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_len_limits=%s\n'%(plif.name,str(plif.limits)))
  12    fid.write('%s_len_penalties=%s\n'%(plif.name,str(plif.penalties)))
  13    fid.write('%s_len_bins=%d\n'%(plif.name,len(plif.limits)))
  14
  15    if plif.name == 'intron':
  16       fid.write('%s_len_min=%d\n'%(plif.name,plif.min_len))
  17       fid.write('%s_len_max=%d\n'%(plif.name,plif.max_len))
  18       fid.write('%s_len_transform=%s\n'%(plif.name,plif.transform))
  19
  20 def export_param(filename,h,d,a,mmatrix):
  21
  22    # Exports a bz2 file with the trained PALMA. Assumes splice sites and intron length used.
  23    h.name = 'intron'
  24    d.name = 'donor'
  25    a.name = 'acceptor'
  26
  27    fid = bz2.BZ2File(filename+'.bz2','w')
  28
  29    fid.write('%palma definition file version: 1.0\n\n')
  30    fid.write('%penalties\n');
  31
  32    writeStruct(fid, h);
  33    writeStruct(fid, a);
  34    writeStruct(fid, d);
  35
  36    # substitution matrix
  37    mmatrix = mmatrix.reshape(6,6)
  38    fid.write('substitution_matrix=[')
  39    for row in range(6):
  40       if row == 5:
  41          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]))
  42       else:
  43          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]))
  44
  45    fid.close()