Sequence * translate_swapped(Sequence * swapped)
{
CodonTable * ct;
int i,j;
Sequence * out;
out = Sequence_alloc();
out->name = stringalloc(swapped->name);
out->seq = calloc(1+swapped->len/3,sizeof(char));
ct = read_CodonTable_file("codon.table");
for(i=0,j=0;i<swapped->len;i+=3,j++) {
out->seq[j] = aminoacid_from_seq(ct,swapped->seq+i);
if( isupper(swapped->seq[i]) && isupper(swapped->seq[i+1]) &&
isupper(swapped->seq[i+2]) ) {
out->seq[j] = toupper(out->seq[j]);
} else{
out->seq[j] = tolower(out->seq[j]);
}
}
out->seq[j] = '\0';
return out;
}
int main(int argc,char ** argv)
{
AlignGeneModelParam * agmp;
SeqAlign * sal;
Sequence * seq;
CompProb * cp;
CodonTable * ct;
DnaProbMatrix * dm;
dm = DnaProbMatrix_from_match(0.8,NMaskType_VARIABLE);
ct = read_CodonTable_file("codon.table");
cp = read_Blast_file_CompProb("wag85");
sal = SeqAlign_alloc_std();
seq = new_Sequence_from_strings("new1","ATGGGG");
add_SeqAlign(sal,seq);
seq = new_Sequence_from_strings("new2","ATGGGT");
add_SeqAlign(sal,seq);
agmp = std_AlignGeneModelParam(cp,dm,ct);
printf("Codon 1 %f vs %f Codon 2 %f v %f \n",
coding_probability_AlignGeneModel(sal,2,agmp),
non_coding_probability_AlignGeneModel(sal,2,agmp),
coding_probability_AlignGeneModel(sal,5,agmp),
non_coding_probability_AlignGeneModel(sal,5,agmp)
);
}
int main(int argc,char **argv)
{
int i;
AlignGeneModelParam * agmp;
GeneStats * gs;
GeneModelParam * gmp = NULL;
CompProb * comp_prob;
DnaProbMatrix * dm;
CodonTable * ct;
RandomModel * rm;
Sequence * test;
ct = read_CodonTable_file("codon.table");
rm = default_RandomModel();
comp_prob = read_Blast_file_CompProb("wag85");
gmp = new_GeneModelParam_from_argv(&argc,argv);
dm = DnaProbMatrix_from_match(0.8,NMaskType_VARIABLE);
if((gs=GeneStats_from_GeneModelParam(gmp)) == NULL ) {
fatal("Could not build gene stats");
}
agmp = std_AlignGeneModelParam(comp_prob,dm,ct,gs);
test = read_fasta_file_Sequence(argv[1]);
assert(test);
for(i=0;i<test->len;i++) {
fprintf(stdout,"%c ss5 %.6f ss3 %.6f\n",test->seq[i],prob_SpliceSiteProb(agmp->ss5,test,i),prob_SpliceSiteProb(agmp->ss3,test,i));
}
}
boolean build_objects(void)
{
boolean ret = TRUE;
Protein * pro_temp;
Genomic * gen_temp;
FILE * ifp;
startend = threestatemodel_mode_from_string(startend_string);
if( startend == TSM_unknown ) {
warn("String %s was unable to converted into a start/end policy\n",startend_string);
ret = FALSE;
}
if( tstart_str != NULL ) {
if( is_integer_string(tstart_str,&tstart) == FALSE || tstart < 0) {
warn("Could not make %s out as target start",tstart);
ret = FALSE;
}
}
if( tend_str != NULL ) {
if( is_integer_string(tend_str,&tend) == FALSE || tend < 0) {
warn("Could not make %s out as target end",tend);
ret = FALSE;
}
}
if( is_integer_string(gap_str,&gap) == FALSE ) {
warn("Could not make %s out as gap penalty (must be integer at the moment)",gap_str);
ret = FALSE;
}
if( is_integer_string(ext_str,&ext) == FALSE ) {
warn("Could not make %s out as gap penalty (must be integer at the moment)",ext_str);
ret = FALSE;
}
if( is_embl == FALSE ) {
if( (gen = read_fasta_file_Genomic(dna_seq_file,length_of_N)) == NULL ) {
ret = FALSE;
warn("Could not read genomic sequence in %s",dna_seq_file);
gen = NULL;
}
} else {
embl = read_EMBL_GenomicRegion_file(dna_seq_file);
if( embl == NULL ) {
warn("Could not read genomic EMBL file in %s",dna_seq_file);
gen = NULL;
ret = FALSE;
} else {
gen = hard_link_Genomic(embl->genomic);
}
}
if( gen != NULL ) {
if( tstart != -1 || tend != -1 ) {
if( tstart == -1 )
tstart = 0;
if( tend == -1 )
tend = gen->baseseq->len;
gen_temp = truncate_Genomic(gen,tstart-1,tend);
if( gen_temp == NULL ){
ret = FALSE;
} else {
free_Genomic(gen);
gen = gen_temp;
}
} else {
/* no truncation required */
}
if( reverse == TRUE ) {
if( tstart > tend ) {
warn("You have already reversed the DNA by using %d - %d truncation. Re-reversing",tstart,tend);
}
gen_temp = reverse_complement_Genomic(gen);
free_Genomic(gen);
gen = gen_temp;
}
}
/*
* Can't truncate on GenomicRegion (for good reasons!).
