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%{
#include "dyna.h"
%}
%{
#include "geneutil.h"
%func
Makes a new GenomicRegion with the genes
predicted from this AlnBlock
Really a wrapper around the add_Genes_to_GenomicRegion_GeneWise
and other functionality
%arg
gen genomic sequence to use
pseudo If true, predicts frameshifted genes as pseudogenes
alb genewise alignment to predict genes from
return a newly allocated structure
%%
GenomicRegion * new_GenomicRegion_from_GeneWise(Genomic * gen,boolean pseudo,AlnBlock * alb)
{
GenomicRegion * out;
out = new_GenomicRegion(gen);
add_Genes_to_GenomicRegion_new(out,alb);
return out;
}
%func
Potential an Alnblock may have more
than one gene due to looping models
This adds all the genes to gr
%arg
gr genomic region to add genes to
org_start start point of the dna to which the alb was made from
org_end end point of the dna to which the alb was made from
alb logical label alignment
pseudo If true, frameshifted genes are predicted as pseudo genes
root the second argument to make_name
make_name fN a pointer to a function to actually make the name of the gene
%%
int add_Genes_to_GenomicRegion_GeneWise(GenomicRegion * gr,int org_start,int org_end,AlnBlock * alb,char * root,boolean pseudo,char * (*make_name)(Wise2_Genomic *,char *,int ,Wise2_Gene * ))
{
int count = 0;
Gene * gene;
AlnColumn * alc;
alc = alb->start;
while( (gene = Gene_from_AlnColumn_GeneWise(alc,org_start,org_end,pseudo,&alc)) != NULL ) {
if( make_name != NULL ) {
gene->name = (*make_name)(gr->genomic,root,gr->len,gene);
}
if( root != NULL ) {
gene->seqname = stringalloc(root);
}
add_Gene_to_GenomicRegion(gr,gene);
count++;
if( alc == NULL )
break;
}
return count;
}
%func
Adds genes using the new gene function
%%
int add_Genes_to_GenomicRegion_new(GenomicRegion * gr,AlnBlock * alb)
{
int count = 0;
Gene * out;
Transcript * tr;
Transcript * new_tr;
Translation * ts;
Exon * exon;
AlnBlock * coll;
AlnColumn * alc;
AlnColumn * exon_start;
AlnColumn * intron_start;
int trace = 1;
int exon_start_coord;
int is_reversed = 0;
int temp;
int i;
coll = collapsed_AlnBlock(alb,1);
/* find start */
for(alc = coll->start;alc != NULL;alc = alc->next ) {
if( strstr(alc->alu[1]->text_label,"CODON") != NULL ) {
if( trace )
fprintf(stderr,"Got %s as first codon\n",alc->alu[1]->text_label);
/* got a gene */
out = Gene_alloc_len(1);
add_Gene_to_GenomicRegion(gr,out);
tr = Transcript_alloc_std();
/* don't add transcript yet, because reversing it requires arsing around with exons */
if( strstr(alc->alu[1]->text_label,"REV") != NULL ) {
is_reversed = 1;
} else {
is_reversed = 0;
}
exon_start_coord = alc->alu[1]->start+1;
out->start = exon_start_coord;
/* first exon is different as there is no 3' splice site */
exon_start = alc;
alc = alc->next;
if( alc == NULL ) {
warn("weird death in gene parsing");
return 1;
}
/* handle single exon genes */
if( strstr(alc->alu[1]->text_label,"SS") == NULL ) {
/* single exon gene */
exon = Exon_alloc_std();
exon->start = 0;
exon->end = alc->alu[1]->start+3 - exon_start->alu[1]->start;
if( trace )
fprintf(stderr,"Single exon gene %s from %d to %d\n",alc->alu[1]->text_label,exon->start,exon->end);
if( is_reversed == 0 ) {
out->start = exon_start->alu[1]->start+1;
out->end = alc->alu[1]->start+4;
} else {
out->end = exon_start->alu[1]->start;
out->start = alc->alu[1]->start+3;
}
add_ex_Transcript(tr,exon);
ts = Translation_alloc();
ts->start = 0;
ts->end = length_Transcript(tr);
ts->parent = tr;
add_Transcript(tr,ts);
tr->parent = out;
add_Gene(out,tr);
continue;
}
/* handle first exon */
exon = Exon_alloc_std();
add_ex_Transcript(tr,exon);
