Mercurial > repos > iuc > funannotate_clean
comparison test-data/funannotate_db/trained_species/fly/augustus/fly_metapars.cfg @ 0:b5ec3983deda draft
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
| author | iuc |
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| date | Thu, 26 Aug 2021 06:57:03 +0000 |
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| -1:000000000000 | 0:b5ec3983deda |
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| 1 # This file contains the list of meta parameters for the coding regions (CDS) which are subject to optimization. | |
| 2 # All other meta parameters are chosen as given in the species parameter file. The order | |
| 3 # of the parameters determines the order in the optimization process. | |
| 4 # Basically, different values for these meta parameters are tried out and the ones | |
| 5 # giving best performance in a cross-validation on the training set are chosen. | |
| 6 # For each parameter the range of possible values is specified after the parameter | |
| 7 # name and at least one white space. | |
| 8 # 3 cases are possible for the range: | |
| 9 # - an explicit list is given, e.g. protein "on" "off" | |
| 10 # - it is an integer range, e.g. window_size "1"-"5" | |
| 11 # - it is a range of floating point numbers, e.g. pseudocount "0.3"_"1.8" | |
| 12 # | |
| 13 # | |
| 14 # Mario Stanke, 19.12.2006 | |
| 15 # | |
| 16 | |
| 17 /Constant/dss_end "1"-"4" | |
| 18 /Constant/dss_start "1"-"3" | |
| 19 /Constant/ass_start "1"-"3" | |
| 20 /Constant/ass_end "0"-"4" | |
| 21 /Constant/ass_upwindow_size "1"-"50" | |
| 22 /IntronModel/d "100"-"950" | |
| 23 /IntronModel/ass_motif_memory "0"-"3" | |
| 24 /IntronModel/ass_motif_radius "0"-"4" | |
| 25 /ExonModel/tis_motif_memory "0"-"3" | |
| 26 /ExonModel/tis_motif_radius "0"-"3" | |
| 27 /Constant/trans_init_window "0"-"25" | |
| 28 /Constant/init_coding_len "0"-"18" | |
| 29 /ExonModel/patpseudocount "0.5"_"5" | |
| 30 /ExonModel/etpseudocount "0"-"10" | |
| 31 /ExonModel/etorder "0"-"3" | |
| 32 /Constant/intterm_coding_len "0"-"13" | |
| 33 /ExonModel/slope_of_bandwidth "0.05"_"0.6" | |
| 34 /ExonModel/minwindowcount "1"-"15" | |
| 35 /IGenicModel/patpseudocount "0.5"_"7" | |
| 36 /IntronModel/patpseudocount "0.5"_"7" | |
| 37 /IntronModel/slope_of_bandwidth "0.05"_"0.6" | |
| 38 /IntronModel/minwindowcount "1"-"8" | |
| 39 /IntronModel/asspseudocount "0.0005"_"0.03" | |
| 40 /IntronModel/dsspseudocount "0.0002"_"0.04" | |
| 41 /IntronModel/dssneighborfactor "0.0001"_"0.01" | |
| 42 /ExonModel/minPatSum "100"_"600" | |
| 43 /Constant/probNinCoding "0.15"_".25" | |
| 44 /Constant/decomp_num_steps "1"-"5" | |
| 45 # comment parameters out that you do not want to be subject of optimization | |
| 46 #/IGenicModel/k "4" "3" "5" | |
| 47 #/IntronModel/k "4" "3" "5" | |
| 48 #/ExonModel/k "4" "3" "5" |