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annotate test-data/funannotate_db/trained_species/fly/augustus/fly_metapars.cfg @ 0:a5baa4ff168d draft

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"planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
author iuc
date Mon, 04 Oct 2021 19:39:38 +0000
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a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
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1 # This file contains the list of meta parameters for the coding regions (CDS) which are subject to optimization.
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2 # All other meta parameters are chosen as given in the species parameter file. The order
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3 # of the parameters determines the order in the optimization process.
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4 # Basically, different values for these meta parameters are tried out and the ones
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5 # giving best performance in a cross-validation on the training set are chosen.
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6 # For each parameter the range of possible values is specified after the parameter
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7 # name and at least one white space.
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8 # 3 cases are possible for the range:
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9 # - an explicit list is given, e.g. protein "on" "off"
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10 # - it is an integer range, e.g. window_size "1"-"5"
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11 # - it is a range of floating point numbers, e.g. pseudocount "0.3"_"1.8"
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12 #
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13 #
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14 # Mario Stanke, 19.12.2006
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15 #
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16
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17 /Constant/dss_end "1"-"4"
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18 /Constant/dss_start "1"-"3"
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19 /Constant/ass_start "1"-"3"
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20 /Constant/ass_end "0"-"4"
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21 /Constant/ass_upwindow_size "1"-"50"
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22 /IntronModel/d "100"-"950"
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23 /IntronModel/ass_motif_memory "0"-"3"
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24 /IntronModel/ass_motif_radius "0"-"4"
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25 /ExonModel/tis_motif_memory "0"-"3"
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26 /ExonModel/tis_motif_radius "0"-"3"
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27 /Constant/trans_init_window "0"-"25"
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28 /Constant/init_coding_len "0"-"18"
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29 /ExonModel/patpseudocount "0.5"_"5"
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30 /ExonModel/etpseudocount "0"-"10"
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31 /ExonModel/etorder "0"-"3"
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32 /Constant/intterm_coding_len "0"-"13"
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33 /ExonModel/slope_of_bandwidth "0.05"_"0.6"
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34 /ExonModel/minwindowcount "1"-"15"
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35 /IGenicModel/patpseudocount "0.5"_"7"
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36 /IntronModel/patpseudocount "0.5"_"7"
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37 /IntronModel/slope_of_bandwidth "0.05"_"0.6"
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38 /IntronModel/minwindowcount "1"-"8"
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39 /IntronModel/asspseudocount "0.0005"_"0.03"
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40 /IntronModel/dsspseudocount "0.0002"_"0.04"
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41 /IntronModel/dssneighborfactor "0.0001"_"0.01"
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42 /ExonModel/minPatSum "100"_"600"
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43 /Constant/probNinCoding "0.15"_".25"
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44 /Constant/decomp_num_steps "1"-"5"
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45 # comment parameters out that you do not want to be subject of optimization
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46 #/IGenicModel/k "4" "3" "5"
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47 #/IntronModel/k "4" "3" "5"
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48 #/ExonModel/k "4" "3" "5"