* but we want only a section of the EMBL file to be used
*
* So... swap genomic now. Positions in EMBL are still valid,
* however - some genes will loose their sequence, which will be damaging. ;)
*/
if( is_embl ) {
free_Genomic(embl->genomic);
embl->genomic = hard_link_Genomic(gen); /* pointer could be dead anyway ;) */
}
if( target_abs == TRUE ) {
if( is_embl == TRUE ) {
warn("Sorry you can't both use absolute positioning and EMBL files as I can't cope with all the coordinate remapping. You'll have to convert to fasta.");
ret = FALSE;
}
gen->baseseq->offset = 1;
gen->baseseq->end = strlen(gen->baseseq->seq);
}
if( alg_str != NULL ) {
alg = gwrap_alg_type_from_string(alg_str);
} else {
if( use_tsm == TRUE ) {
alg_str = "623L";
} else {
alg_str = "623";
}
alg = gwrap_alg_type_from_string(alg_str);
}
if( qstart_str != NULL ) {
if( is_integer_string(qstart_str,&qstart) == FALSE || qstart < 0) {
warn("Could not make %s out as query start",qstart);
ret = FALSE;
}
}
if( qend_str != NULL ) {
if( is_integer_string(qend_str,&qend) == FALSE || qend < 0) {
warn("Could not make %s out as query end",qend);
ret = FALSE;
}
}
if( use_tsm == FALSE ) {
if( startend != TSM_default && startend != TSM_global && startend != TSM_local && startend != TSM_endbiased) {
warn("Proteins can only have local/global/endbias startend policies set, not %s",startend_string);
ret = FALSE;
}
if( (pro = read_fasta_file_Protein(protein_file)) == NULL ) {
ret = FALSE;
warn("Could not read Protein sequence in %s",protein_file);
} else {
if( qstart != -1 || qend != -1 ) {
if( qstart == -1 )
qstart = 0;
if( qend == -1 )
qend = pro->baseseq->len;
pro_temp = truncate_Protein(pro,qstart-1,qend);
if( pro_temp == NULL ){
ret = FALSE;
} else {
free_Protein(pro);
pro = pro_temp;
}
}
}
} else {
/** using a HMM **/
/*tsm = read_HMMer_1_7_ascii_file(hmm_file);*/
/*tsm = Wise2_read_ThreeStateModel_from_hmmer1_file(hmm_file);*/
tsm = HMMer2_read_ThreeStateModel(hmm_file);
if( tsm == NULL ) {
warn("Could not read hmm from %s\n",hmm_file);
ret = FALSE;
} else {
display_char_in_ThreeStateModel(tsm);
if( hmm_name != NULL ) {
if( tsm->name != NULL )
ckfree(tsm->name);
tsm->name = stringalloc(hmm_name);
}
if( tsm == NULL ) {
warn("Could not read %s as a hmm",hmm_file);
}
/** have to set start/end **/
set_startend_policy_ThreeStateModel(tsm,startend,30,0.1);
}
} /* end of else tsm != NULL */
if( main_block_str != NULL ) {
if( is_integer_string(main_block_str,&main_block) == FALSE ) {
warn("Could not get maximum main_block number %s",main_block_str);
ret = FALSE;
}
}
if( is_double_string(subs_string,&subs_error) == FALSE ) {
warn("Could not convert %s to a double",subs_error);
ret = FALSE;
}
if( is_double_string(indel_string,&indel_error) == FALSE ) {
warn("Could not convert %s to a double",indel_error);
ret = FALSE;
}
if( is_double_string(allN_string,&allN) == FALSE ) {
warn("Could not convert %s to a double",allN_string);
ret = FALSE;
}
if( strcmp(cfreq_string,"model") == 0 ) {
model_codon = TRUE;
} else if ( strcmp(cfreq_string,"flat") == 0 ) {
model_codon = FALSE;
} else {
warn("Cannot interpret [%s] as a codon modelling parameter\n",cfreq_string);
ret = FALSE;
}
if( strcmp(splice_string,"model") == 0 ) {
model_splice = TRUE;
} else if ( strcmp(splice_string,"flat") == 0 ) {
model_splice = FALSE;
gmp->use_gtag_splice = TRUE;
} else {
warn("Cannot interpret [%s] as a splice modelling parameter\n",splice_string);
ret = FALSE;
}
if( strcmp(null_string,"syn") == 0 ) {
use_syn = TRUE;
} else if ( strcmp(null_string,"flat") == 0 ) {
use_syn = FALSE;
} else {
warn("Cannot interpret [%s] as a null model string\n",null_string);
ret = FALSE;
}
if( strcmp(intron_string,"model") == 0 ) {
use_tied_model = FALSE;
} else if ( strcmp(intron_string,"tied") == 0 ) {
use_tied_model = TRUE;
} else {
