diff test-data/funannotate_db/trained_species/fly/augustus/fly_parameters.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_parameters.cfg	Mon Oct 04 19:39:38 2021 +0000
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+#
+# parameters for all Drosophila versions
+# 
+# date : 11.8.2009
+#
+
+#
+# Properties for augustus
+#------------------------------------
+/augustus/verbosity 3     # 0-3, 0: only print the necessary
+maxDNAPieceSize    200000 # maximum segment that is predicted in one piece
+stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction)
+
+# gff output options:
+protein             on    # output predicted protein sequence
+codingseq           off   # output the coding sequence
+cds                 on    # output 'cds' as feature for exons
+start               on    # output start codons (translation start)
+stop                on    # output stop codons  (translation stop)
+introns             on    # output introns
+tss                 on    # output transcription start site
+tts                 on    # output transcription termination site
+print_utr           off   # output 5'UTR and 3'UTR lines in addition to exon lines
+
+checkExAcc          off   # internal parameter for extrinsic accuracy
+
+# alternative transcripts and posterior probabilities
+sample                      100   # the number of sampling iterations
+alternatives-from-sampling  false # output alternative transcripts
+minexonintronprob           0.08  # minimal posterior probability of all (coding) exons
+minmeanexonintronprob       0.4   # minimal geometric mean of the posterior probs of introns and exons
+maxtracks                   -1    # maximum number of reported transcripts per gene (-1: no limit)
+keep_viterbi                true  # set to true if all Viterbi transcripts should be reported
+uniqueCDS                   true  # don't report transcripts that differ only in the UTR
+UTR                         on    # predict untranslated regions
+
+#
+# 
+# The rest of the file contains mainly meta parameters used for training.
+#
+
+# global constants
+# ----------------------------
+
+/Constant/trans_init_window           25
+/Constant/ass_upwindow_size           32
+/Constant/ass_start                   1
+/Constant/ass_end                     4
+/Constant/dss_start                   3
+/Constant/dss_end                     4
+/Constant/init_coding_len	      9
+/Constant/intterm_coding_len	      0
+/Constant/tss_upwindow_size           45
+/Constant/decomp_num_at               1
+/Constant/decomp_num_gc               1
+/Constant/gc_range_min		      0.32   # This range has an effect only when decomp_num_steps>1. 
+/Constant/gc_range_max                0.50   # States the minimal and maximal percentage of c or g
+/Constant/decomp_num_steps            1      # I recommend keeping this to 1 for most species.
+/Constant/min_coding_len              201    # no gene with a coding sequence shorter than this is predicted
+/Constant/probNinCoding               0.23   # divide this by .25 to get a malus for making one masked letter part of the coding sequence
+/Constant/amberprob                   0.34   # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid
+/Constant/ochreprob                   0.41   # Prob(stop codon = taa), if 0 taa is assumed to code for amino acid
+/Constant/opalprob                    0.25   # Prob(stop codon = tga), if 0 tga is assumed to code for amino acid
+/Constant/subopt_transcript_threshold 0.7
+/Constant/almost_identical_maxdiff    10
+
+# type of weighing, one of  1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel
+/BaseCount/weighingType    3
+# file with the weight matrix (only for multiNormalKernel type weighing)
+/BaseCount/weightMatrixFile   fly_weightmatrix.txt # change this to your species if at all necessary
+
+# Properties for IGenicModel
+# ----------------------------
+/IGenicModel/verbosity      0
+/IGenicModel/infile         fly_igenic_probs.pbl   # change this and the other five filenames *_probs.pbl below to your species
+/IGenicModel/outfile        fly_igenic_probs.pbl
+/IGenicModel/patpseudocount 5.0
+/IGenicModel/k              4        # order of the Markov chain for content model, keep equal to /ExonModel/k
+
+# Properties for ExonModel
+# ----------------------------
+/ExonModel/verbosity          3
+/ExonModel/infile             fly_exon_probs.pbl
+/ExonModel/outfile            fly_exon_probs.pbl
+/ExonModel/patpseudocount     5.0
+/ExonModel/minPatSum          350
+/ExonModel/k                  4       # order of the Markov chain for content model
+/ExonModel/etorder	      2
+/ExonModel/etpseudocount      3
+/ExonModel/exonlengthD        3000    # beyond this the distribution is geometric
+/ExonModel/maxexonlength      15000
+/ExonModel/slope_of_bandwidth 0.3
+/ExonModel/minwindowcount     8
+/ExonModel/tis_motif_memory   3
+/ExonModel/tis_motif_radius   2
+ 
+# Properties for IntronModel
+# ----------------------------
+/IntronModel/verbosity          0
+/IntronModel/infile             fly_intron_probs.pbl
+/IntronModel/outfile            fly_intron_probs.pbl
+/IntronModel/patpseudocount     5.0
+/IntronModel/k                  4     # order of the Markov chain for content model, keep equal to /ExonModel/k
+/IntronModel/slope_of_bandwidth 0.4
+/IntronModel/minwindowcount     3
+/IntronModel/asspseudocount     0.01
+/IntronModel/dsspseudocount     0.01015
+/IntronModel/dssneighborfactor  0.001
+#/IntronModel/splicefile         fly_splicefile.txt # this optional file contains additional windows around splice sites for training, uncomment if you have one
+/IntronModel/sf_with_motif	false           # if true the splice file is also used to train the branch point region
+/IntronModel/d                  929  # constraint: this must be larger than 4 + /Constant/dss_end + /Constant/ass_upwindow_size + /Constant/ass_start
+/IntronModel/ass_motif_memory   1
+/IntronModel/ass_motif_radius   4
+
+# Properties for UtrModel
+# ----------------------------
+/UtrModel/verbosity             3
+/UtrModel/infile                fly_utr_probs.pbl
+/UtrModel/outfile               fly_utr_probs.pbl
+/UtrModel/k                     4
+/UtrModel/utr5patternweight     0.3    #0.7625
+/UtrModel/utr3patternweight     0.3   #0.5
+/UtrModel/patpseudocount        1
+/UtrModel/tssup_k               1
+/UtrModel/tssup_patpseudocount  1
+/UtrModel/slope_of_bandwidth    0.25
+/UtrModel/minwindowcount        1
+/UtrModel/exonlengthD           800
+/UtrModel/maxexonlength         1200
+/UtrModel/max3singlelength      2000    # excludes roughly 1%
+/UtrModel/max3termlength        1200    # excludes ~ 0.3%
+/UtrModel/tss_start             8
+/UtrModel/tss_end               5
+/UtrModel/tata_start            2
+/UtrModel/tata_end              10
+/UtrModel/tata_pseudocount      2
+/UtrModel/d_tss_tata_min        26      # minimal distance between start of tata box (if existent) and tss 
+/UtrModel/d_tss_tata_max        37      # maximal distance between start of tata box (if existent) and tss
+/UtrModel/polyasig_consensus    aataaa  # polyadenylation signal training not fully automated yet
+/UtrModel/d_polyasig_cleavage   14      # the transcription end is predicted this many bases after the polyadenylation signal
+/UtrModel/d_polya_cleavage_min  9
+/UtrModel/d_polya_cleavage_max  35
+/UtrModel/prob_polya            0.95
+/UtrModel/tts_motif_memory      1