+ moved penalty lookup and compute_doncc to Plif module
[qpalma.git] / qpalma / TrainingParam.py
1 #!/usr/bin/env python
2 # -*- coding: utf-8 -*-
3
4 class Param:
5
6 def __init__(self):
7 """ default parameters """
8
9 self.basedir = '/fml/ag-raetsch/share/projects/qpalma/elegans_palma2'
10 #self.basedir = '/fml/ag-raetsch/share/projects/qpalma/zebrafish'
11 self.MAX_MEM = 31000;
12 self.LOCAL_ALIGN = 1;
13 self.init_param = 1;
14 self.train_with_splicesitescoreinformation = 1;
15 self.train_with_intronlengthinformation = 1;
16 self.C = 0.001;
17 self.microexon = 0;
18 self.prob = 0;
19 self.organism = 'elegans'
20 self.expt = 'training'
21
22 self.insertion_prob = self.prob/3 ;
23 self.deletion_prob = self.prob/3 ;
24 self.mutation_prob = self.prob/3 ;