+ added information on cut positions of spliced reads
[qpalma.git] / scripts / createNewDataset.py
1 #!/usr/bin/env python
2 # -*- coding: utf-8 -*-
3
4 import qpalma.Configuration as Conf
5 from compile_dataset import compile_d
6
7 #filtered_fn = '/fml/ag-raetsch/share/projects/qpalma/solexa/filteredReads_11_02_2008_subset'
8 #remapped_fn = '/fml/ag-raetsch/share/projects/qpalma/solexa/halleluja.txt_1000'
9
10 #filtered_fn = '/fml/ag-raetsch/share/projects/qpalma/solexa/filteredReads_11_02_2008'
11 #filtered_fn = '/fml/ag-raetsch/share/projects/qpalma/solexa/filteredReads_18_03_2008'
12 #remapped_fn = '/fml/ag-raetsch/share/projects/qpalma/solexa/map.vm_18_03_2008'
13
14 filtered_fn = '/fml/ag-raetsch/share/projects/qpalma/solexa/allFilteredReads_20_03_2008'
15
16 remapped_fn = '/fml/ag-raetsch/share/projects/qpalma/solexa/map.vm_05_04_2008_tmp'
17
18 #remapped_fn = '/fml/ag-raetsch/share/projects/qpalma/solexa/map.vm_1k'
19 #remapped_fn = '/fml/ag-raetsch/share/projects/qpalma/solexa/halleluja.txt'
20
21 compile_d(Conf.gff_fn,Conf.dna_flat_fn,filtered_fn,remapped_fn,Conf.tmp_dir,'dataset_remapped',True)