f, %f, %f, %f, %f]\n'%(mmatrix[row,0],mmatrix[row,1],mmatrix[row,2],mmatrix[row,3],mmatrix[row,4],mmatrix[row,5]))
  45       else:
  46          fid.write('%f, %f, %f, %f, %f, %f;\n'%(mmatrix[row,0],mmatrix[row,1],mmatrix[row,2],mmatrix[row,3],mmatrix[row,4],mmatrix[row,5]))
  47
  48    fid.close()