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
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