warn("Cannot interpret [%s] as a intron tieing switch\n",intron_string);
ret = FALSE;
}
if( (rm = default_RandomModel()) == NULL) {
warn("Could not make default random model\n");
ret = FALSE;
}
if( use_new_stats == 0 ) {
if( (gf = read_GeneFrequency21_file(gene_file)) == NULL) {
ret = FALSE;
warn("Could not read a GeneFrequency file in %s",gene_file);
}
} else {
if( (gs = GeneStats_from_GeneModelParam(gmp)) == NULL ){
ret=FALSE;
warn("Could not read gene statistics in %s",new_gene_file);
}
} /* end of else using new gene stats */
if( (mat = read_Blast_file_CompMat(matrix_file)) == NULL) {
if( use_tsm == TRUE ) {
info("I could not read the Comparison matrix file in %s; however, you are using a HMM so it is not needed. Please set the WISECONFIGDIR or WISEPERSONALDIR variable correctly to prevent this message.",matrix_file);
} else {
warn("Could not read Comparison matrix file in %s",matrix_file);
ret = FALSE;
}
}
if( (ct = read_CodonTable_file(codon_file)) == NULL) {
ret = FALSE;
warn("Could not read codon table file in %s",codon_file);
}
if( (ofp = openfile(output_file,"W")) == NULL) {
warn("Could not open %s as an output file",output_file);
ret = FALSE;
}
rmd = RandomModelDNA_std();
return ret;
}
int main(int argc,char ** argv)
{
Sequence * gen;
Genomic * genomic;
CodonTable * ct = NULL;
GenomeEvidenceSet * ges = NULL;
RandomCodonScore * rcs;
FILE * ifp = NULL;
ComplexSequence * cs = NULL;
ComplexSequenceEvalSet * cses = NULL;
AlnBlock * alb;
PackAln * pal;
GenomicRegion * gr;
int i;
Protein * trans;
cDNA * cdna;
int kbyte = 10000;
int stop_codon_pen = 200;
int start_codon_pen = 30;
int new_gene = 5000;
int switch_cost = 100;
int smell = 8;
DPRunImpl * dpri = NULL;
EstEvidence * est;
boolean show_trans = TRUE;
boolean show_cdna = FALSE;
boolean show_genes = TRUE;
boolean show_alb = FALSE;
boolean show_pal = FALSE;
boolean show_gff = TRUE;
boolean show_debug = FALSE;
boolean show_geneu = TRUE;
char * divide_string = "//";
strip_out_boolean_def_argument(&argc,argv,"geneutr",&show_geneu);
strip_out_boolean_def_argument(&argc,argv,"genes",&show_genes);
strip_out_boolean_def_argument(&argc,argv,"trans",&show_trans);
strip_out_boolean_def_argument(&argc,argv,"gff",&show_gff);
strip_out_boolean_def_argument(&argc,argv,"alb",&show_alb);
strip_out_boolean_def_argument(&argc,argv,"pal",&show_pal);
strip_out_boolean_def_argument(&argc,argv,"debug",&show_debug);
strip_out_boolean_def_argument(&argc,argv,"cdna",&show_cdna);
strip_out_integer_argument(&argc,argv,"stop",&stop_codon_pen);
strip_out_integer_argument(&argc,argv,"start",&start_codon_pen);
strip_out_integer_argument(&argc,argv,"gene",&new_gene);
strip_out_integer_argument(&argc,argv,"switch",&switch_cost);
strip_out_integer_argument(&argc,argv,"smell",&smell);
dpri = new_DPRunImpl_from_argv(&argc,argv);
if( dpri == NULL ) {
fatal("Unable to build DPRun implementation. Bad arguments");
}
strip_out_standard_options(&argc,argv,show_help,show_version);
if( argc != 3 ) {
show_help(stdout);
exit(12);
}
ct = read_CodonTable_file("codon.table");
gen = read_fasta_file_Sequence(argv[1]);
ifp = openfile(argv[2],"r");
ges = read_est_evidence(ifp,ct);
for(i=0;i<ges->len;i++) {
est = (EstEvidence *) ges->geu[i]->data;
est->in_smell = smell;
}
rcs= RandomCodonScore_alloc();
for(i=0;i<125;i++) {
if( is_stop_codon(i,ct) ) {
rcs->codon[i] = -1000000;
} else {
rcs->codon[i] = 0;
}
/* fprintf(stderr,"Got %d for %d\n",rcs->codon[i],i); */
}
cses = default_genomic_ComplexSequenceEvalSet();
cs = new_ComplexSequence(gen,cses);
pal = PackAln_bestmemory_GenomeWise9(ges,cs,-switch_cost,-new_gene,-start_codon_pen,-stop_codon_pen,rcs,NULL,dpri);
alb = convert_PackAln_to_AlnBlock_GenomeWise9(pal);
genomic = Genomic_from_Sequence(gen);
gr = new_GenomicRegion(genomic);
add_Genes_to_GenomicRegion_GeneWise(gr,1,gen->len,alb,gen->name,0,NULL);
