1 #include "aligngenemodel.h"
2
3
4
5
main(int argc,char ** argv)6 int main(int argc,char **argv)
7 {
8 int i;
9 AlignGeneModelParam * agmp;
10 GeneStats * gs;
11 GeneModelParam * gmp = NULL;
12 CompProb * comp_prob;
13 DnaProbMatrix * dm;
14 CodonTable * ct;
15 RandomModel * rm;
16
17 Sequence * test;
18
19 ct = read_CodonTable_file("codon.table");
20
21 rm = default_RandomModel();
22
23 comp_prob = read_Blast_file_CompProb("wag85");
24
25 gmp = new_GeneModelParam_from_argv(&argc,argv);
26
27 dm = DnaProbMatrix_from_match(0.8,NMaskType_VARIABLE);
28
29 if((gs=GeneStats_from_GeneModelParam(gmp)) == NULL ) {
30 fatal("Could not build gene stats");
31 }
32
33 agmp = std_AlignGeneModelParam(comp_prob,dm,ct,gs);
34
35 test = read_fasta_file_Sequence(argv[1]);
36
37 assert(test);
38
39 for(i=0;i<test->len;i++) {
40 fprintf(stdout,"%c ss5 %.6f ss3 %.6f\n",test->seq[i],prob_SpliceSiteProb(agmp->ss5,test,i),prob_SpliceSiteProb(agmp->ss3,test,i));
41 }
42
43
44 }
45
46