+ changed check for intial setting of old_w. (matrix != None does not work in cvxopt)
[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 # In order to align short reads QPalma relies on additional information such as
43 # splice site score prediction.
44 #
45
46 genome_dir = /fml/ag-raetsch/share/projects/genomes/A_thaliana_best/genome
47 acceptor_scores_loc = /fml/ag-raetsch/home/fabio/tmp/interval_query_files/acc
48 donor_scores_loc = /fml/ag-raetsch/home/fabio/tmp/interval_query_files/don
49
50 genome_file_fmt = chr%d.dna.flat
51 splice_score_file_fmt= contig_%d%s
52
53 #allowed_fragments = [1,2,3,4,5]
54 allowed_fragments = [1]
55
56
57 #
58 # Settings concerning the prediction algorithm
59 #
60
61 #
62 #
63 #
64
65
66
67 #
68 # This defines
69 #
70
71 half_window_size = 1500
72
73 #
74 # Settings concerning the training algorithm
75 #
76 #
77
78 optimizer = MOSEK
79 optimizer = CPLEX
80 optimizer = CVXOPT
81
82 #
83 # The output format can be one of BLAT, ShoRe or mGene
84 #
85
86 output_format = blat
87
88 #prb_offset = 50
89 prb_offset = 64
90
91 enable_quality_scores = True
92 enable_splice_scores = True
93 enable_intron_length = True
94
95 C = 100
96
97 remove_duplicate_scores = False
98
99 matchmatrixCols = 1
100 matchmatrixRows = 6
101 numAccSuppPoints = 10
102 numConstraintsPerRound = 50
103 numDonSuppPoints = 10
104 numLengthSuppPoints = 10
105 numQualPlifs = 30
106 numQualSuppPoints = 10
107
108 anzpath = 2
109
110 #enable_intron_length = True
111 #enable_quality_scores = True
112 #enable_splice_signals = True
113 #
114 iter_steps = 40
115 max_intron_len = 2000
116 max_qual = 40
117 max_svm_score = 1.0
118 min_intron_len = 20
119 min_qual = -5
120 min_svm_score = 0.0
121 print_matrix = False