if( show_genes ) {
show_pretty_GenomicRegion(gr,0,stdout);
fprintf(stdout,"%s\n",divide_string);
}
if( show_gff ) {
show_GFF_GenomicRegion(gr,gen->name,"genomwise",stdout);
fprintf(stdout,"%s\n",divide_string);
}
if( show_trans ) {
for(i=0;i<gr->len;i++) {
if( gr->gene[i]->ispseudo == TRUE ) {
fprintf(stdout,"#Gene %d is a pseudo gene - no translation possible\n",i);
} else {
trans = get_Protein_from_Translation(gr->gene[i]->transcript[0]->translation[0],ct);
write_fasta_Sequence(trans->baseseq,stdout);
}
}
fprintf(stdout,"%s\n",divide_string);
}
if( show_cdna ) {
for(i=0;i<gr->len;i++) {
cdna = get_cDNA_from_Transcript(gr->gene[i]->transcript[0]);
write_fasta_Sequence(cdna->baseseq,stdout);
}
fprintf(stdout,"%s\n",divide_string);
}
if( show_geneu ) {
show_utr_exon_genomewise(alb,stdout);
fprintf(stdout,"%s\n",divide_string);
}
if( show_alb ) {
mapped_ascii_AlnBlock(alb,id,1,stdout);
fprintf(stdout,"%s\n",divide_string);
}
if( show_debug ) {
debug_genomewise(alb,ges,ct,gen,stdout);
fprintf(stdout,"%s\n",divide_string);
}
if( show_pal ) {
show_simple_PackAln(pal,stdout);
fprintf(stdout,"%s\n",divide_string);
}
return 0;
}
boolean build_objects(void)
{
boolean ret = TRUE;
Protein * pro_temp;
SequenceDB * psdb;
startend = threestatemodel_mode_from_string(startend_string);
if( startend == TSM_unknown ) {
warn("String %s was unable to converted into a start/end policy\n",startend_string);
ret = FALSE;
}
if( use_single_dna == TRUE ) {
cdna = read_fasta_file_cDNA(dna_seq_file);
if( cdna == NULL ) {
warn("Could not open single dna sequence in %s",dna_seq_file);
ret = FALSE;
}
} else {
sdb = single_fasta_SequenceDB(dna_seq_file);
if( sdb == NULL ) {
warn("Could not build a sequence database on %s",dna_seq_file);
ret = FALSE;
}
}
rm = default_RandomModel();
if( (mat = read_Blast_file_CompMat(matrix_file)) == NULL) {
if( use_tsm == TRUE ) {
info("I could not read the Comparison matrix file in %s; however, you are using a HMM so it is not needed. Please set the WISECONFIGDIR or WISEPERSONALDIR variable correctly to prevent this message.",matrix_file);
} else {
warn("Could not read Comparison matrix file in %s",matrix_file);
ret = FALSE;
}
}
if( is_integer_string(gap_str,&gap) == FALSE ) {
warn("Could not get gap string number %s",gap_str);
ret = FALSE;
}
if( is_integer_string(ext_str,&ext) == FALSE ) {
warn("Could not get ext string number %s",ext_str);
ret = FALSE;
}
if( qstart_str != NULL ) {
if( is_integer_string(qstart_str,&qstart) == FALSE || qstart < 0) {
warn("Could not make %s out as query start",qstart);
ret = FALSE;
}
}
if( qend_str != NULL ) {
if( is_integer_string(qend_str,&qend) == FALSE || qend < 0) {
warn("Could not make %s out as query end",qend);
ret = FALSE;
}
}
if( aln_number_str != NULL ) {
if( is_integer_string(aln_number_str,&aln_number) == FALSE || aln_number < 0) {
warn("Weird aln number string %s...\n",aln_number_str);
ret = FALSE;
}
}
if( report_str != NULL ) {
if( is_integer_string(report_str,&report_stagger) == FALSE ) {
warn("Weird report stagger asked for %s",report_str);
ret = FALSE;
}
}
if( use_pfam1 == TRUE ) {
tsmdb = new_PfamHmmer1DB_ThreeStateDB(protein_file);
if( set_search_type_ThreeStateDB(tsmdb,startend_string) == FALSE) {
warn("Unable to set global/local switch on threestatedb");
ret = FALSE;
}
} else if ( use_pfam2 == TRUE ) {
tsmdb = HMMer2_ThreeStateDB(protein_file);
if( set_search_type_ThreeStateDB(tsmdb,startend_string) == FALSE) {
warn("Unable to set global/local switch on threestatedb");
ret = FALSE;
}
} else if ( use_tsm == TRUE) {
/** using a HMM **/
tsm = HMMer2_read_ThreeStateModel(protein_file);
if( tsm == NULL ) {
warn("Could not read hmm from %s\n",protein_file);
ret = FALSE;
} else {
display_char_in_ThreeStateModel(tsm);
if( hmm_name != NULL ) {
if( tsm->name != NULL )
ckfree(tsm->name);
