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annotate test-data/funannotate_db/trained_species/fly/augustus/fly_metapars.utr.cfg @ 0:998b719a94cb draft

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"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
author iuc
date Thu, 26 Aug 2021 06:56:18 +0000
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998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
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1 # This file contains the list of meta parameters for the Untranslated Regions (UTRs), which are subject to optimization.
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2 # All other parameters are chosen as given in the species parameter file. The order
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
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3 # of the parameters determines the order in the optimization process.
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
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4 # Basically, different values for these meta parameters are tried out and the ones
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
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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, 9.5.2008
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15 #
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17 /UtrModel/prob_polya "0.0"_"1.0"
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18 /UtrModel/d_polya_cleavage_min "6"-"14"
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19 /UtrModel/d_polya_cleavage_max "17"-"27"
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20 /UtrModel/tss_start "0"-"12"
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21 /UtrModel/tss_end "0"-"8"
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22 /UtrModel/tts_motif_memory "0"-"2"
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23 /UtrModel/utr5patternweight "0.1"_"1.0"
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24 /UtrModel/utr3patternweight "0.1"_"1.0"
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25 /UtrModel/patpseudocount "1"_"3"
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26 /UtrModel/tssup_k "0"-"2"
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27 /UtrModel/slope_of_bandwidth "0.2"_"0.4"
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28 /UtrModel/minwindowcount "1"-"4"
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29 #/UtrModel/k "2"-"4"
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