Mercurial > repos > iuc > funannotate_predict
annotate test-data/funannotate_db/trained_species/fly/augustus/fly_metapars.cfg @ 0:40b87aef5241 draft
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
author | iuc |
---|---|
date | Thu, 26 Aug 2021 06:55:33 +0000 |
parents | |
children |
rev | line source |
---|---|
0
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
1 # This file contains the list of meta parameters for the coding regions (CDS) which are subject to optimization. |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
2 # All other meta parameters are chosen as given in the species parameter file. The order |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
3 # of the parameters determines the order in the optimization process. |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
4 # Basically, different values for these meta parameters are tried out and the ones |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
5 # giving best performance in a cross-validation on the training set are chosen. |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
6 # For each parameter the range of possible values is specified after the parameter |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
7 # name and at least one white space. |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
8 # 3 cases are possible for the range: |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
9 # - an explicit list is given, e.g. protein "on" "off" |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
10 # - it is an integer range, e.g. window_size "1"-"5" |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
11 # - it is a range of floating point numbers, e.g. pseudocount "0.3"_"1.8" |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
12 # |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
13 # |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
14 # Mario Stanke, 19.12.2006 |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
15 # |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
16 |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
17 /Constant/dss_end "1"-"4" |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
18 /Constant/dss_start "1"-"3" |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
19 /Constant/ass_start "1"-"3" |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
20 /Constant/ass_end "0"-"4" |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
21 /Constant/ass_upwindow_size "1"-"50" |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
22 /IntronModel/d "100"-"950" |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
23 /IntronModel/ass_motif_memory "0"-"3" |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
24 /IntronModel/ass_motif_radius "0"-"4" |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
25 /ExonModel/tis_motif_memory "0"-"3" |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
26 /ExonModel/tis_motif_radius "0"-"3" |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
27 /Constant/trans_init_window "0"-"25" |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
28 /Constant/init_coding_len "0"-"18" |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
29 /ExonModel/patpseudocount "0.5"_"5" |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
30 /ExonModel/etpseudocount "0"-"10" |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
31 /ExonModel/etorder "0"-"3" |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
32 /Constant/intterm_coding_len "0"-"13" |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
33 /ExonModel/slope_of_bandwidth "0.05"_"0.6" |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
34 /ExonModel/minwindowcount "1"-"15" |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
35 /IGenicModel/patpseudocount "0.5"_"7" |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
36 /IntronModel/patpseudocount "0.5"_"7" |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
37 /IntronModel/slope_of_bandwidth "0.05"_"0.6" |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
38 /IntronModel/minwindowcount "1"-"8" |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
39 /IntronModel/asspseudocount "0.0005"_"0.03" |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
40 /IntronModel/dsspseudocount "0.0002"_"0.04" |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
41 /IntronModel/dssneighborfactor "0.0001"_"0.01" |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
42 /ExonModel/minPatSum "100"_"600" |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
43 /Constant/probNinCoding "0.15"_".25" |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
44 /Constant/decomp_num_steps "1"-"5" |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
45 # comment parameters out that you do not want to be subject of optimization |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
46 #/IGenicModel/k "4" "3" "5" |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
47 #/IntronModel/k "4" "3" "5" |
40b87aef5241
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
48 #/ExonModel/k "4" "3" "5" |