tsm->name = stringalloc(hmm_name);
} else {
if( tsm->name == NULL ) {
tsm->name = stringalloc(protein_file);
}
}
/** have to set start/end **/
set_startend_policy_ThreeStateModel(tsm,startend,15,0.2);
tsmdb = new_single_ThreeStateDB(tsm,rm);
if( tsmdb == NULL ) {
warn("Could not build a threestatemodel database from a single tsm. Weird!");
ret = FALSE;
}
} /* end of else tsm != NULL */
} /* end of else is tsm */
else if( use_single_pro ) {
if( startend != TSM_default && startend != TSM_global && startend != TSM_local ) {
warn("Proteins can only have local/global startend policies set, not %s",startend_string);
ret = FALSE;
}
if( (pro = read_fasta_file_Protein(protein_file)) == NULL ) {
ret = FALSE;
warn("Could not read Protein sequence in %s",protein_file);
} else {
if( qstart != -1 || qend != -1 ) {
if( qstart == -1 )
qstart = 0;
if( qend == -1 )
qend = pro->baseseq->len;
pro_temp = truncate_Protein(pro,qstart-1,qend);
if( pro_temp == NULL ){
ret = FALSE;
} else {
free_Protein(pro);
pro = pro_temp;
}
}
if( startend == TSM_global)
tsm = global_ThreeStateModel_from_half_bit_Sequence(pro,mat,rm,-gap,-ext);
else
tsm = ThreeStateModel_from_half_bit_Sequence(pro,mat,rm,-gap,-ext);
if( tsm == NULL ) {
warn("Could not build ThreeStateModel from a single protein sequence...");
ret = FALSE;
} else {
tsmdb = new_single_ThreeStateDB(tsm,rm);
if( tsmdb == NULL ) {
warn("Could not build a threestatemodel database from a single tsm. Weird!");
ret = FALSE;
}
} /* end of could build a TSM */
} /* else is a real protein */
} /* end of else is single protein */
else if (use_db_pro == TRUE ) {
psdb = single_fasta_SequenceDB(protein_file);
tsmdb = new_proteindb_ThreeStateDB(psdb,mat,-gap,-ext);
free_SequenceDB(psdb);
}
else {
warn("No protein input file! Yikes!");
}
/***
if( use_tsm == FALSE ) {
} else {
****/
if( main_block_str != NULL ) {
if( is_integer_string(main_block_str,&main_block) == FALSE ) {
warn("Could not get maximum main_block number %s",main_block_str);
ret = FALSE;
}
}
if( evalue_search_str != NULL && is_double_string(evalue_search_str,&evalue_search_cutoff) == FALSE ) {
warn("Could not convert %s to a double",evalue_search_str);
ret = FALSE;
}
if( is_double_string(search_cutoff_str,&search_cutoff) == FALSE ) {
warn("Could not convert %s to a double",search_cutoff_str);
ret = FALSE;
}
if( is_double_string(subs_string,&subs_error) == FALSE ) {
warn("Could not convert %s to a double",subs_error);
ret = FALSE;
}
if( is_double_string(indel_string,&indel_error) == FALSE ) {
warn("Could not convert %s to a double",indel_error);
ret = FALSE;
}
if( is_double_string(allN_string,&allN) == FALSE ) {
warn("Could not convert %s to a double",allN_string);
ret = FALSE;
}
if( strcmp(null_string,"syn") == 0 ) {
use_syn = TRUE;
} else if ( strcmp(null_string,"flat") == 0 ) {
use_syn = FALSE;
} else {
warn("Cannot interpret [%s] as a null model string\n",null_string);
ret = FALSE;
}
if( alg_str != NULL ) {
alg = alg_estwrap_from_string(alg_str);
} else {
alg_str = "312";
alg = alg_estwrap_from_string(alg_str);
}
if( aln_alg_str != NULL ) {
aln_alg = alg_estwrap_from_string(aln_alg_str);
} else {
/* if it is a protein, don't loop */
if( use_single_pro == TRUE || use_db_pro == TRUE )
aln_alg_str = "333";
else
aln_alg_str = "333L";
aln_alg = alg_estwrap_from_string(aln_alg_str);
}
if( (rm = default_RandomModel()) == NULL) {
warn("Could not make default random model\n");
ret = FALSE;
}
if( (ct = read_CodonTable_file(codon_file)) == NULL) {
ret = FALSE;
warn("Could not read codon table file in %s",codon_file);
}
if( (ofp = openfile(output_file,"W")) == NULL) {
warn("Could not open %s as an output file",output_file);
ret = FALSE;
}
rmd = RandomModelDNA_std();
cps = flat_cDNAParser(indel_error);
cm = flat_CodonMapper(ct);
sprinkle_errors_over_CodonMapper(cm,subs_error);
