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

"planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/funannotate_db/trained_species/fly/augustus/fly_metapars.utr.cfg	Mon Oct 04 19:39:38 2021 +0000
@@ -0,0 +1,30 @@
+# This file contains the list of meta parameters for the Untranslated Regions (UTRs), which are subject to optimization. 
+# All other parameters are chosen as given in the species parameter file. The order 
+# of the parameters determines the order in the optimization process.
+# Basically, different values for these meta parameters are tried out and the ones
+# giving best performance in a cross-validation on the training set are chosen.
+# For each parameter the range of possible values is specified after the parameter
+# name and at least one white space.
+# 3 cases are possible for the range:
+# - an explicit list is given, e.g. protein	"on" "off"
+# - it is an integer range, e.g. window_size	"1"-"5"
+# - it is a range of floating point numbers, e.g. pseudocount	"0.3"_"1.8"
+#
+# 
+# Mario Stanke, 9.5.2008
+#
+
+/UtrModel/prob_polya            "0.0"_"1.0"
+/UtrModel/d_polya_cleavage_min  "6"-"14"
+/UtrModel/d_polya_cleavage_max  "17"-"27"
+/UtrModel/tss_start             "0"-"12"
+/UtrModel/tss_end               "0"-"8"
+/UtrModel/tts_motif_memory      "0"-"2"
+/UtrModel/utr5patternweight     "0.1"_"1.0"
+/UtrModel/utr3patternweight     "0.1"_"1.0"
+/UtrModel/patpseudocount        "1"_"3"
+/UtrModel/tssup_k               "0"-"2"
+/UtrModel/slope_of_bandwidth    "0.2"_"0.4"
+/UtrModel/minwindowcount        "1"-"4"
+#/UtrModel/k                     "2"-"4"
+