1 2 3%{ 4#include "dyna.h" 5#include "genome_evidence.h" 6 7%} 8 9 10 11 12 13matrix GenomeWise9 14query name="evi" type="GenomeEvidenceSet*" 15target name="gen" type="GENOMIC" 16resource name="switchcost" type="int" 17resource name="newgenecost" type="int" 18resource name="non_start_codon" type="int" 19resource name="non_stop_codon" type="int" 20resource type="RandomCodonScore *" name="rndcodon" 21state UTR5 offi="0" offj="1" 22 source UTR5 23 calc="GNE_UTR(evi,i,gen,j)" 24 endsource 25 source UTR5_INTRON 26 calc="GNE_UTR_3SS(evi,i,gen,j)" 27 endsource 28 source SPECIAL_UTR5 29 calc="GNE_UTR(evi,i,gen,j)" 30 endsource 31 source START 32 calc="GNE_UTR5_START(evi,i,gen,j)" 33 endsource 34 source INTERGENIC 35 calc="GNE_UTR(evi,i,gen,j) + GNE_UTR5_START(evi,i,gen,j)" 36 endsource 37 source PREGENE_INTERGENIC 38 calc="GNE_UTR(evi,i,gen,j)" 39 endsource 40 query_label UTR5 41 target_label UTR5 42endstate 43state UTR5_INTRON offj="1" 44 source UTR5_INTRON 45 calc="GNE_UTR_INTRON(evi,i,gen,j)" 46 endsource 47 source UTR5 48 calc="GNE_UTR_5SS(evi,i,gen,j)" 49 endsource 50 query_label UTR5 51 target_label UTR5_INTRON 52endstate 53state START_CODON offi="0" offj="3" 54 source UTR5_INTRON 55 calc="GNE_START_CODON(evi,i,gen,j)" 56 query_label START_CODON 57 target_label CODON 58 endsource 59 source UTR5 60 calc="GNE_START_CODON(evi,i,gen,j)" 61 query_label START_CODON 62 target_label CODON 63 endsource 64endstate 65state CDS offi="0" offj="3" 66 source CDS 67 calc="GNE_CDS(evi,i,gen,j)" 68 endsource 69 source CDS_INTRON_0 offj="6" 70 calc="GNE_CDS_3SS(evi,i,gen,j-3,0)" 71 target_label 3SS_PHASE_0 72 endsource 73 source CDS_INTRON_1 offj="5" 74 calc="GNE_CDS_3SS(evi,i,gen,j-2,1)" 75 target_label 3SS_PHASE_1 76 endsource 77 source CDS_INTRON_2 offj="4" 78 calc="GNE_CDS_3SS(evi,i,gen,j-1,2)" 79 target_label 3SS_PHASE_2 80 endsource 81 source CDS offj="2" 82 calc="GNE_CDS_FRAMESHIFT(evi,i,gen,j,2)" 83 target_label SEQUENCE_DELETION 84 endsource 85 source CDS offj="4" 86 calc="GNE_CDS_FRAMESHIFT(evi,i,gen,j,4)" 87 target_label SEQUENCE_DELETION 88 endsource 89 source UTR5 90 calc="GNE_CDS(evi,i,gen,j)+non_start_codon" 91 endsource 92 source START_CODON 93 calc="GNE_CDS(evi,i,gen,j)" 94 endsource 95 source SPECIAL_CDS 96 calc="GNE_CDS(evi,i,gen,j)" 97 endsource 98 source INTERGENIC 99 calc="GNE_CDS(evi,i,gen,j) + GNE_UTR5_START(evi,i,gen,j)" 100 endsource 101 query_label CDS 102 target_label CODON 103endstate 104state CDS_INTRON_0 offj="1" 105 source CDS_INTRON_0 offj="1" 106 calc="GNE_CDS_INTRON(evi,i,gen,j)" 107 endsource 108 source CDS offj="8" 109 calc="GNE_CDS_5SS(evi,i,gen,j-7,0)" 110 target_label 5SS_PHASE_0 111 endsource 112 query_label CDS_INTRON 113 target_label CDS_INTRON 114endstate 115state CDS_INTRON_1 offj="1" 116 source CDS_INTRON_1 117 calc="GNE_CDS_INTRON(evi,i,gen,j)" 118 endsource 119 source CDS offj="9" 120 calc="GNE_CDS_5SS(evi,i,gen,j-7,1)" 121 target_label 5SS_PHASE_1 122 endsource 