return ret;
}
int main(int argc,char ** argv)
{
int i;
DPRunImpl * dpri = NULL;
GeneModelParam * gmp = NULL;
GeneModel * gm = NULL;
Sequence * seq;
RandomCodon * rc;
RandomModelDNA * rmd;
RandomCodonScore * rcs;
ComplexSequenceEval * splice5;
ComplexSequenceEval * splice3;
ComplexSequenceEvalSet * cses;
ComplexSequence * cseq;
SyExonScore * exonscore;
PackAln * pal;
AlnBlock * alb;
Genomic * genomic;
GenomicRegion * gr;
Protein * trans;
dpri = new_DPRunImpl_from_argv(&argc,argv);
if( dpri == NULL ) {
fatal("Unable to build DPRun implementation. Bad arguments");
}
gmp = new_GeneModelParam_from_argv(&argc,argv);
ct= read_CodonTable_file("codon.table");
strip_out_standard_options(&argc,argv,show_help,show_version);
if( argc != 2 ) {
show_help(stdout);
exit(12);
}
if((gm=GeneModel_from_GeneModelParam(gmp)) == NULL ) {
fatal("Could not build gene model");
}
seq = read_fasta_file_Sequence(argv[1]);
assert(seq);
cses = new_ComplexSequenceEvalSet_from_GeneModel(gm);
cseq = new_ComplexSequence(seq,cses);
rc = flat_RandomCodon(ct);
rmd = RandomModelDNA_std();
fold_in_RandomModelDNA_into_RandomCodon(rc,rmd);
rcs = RandomCodonScore_from_RandomCodon(rc);
exonscore = SyExonScore_flat_model(200,250,0.1,0.1);
/*
for(i=0;i<cseq->length;i++) {
fprintf(stdout,"%d PairSeq is %d score %d\n",i,CSEQ_PAIR_PAIRBASE(cseq,i),nonc_score->base[CSEQ_PAIR_PAIRBASE(cseq,i)]);
}
exit(0);
*/
/*
show_RandomCodonScore(rcs,stdout);
for(i=3;i<seq->len;i++) {
fprintf(stdout,"seq %d is %c with score %d\n",i,aminoacid_from_seq(ct,seq->seq+i-2),rcs->codon[CSEQ_GENOMIC_CODON(cseq,i)]);
}
exit(0);
*/
pal = PackAln_bestmemory_StatWise10(exonscore,cseq,rcs,Probability2Score(1.0/10.0),Probability2Score(1.0/10.0),NULL,dpri);
alb = convert_PackAln_to_AlnBlock_StatWise10(pal);
mapped_ascii_AlnBlock(alb,id,1,stdout);
genomic = Genomic_from_Sequence(seq);
gr = new_GenomicRegion(genomic);
add_Genes_to_GenomicRegion_GeneWise(gr,1,seq->len,alb,"bollocks",0,NULL);
for(i=0;i<gr->len;i++) {
if( gr->gene[i]->ispseudo == TRUE ) {
fprintf(stdout,"#Gene %d is a pseudo gene - no translation possible\n",i);
} else {
trans = get_Protein_from_Translation(gr->gene[i]->transcript[0]->translation[0],ct);
write_fasta_Sequence(trans->baseseq,stdout);
}
}
return 0;
}
int main(int argc,char ** argv)
{
int i;
SequenceSet * in;
Sequence * trans;
ThreeStateDB * tsd;
DPRunImpl * dpri;
CodonTable * ct;
int return_status;
ThreeStateModel * tsm;
ThreeStateScore * tss;
Protein * hmmp;
ComplexSequence * cs;
ComplexSequenceEvalSet * cses;
PackAln * pal;
AlnBlock * alb;
int show_align = 0;
int show_alb = 0;
int show_verbose = 1;
int show_trans = 0;
ct = read_CodonTable_file("codon.table");
cses = default_aminoacid_ComplexSequenceEvalSet();
dpri = new_DPRunImpl_from_argv(&argc,argv);
strip_out_boolean_def_argument(&argc,argv,"pretty",&show_align);
strip_out_boolean_def_argument(&argc,argv,"alb",&show_alb);
strip_out_boolean_def_argument(&argc,argv,"trans",&show_trans);
if( argc != 3 ) {
show_help(stdout);
exit(63);
}
in = read_fasta_SequenceSet_file(argv[1]);
tsd = HMMer2_ThreeStateDB(argv[2]);
assert(in);
assert(tsd);
assert(in->len == 2);
trans = translate_Sequence(in->set[0],ct);
if( show_trans ) {
write_fasta_Sequence(trans,stdout);
}
cs = new_ComplexSequence(trans,cses);
open_ThreeStateDB(tsd);
while( (tsm = read_TSM_ThreeStateDB(tsd,&return_status)) != NULL ) {
fold_RandomModel_into_ThreeStateModel(tsm,tsm->rm);
set_startend_policy_ThreeStateModel(tsm,TSM_local,10,1.0);
tss = ThreeStateScore_from_ThreeStateModel(tsm);
hmmp = pseudo_Protein_from_ThreeStateModel(tsm);
pal = PackAln_bestmemory_ThreeStateLoop(tss,cs,NULL,dpri);
alb = convert_PackAln_to_AlnBlock_ThreeStateLoop(pal);
if( show_alb ) {
show_flat_AlnBlock(alb,stdout);
}
if( show_align ) {
write_pretty_seq_align(alb,hmmp->baseseq,trans,15,50,stdout);
