Mercurial > repos > iuc > funannotate_annotate

annotate test-data/funannotate_db/trained_species/fly/augustus/fly_parameters.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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1 #
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2 # parameters for all Drosophila versions
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3 #
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4 # date : 11.8.2009
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5 #
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7 #
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8 # Properties for augustus
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9 #------------------------------------
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10 /augustus/verbosity 3 # 0-3, 0: only print the necessary
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11 maxDNAPieceSize 200000 # maximum segment that is predicted in one piece
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12 stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction)
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14 # gff output options:
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15 protein on # output predicted protein sequence
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16 codingseq off # output the coding sequence
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17 cds on # output 'cds' as feature for exons
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18 start on # output start codons (translation start)
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19 stop on # output stop codons (translation stop)
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20 introns on # output introns
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21 tss on # output transcription start site
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22 tts on # output transcription termination site
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23 print_utr off # output 5'UTR and 3'UTR lines in addition to exon lines
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25 checkExAcc off # internal parameter for extrinsic accuracy
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27 # alternative transcripts and posterior probabilities
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28 sample 100 # the number of sampling iterations
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29 alternatives-from-sampling false # output alternative transcripts
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30 minexonintronprob 0.08 # minimal posterior probability of all (coding) exons
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31 minmeanexonintronprob 0.4 # minimal geometric mean of the posterior probs of introns and exons
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32 maxtracks -1 # maximum number of reported transcripts per gene (-1: no limit)
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33 keep_viterbi true # set to true if all Viterbi transcripts should be reported
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34 uniqueCDS true # don't report transcripts that differ only in the UTR
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35 UTR on # predict untranslated regions
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36
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37 #
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38 #
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39 # The rest of the file contains mainly meta parameters used for training.
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40 #
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41
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42 # global constants
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43 # ----------------------------
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44
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45 /Constant/trans_init_window 25
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46 /Constant/ass_upwindow_size 32
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47 /Constant/ass_start 1
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48 /Constant/ass_end 4
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49 /Constant/dss_start 3
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50 /Constant/dss_end 4
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51 /Constant/init_coding_len 9
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52 /Constant/intterm_coding_len 0
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53 /Constant/tss_upwindow_size 45
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54 /Constant/decomp_num_at 1
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55 /Constant/decomp_num_gc 1
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56 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1.
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57 /Constant/gc_range_max 0.50 # States the minimal and maximal percentage of c or g
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58 /Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species.
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59 /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted
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60 /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence
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61 /Constant/amberprob 0.34 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid
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62 /Constant/ochreprob 0.41 # Prob(stop codon = taa), if 0 taa is assumed to code for amino acid
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63 /Constant/opalprob 0.25 # Prob(stop codon = tga), if 0 tga is assumed to code for amino acid
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64 /Constant/subopt_transcript_threshold 0.7
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65 /Constant/almost_identical_maxdiff 10
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66
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67 # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel
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68 /BaseCount/weighingType 3
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69 # file with the weight matrix (only for multiNormalKernel type weighing)
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70 /BaseCount/weightMatrixFile fly_weightmatrix.txt # change this to your species if at all necessary
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71
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72 # Properties for IGenicModel
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73 # ----------------------------
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74 /IGenicModel/verbosity 0
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75 /IGenicModel/infile fly_igenic_probs.pbl # change this and the other five filenames *_probs.pbl below to your species
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76 /IGenicModel/outfile fly_igenic_probs.pbl
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77 /IGenicModel/patpseudocount 5.0
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78 /IGenicModel/k 4 # order of the Markov chain for content model, keep equal to /ExonModel/k
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79
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80 # Properties for ExonModel
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81 # ----------------------------
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82 /ExonModel/verbosity 3
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83 /ExonModel/infile fly_exon_probs.pbl
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84 /ExonModel/outfile fly_exon_probs.pbl
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85 /ExonModel/patpseudocount 5.0
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86 /ExonModel/minPatSum 350
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87 /ExonModel/k 4 # order of the Markov chain for content model
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88 /ExonModel/etorder 2
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89 /ExonModel/etpseudocount 3
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90 /ExonModel/exonlengthD 3000 # beyond this the distribution is geometric
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91 /ExonModel/maxexonlength 15000
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92 /ExonModel/slope_of_bandwidth 0.3
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93 /ExonModel/minwindowcount 8
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94 /ExonModel/tis_motif_memory 3
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95 /ExonModel/tis_motif_radius 2
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96
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97 # Properties for IntronModel
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98 # ----------------------------
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99 /IntronModel/verbosity 0
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100 /IntronModel/infile fly_intron_probs.pbl
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101 /IntronModel/outfile fly_intron_probs.pbl
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102 /IntronModel/patpseudocount 5.0
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103 /IntronModel/k 4 # order of the Markov chain for content model, keep equal to /ExonModel/k
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104 /IntronModel/slope_of_bandwidth 0.4
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105 /IntronModel/minwindowcount 3
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106 /IntronModel/asspseudocount 0.01
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107 /IntronModel/dsspseudocount 0.01015
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108 /IntronModel/dssneighborfactor 0.001
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109 #/IntronModel/splicefile fly_splicefile.txt # this optional file contains additional windows around splice sites for training, uncomment if you have one
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110 /IntronModel/sf_with_motif false # if true the splice file is also used to train the branch point region
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111 /IntronModel/d 929 # constraint: this must be larger than 4 + /Constant/dss_end + /Constant/ass_upwindow_size + /Constant/ass_start
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112 /IntronModel/ass_motif_memory 1
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113 /IntronModel/ass_motif_radius 4
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114
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115 # Properties for UtrModel
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116 # ----------------------------
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117 /UtrModel/verbosity 3
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118 /UtrModel/infile fly_utr_probs.pbl
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119 /UtrModel/outfile fly_utr_probs.pbl
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120 /UtrModel/k 4
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121 /UtrModel/utr5patternweight 0.3 #0.7625
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122 /UtrModel/utr3patternweight 0.3 #0.5
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123 /UtrModel/patpseudocount 1
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124 /UtrModel/tssup_k 1
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125 /UtrModel/tssup_patpseudocount 1
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126 /UtrModel/slope_of_bandwidth 0.25
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127 /UtrModel/minwindowcount 1
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128 /UtrModel/exonlengthD 800
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129 /UtrModel/maxexonlength 1200
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130 /UtrModel/max3singlelength 2000 # excludes roughly 1%
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131 /UtrModel/max3termlength 1200 # excludes ~ 0.3%
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132 /UtrModel/tss_start 8
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133 /UtrModel/tss_end 5
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134 /UtrModel/tata_start 2
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135 /UtrModel/tata_end 10
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136 /UtrModel/tata_pseudocount 2
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137 /UtrModel/d_tss_tata_min 26 # minimal distance between start of tata box (if existent) and tss
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138 /UtrModel/d_tss_tata_max 37 # maximal distance between start of tata box (if existent) and tss
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139 /UtrModel/polyasig_consensus aataaa # polyadenylation signal training not fully automated yet
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140 /UtrModel/d_polyasig_cleavage 14 # the transcription end is predicted this many bases after the polyadenylation signal
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141 /UtrModel/d_polya_cleavage_min 9
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142 /UtrModel/d_polya_cleavage_max 35
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143 /UtrModel/prob_polya 0.95
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144 /UtrModel/tts_motif_memory 1