123 query_label CDS_INTRON 124 target_label CDS_INTRON 125endstate 126state CDS_INTRON_2 offj="1" 127 source CDS_INTRON_2 128 calc="GNE_CDS_INTRON(evi,i,gen,j)" 129 endsource 130 source CDS offj="10" 131 calc="GNE_CDS_5SS(evi,i,gen,j-7,2)" 132 target_label 5SS_PHASE_2 133 endsource 134 query_label CDS_INTRON 135 target_label CDS_INTRON 136endstate 137state STOP_CODON offi="0" offj="3" 138 source CDS 139 calc="GNE_STOP_CODON(evi,i,gen,j)" 140 query_label STOP_CODON 141 target_label STOP_CODON 142 endsource 143endstate 144state UTR3 offi="0" offj="1" 145 source UTR3 146 calc="GNE_UTR(evi,i,gen,j)" 147 endsource 148 source CDS 149 calc="GNE_UTR(evi,i,gen,j) + non_stop_codon" 150 endsource 151 source STOP_CODON 152 calc="GNE_UTR(evi,i,gen,j)" 153 endsource 154 source UTR3_INTRON 155 calc="GNE_UTR_3SS(evi,i,gen,j)" 156 endsource 157 source INTERGENIC !left 158 calc="GNE_UTR(evi,i,gen,j)" 159 endsource 160 query_label UTR3 161 target_label UTR3 162endstate 163state UTR3_INTRON offj="1" 164 source UTR3_INTRON 165 calc="GNE_UTR_INTRON(evi,i,gen,j)" 166 endsource 167 source UTR3 168 calc="GNE_UTR_5SS(evi,i,gen,j)" 169 endsource 170 source SPECIAL_UTR3 171 calc="GNE_UTR(evi,i,gen,j)" 172 endsource 173 query_label UTR3 174 target_label UTR3_INTRON 175endstate 176state PREGENE_INTERGENIC !special 177 source START offi="0" offj="1" 178 calc="0" 179 endsource 180 query_label INTERGENIC 181 target_label RANDOM_DNA 182endstate 183state POSTGENE_INTERGENIC !special 184 source UTR3 offj="0" 185 calc="newgenecost + GNE_UTR3_END(evi,i,gen,j)" 186 endsource 187 query_label INTERGENIC 188 target_label RANDOM_DNA 189endstate 190state INTERGENIC !special offj="1" 191 source INTERGENIC offi="0" offj="1" 192 calc="0" 193 endsource 194 source CDS offj="0" 195 calc="newgenecost + GNE_UTR3_END(evi,i,gen,j)" 196 endsource 197 source UTR3 offj="0" 198 calc="newgenecost + GNE_UTR3_END(evi,i,gen,j)" 199 endsource 200 query_label INTERGENIC 201 target_label RANDOM_DNA 202endstate 203state SPECIAL_UTR5 !special 204 source UTR5 205 calc="switchcost" 206 endsource 207 query_label SPECIAL 208 target_label UTR5 209endstate 210state SPECIAL_UTR3 !special 211 source UTR3 212 calc="switchcost" 213 endsource 214 query_label SPECIAL 215 target_label UTR3 216endstate 217state SPECIAL_CDS !special 218 source CDS 219 calc="switchcost + rndcodon->codon[GENOMIC_CODON(gen,j)]" 220 endsource 221 source SPECIAL_CDS offj="3" 222 calc="rndcodon->codon[GENOMIC_CODON(gen,j)]" 223 endsource 224 query_label SPECIAL 225 target_label CODON 226endstate 227state START !start !special 228endstate 229state END !end !special 230 source INTERGENIC offj="1" !right 231 calc="0" 232 endsource 233 target_label END 234 query_label END 235endstate 236collapse UTR5 UTR5 237collapse UTR3 UTR3 238collapse UTR5 UTR5_INTRON 239collapse UTR3 UTR3_INTRON 240collapse INTERGENIC RANDOM_DNA 241collapse CDS_INTRON CDS_INTRON 242endmatrix 243 244 245 246 247 248 249 250