}
if( show_verbose ) {
show_verbose_evo(alb,tsm,in->set[0],in->set[1],ct,stdout);
}
}
}
int main(int argc,char ** argv)
{
int i;
DPRunImpl * dpri = NULL;
GeneModelParam * gmp = NULL;
GeneModel * gm = NULL;
FILE * ifp;
SeqAlign * al;
PairBaseSeq * pbs;
ComplexSequenceEval * splice5;
ComplexSequenceEval * splice3;
ComplexSequence * cseq;
CompMat * score_mat;
CompProb * comp_prob;
RandomModel * rm;
PairBaseCodonModelScore * codon_score;
PairBaseModelScore* nonc_score;
PairBaseCodonModelScore * start;
PairBaseCodonModelScore * stop;
SyExonScore * exonscore;
PackAln * pal;
AlnBlock * alb;
Genomic * genomic;
GenomicRegion * gr;
GenomicRegion * gr2;
Protein * trans;
StandardOutputOptions * std_opt;
ShowGenomicRegionOptions * sgro;
char * dump_packaln = NULL;
char * read_packaln = NULL;
FILE * packifp = NULL;
boolean show_trans = 1;
boolean show_gene_raw = 0;
ct = read_CodonTable_file(codon_table);
/*
score_mat = read_Blast_file_CompMat("blosum62.bla");
comp_prob = CompProb_from_halfbit(score_mat);
*/
rm = default_RandomModel();
comp_prob = read_Blast_file_CompProb("wag85");
fold_column_RandomModel_CompProb(comp_prob,rm);
dpri = new_DPRunImpl_from_argv(&argc,argv);
if( dpri == NULL ) {
fatal("Unable to build DPRun implementation. Bad arguments");
}
gmp = new_GeneModelParam_from_argv(&argc,argv);
std_opt = new_StandardOutputOptions_from_argv(&argc,argv);
sgro = new_ShowGenomicRegionOptions_from_argv(&argc,argv);
dump_packaln = strip_out_assigned_argument(&argc,argv,"dump");
read_packaln = strip_out_assigned_argument(&argc,argv,"recover");
strip_out_standard_options(&argc,argv,show_help,show_version);
if( argc != 2 ) {
show_help(stdout);
exit(12);
}
if((gm=GeneModel_from_GeneModelParam(gmp)) == NULL ) {
fatal("Could not build gene model");
}
codon_score = make_PairBaseCodonModelScore(comp_prob);
nonc_score = make_PairBaseModelScore();
splice5 = ComplexSequenceEval_from_pwmDNAScore_splice(gm->splice5score);
splice3 = ComplexSequenceEval_from_pwmDNAScore_splice(gm->splice3score);
if((ifp = openfile(argv[1],"r")) == NULL ) {
fatal("Could not open file %s",argv[1]);
}
al = read_fasta_SeqAlign(ifp);
assert(al);
assert(al->len == 2);
assert(al->seq[0]->len > 0);
assert(al->seq[1]->len > 0);
/* write_fasta_SeqAlign(al,stdout);*/
pbs = new_PairBaseSeq_SeqAlign(al);
if( read_packaln == NULL ) {
cseq = ComplexSequence_from_PairBaseSeq(pbs,splice5,splice3);
}
start = make_start_PairBaseCodonModelScore(ct);
stop = make_stop_PairBaseCodonModelScore(ct);
/* show_PairBaseCodonModelScore(stop,ct,stdout); */
/*
for(i=0;i<pbs->anchor->len;i++) {
printf("%3d %c For %-6d %-6d %c Rev %-6d %-6d\n",i,pbs->anchor->seq[i],
CSEQ_PAIR_5SS(cseq,i),CSEQ_PAIR_3SS(cseq,i),
char_complement_base(pbs->anchor->seq[i]),
CSEQ_REV_PAIR_5SS(cseq,i),CSEQ_REV_PAIR_3SS(cseq,i));
}
*/
/* show_ComplexSequence(cseq,stdout);
*/
exonscore = SyExonScore_flat_model(100,150,0.1,1.0);
/*
for(i=0;i<cseq->length;i++) {
fprintf(stdout,"%d PairSeq is %d score %d\n",i,CSEQ_PAIR_PAIRBASE(cseq,i),nonc_score->base[CSEQ_PAIR_PAIRBASE(cseq,i)]);
}
exit(0);
*/
if( read_packaln != NULL ) {
packifp = openfile(read_packaln,"r");
if( packifp == NULL ) {
fatal("File %s is unopenable - ignoring dump command",dump_packaln);
} else {
pal = read_simple_PackAln(packifp);
}
} else {
pal = PackAln_bestmemory_SyWise20(exonscore,cseq,codon_score,nonc_score,start,stop,Probability2Score(1.0/100.0),Probability2Score(1.0/10000.0),Probability2Score(1.0/10.0),NULL,dpri);
}
alb = convert_PackAln_to_AlnBlock_SyWise20(pal);
if( dump_packaln != NULL ) {
packifp = openfile(dump_packaln,"w");
if( packifp == NULL ) {
warn("File %s is unopenable - ignoring dump command",dump_packaln);
} else {
show_simple_PackAln(pal,packifp);
}
}
show_score_sequence(alb,pbs,nonc_score,stdout);
/*
show_StandardOutputOptions(std_opt,alb,pal,"//",stdout);
