+ added sample configuration file
[qpalma.git] / test.conf
1 #
2 # Global settings
3 #
4
5
6 #
7 # Set this variable to True if you want to allow QPalma to perform more extensive checks
8 #
9
10 perform_checks = True
11
12 #
13 # You can set the platform.
14 # Currently supported:
15 #
16 # - Set IGA for Illumina Genome Analyzer
17 # - Set 454 for the Roche 454 platform (not implemented yet)
18
19 platform = IGA
20
21 #
22 # This variable stores the path to the toplevel result directory
23 #
24
25 result_dir = /fml/ag-raetsch/home/fabio/tmp/sandbox/first_test
26
27 #
28 # These variables store the filename of the raw read data
29 #
30
31 spliced_reads_fn = /fml/ag-raetsch/home/fabio/tmp/sandbox/map_2nd.vm
32
33 unspliced_reads_fn = /fml/ag-raetsch/home/fabio/tmp/sandbox/map.vm
34
35 #
36 # You can specify how many nodes you want to use via this variable
37 #
38
39 num_splits = 5
40
41 #
42 # Specifiy here the filename of the global logfile QPalma uses to report everything
43 #
44
45 global_log_fn = /fml/ag-raetsch/home/fabio/tmp/sandbox/first_test/qpalma.log
46
47 #
48 # The parameter you want to do prediction with:
49 #
50
51 prediction_parameter_fn = /fml/ag-raetsch/home/fabio/tmp/newest_run/alignment/run_enable_quality_scores_+_enable_splice_signals_+_enable_intron_length_+/param_526.pickle
52
53 #
54 # The run object which should become at some point obsolete but is still needed for now
55 #
56
57 run_fn = /fml/ag-raetsch/home/fabio/tmp/newest_run/alignment/run_enable_quality_scores_+_enable_splice_signals_+_enable_intron_length_+/run_obj.pickle
58
59 #
60 # In order to align short reads QPalma relies on additional information such as
61 # splice site score prediction.
62 #
63
64 genome_dir = /fml/ag-raetsch/share/projects/genomes/A_thaliana_best/genome
65 acceptor_scores_loc = /fml/ag-raetsch/home/fabio/tmp/interval_query_files/acc
66 donor_scores_loc = /fml/ag-raetsch/home/fabio/tmp/interval_query_files/don
67
68 genome_file_fmt = chr%d.dna.flat
69 splice_score_file_fmt= contig_%d%s
70
71 #allowed_fragments = [1,2,3,4,5]
72 allowed_fragments = [1]
73
74
75 #
76 # Settings concerning the prediction algorithm
77 #
78
79 #
80 #
81 #
82
83
84
85 #
86 # This defines
87 #
88
89 half_window_size = 1500
90
91 #
92 # Settings concerning the training algorithm
93 #
94 #
95
96 numLengthSuppPoints = 10
97 numDonSuppPoints = 10
98 numAccSuppPoints = 10
99 matchmatrixRows = 10
100 matchmatrixCols = 10
101 numQualSuppPoints = 10
102 totalQualSuppPoints = 10
103
104 optimizer = MOSEK
105 optimizer = CPLEX
106 optimizer = CVXOPT
107
108 #
109 # BLAT, ShoRe and mGene
110 #
111
112 output_format = BLAT
113
114
115 #prb_offset = 50
116 prb_offset = 64