*/
genomic = Genomic_from_Sequence(al->seq[0]);
gr = new_GenomicRegion(genomic);
gr2 = new_GenomicRegion(genomic);
add_Genes_to_GenomicRegion_new(gr,alb);
show_GenomicRegionOptions(sgro,gr,ct,"//",stdout);
return 0;
}
int main(int argc,char ** argv)
{
Sequence * cdna;
Sequence * gen;
Sequence * active_gen;
Sequence * active_cdna;
int i;
int dstart = -1;
int dend = -1;
int cstart = -1;
int cend = -1;
CodonTable * ct = NULL;
CodonMatrixScore * cm = NULL;
RandomCodon * rndcodon = NULL;
RandomCodonScore * rndcodonscore = NULL;
DnaMatrix * dm = NULL;
DPRunImpl * dpri = NULL;
GeneModel * gm;
GeneModelParam * gmp;
GeneStats * gs;
GeneParser21 * gp21;
GeneParser21Score * gp21s;
GeneParser4Score * gp;
ComplexSequenceEvalSet * cdna_cses;
ComplexSequenceEvalSet * gen_cses;
ComplexSequence * cs_cdna;
ComplexSequence * cs_gen;
Genomic * gent;
GenomicRegion * gr;
CompMat * cmat;
CompProb * cprob;
char * matfile = "blosum62.bla";
Protein * trans;
PackAln * pal;
AlnBlock * alb;
FILE * ofp = stdout;
dpri = new_DPRunImpl_from_argv(&argc,argv);
gmp = new_GeneModelParam_from_argv(&argc,argv);
strip_out_integer_argument(&argc,argv,"u",&dstart);
strip_out_integer_argument(&argc,argv,"v",&dend);
strip_out_integer_argument(&argc,argv,"s",&cstart);
strip_out_integer_argument(&argc,argv,"t",&cend);
strip_out_standard_options(&argc,argv,show_help,show_version);
ct = read_CodonTable_file(codon_file);
cmat = read_Blast_file_CompMat(matfile);
cprob = CompProb_from_halfbit(cmat);
cm = naive_CodonMatrixScore_from_prob(ct,cprob);
gm = GeneModel_from_GeneModelParam(gmp);
cdna = read_fasta_file_Sequence(argv[1]);
gen = read_fasta_file_Sequence(argv[2]);
if( dstart != -1 || dend != -1 ) {
if( dstart == -1 ) {
dstart = 1;
}
if( dend == -1 ) {
dend = gen->len;
}
active_gen = magic_trunc_Sequence(gen,dstart,dend);
} else {
active_gen = hard_link_Sequence(gen);
}
if( cstart != -1 || cend != -1 ) {
if( cstart == -1 ) {
cstart = 1;
}
if( cend == -1 ) {
cend = gen->len;
}
active_cdna = magic_trunc_Sequence(gen,cstart,cend);
} else {
active_cdna = hard_link_Sequence(gen);
}
rndcodon = RandomCodon_from_raw_CodonFrequency(gm->codon,ct);
fold_in_RandomModelDNA_into_RandomCodon(rndcodon,gm->rnd);
rndcodonscore = RandomCodonScore_from_RandomCodon(rndcodon);
assert(active_cdna);
assert(active_gen);
cdna_cses = default_cDNA_ComplexSequenceEvalSet();
gen_cses = new_ComplexSequenceEvalSet_from_GeneModel(gm);
cs_cdna = new_ComplexSequence(active_cdna,cdna_cses);
cs_gen = new_ComplexSequence(active_gen,gen_cses);
gp21 = std_GeneParser21();
GeneParser21_fold_in_RandomModelDNA(gp21,gm->rnd);
gp21s = GeneParser21Score_from_GeneParser21(gp21);
gp = GeneParser4Score_from_GeneParser21Score(gp21s);
dm = identity_DnaMatrix(Probability2Score(halfbit2Probability(1)),Probability2Score(halfbit2Probability(-1)));
assert(cs_cdna);
assert(cs_gen);
assert(gp);
assert(rndcodonscore);
assert(dm);
assert(dpri);
/* show_CodonMatrixScore(cm,ct,ofp);*/
pal = PackAln_bestmemory_CdnaWise10(cs_cdna,cs_gen,gp,cm,rndcodonscore,dm,
Probability2Score(halfbit2Probability(-12)),
Probability2Score(halfbit2Probability(-2)),
Probability2Score(halfbit2Probability(-5)),
Probability2Score(halfbit2Probability(0)),
NULL,
dpri);
alb = convert_PackAln_to_AlnBlock_CdnaWise10(pal);
gent = Genomic_from_Sequence(gen);
assert(gent);
gr = new_GenomicRegion(gent);
assert(gr);
add_Genes_to_GenomicRegion_GeneWise(gr,active_gen->offset,active_gen->end,alb,cdna->name,0,NULL);
mapped_ascii_AlnBlock(alb,Score2Bits,0,ofp);
show_pretty_GenomicRegion(gr,0,ofp);
for(i=0;i<gr->len;i++) {
if( gr->gene[i]->ispseudo == TRUE ) {
fprintf(ofp,"#Gene %d is a pseudo gene - no translation possible\n",i);
} else {
trans = get_Protein_from_Translation(gr->gene[i]->transcript[0]->translation[0],ct);
write_fasta_Sequence(trans->baseseq,ofp);
}
}
}