exon->start = exon_start->alu[1]->start+1 - exon_start_coord;
if( strstr(alc->alu[1]->text_label,"PHASE_0") != NULL) {
exon->end = alc->alu[1]->start +1 - out->start;
} else if ( strstr(alc->alu[1]->text_label,"PHASE_1") != NULL) {
exon->end = alc->alu[1]->start +2 - out->start;
} else if ( strstr(alc->alu[1]->text_label,"PHASE_2") != NULL) {
exon->end = alc->alu[1]->start +3 - out->start;
}
/* loop over internal exons. Alc is current on leftmost splice site */
for( ;; ) {
if( trace )
fprintf(stderr,"internal exon - this should be leftmost splice %s\n",alc->alu[1]->text_label);
if( strstr(alc->next->alu[1]->text_label,"SS") != NULL ) {
warn("Have a no-base intron. Conceptually possible, but highly unlikely. Probably misparamterisation somewhere...");
} else {
alc = alc->next;
if( trace )
fprintf(stderr,"internal exon - this should be INTRON %s\n",alc->alu[1]->text_label);
}
if( alc == NULL ) {
warn("Weird death inside Intron of gene parsing");
return 1;
}
alc = alc->next;
if( trace )
fprintf(stderr,"internal exon - this should be rightmost splice %s\n",alc->alu[1]->text_label);
if( alc == NULL ) {
warn("Weird death inside Intron of gene parsing");
return 1;
}
if( strstr(alc->alu[1]->text_label,"SS") == NULL ) {
warn("At end of intron , non splice label %s",alc->alu[1]->text_label);
return 1;
}
exon_start = alc;
alc = alc->next;
if( trace )
fprintf(stderr,"internal exon - this should be CODON %s\n",alc->alu[1]->text_label);
if( alc == NULL ) {
warn("Weird death inside Intron of gene parsing");
return 1;
}
alc = alc->next;
if( alc == NULL ) {
warn("Weird death inside Intron of gene parsing");
return 1;
}
if( trace )
fprintf(stderr,"internal exon - this should be 5SS %s\n",alc->alu[1]->text_label);
/* should have a 3'SS whatever */
exon = Exon_alloc_std();
add_ex_Transcript(tr,exon);
if( strstr(exon_start->alu[1]->text_label,"PHASE_0") != NULL) {
exon->start = exon_start->alu[1]->start +4 - out->start;
} else if ( strstr(exon_start->alu[1]->text_label,"PHASE_1") == NULL) {
exon->start = exon_start->alu[1]->start +4 - out->start;
} else if ( strstr(exon_start->alu[1]->text_label,"PHASE_2") == NULL) {
exon->start = exon_start->alu[1]->start +4 - out->start;
}
if( strstr(alc->alu[1]->text_label,"SS") == NULL ) {
fprintf(stderr,"Breaking with no 5'SS on %s with %d\n",alc->alu[1]->text_label,alc->alu[1]->start);
exon->end = alc->alu[1]->start +1 - out->start;
break;
} else {
if( strstr(alc->alu[1]->text_label,"PHASE_0") != NULL) {
exon->end = alc->alu[1]->start +1 - out->start;
} else if ( strstr(alc->alu[1]->text_label,"PHASE_1") != NULL) {
exon->end = alc->alu[1]->start +2 - out->start;
} else if ( strstr(alc->alu[1]->text_label,"PHASE_2") != NULL) {
exon->end = alc->alu[1]->start +3 - out->start;
}
}
/* alc is left on the 5'SS for the next exon */
} /* end of for (;;) over internal exons*/
/* end of a gene. exon is the last exon */
out->end = exon->end + out->start;
ts = Translation_alloc();
ts->start = 0;
ts->end = length_Transcript(tr);
if( ts->end % 3 != 0 ) {
warn("Transcript is not mod 3 size. It is %d doh!",ts->end);
}
if( is_reversed == 1 ) {
if( trace )
fprintf(stderr,"Reversing gene %d to %d\n",out->start,out->end);
temp = out->end;
temp = temp;
out->end = out->start;
out->start = temp;
/* reversed genes have an off by one convention */
out->end -= 1;
out->start -= 1;
/* now have to reverse transcript. doh! */
new_tr = Transcript_alloc_std();
temp = out->start - out->end;
for(i=tr->ex_len-1;i >= 0;i-- ) {
exon = Exon_alloc_std();
exon->start = temp - tr->exon[i]->end;
exon->end = temp - tr->exon[i]->start;
fprintf(stderr,"Adding exon %d %d which used to be %d %d\n",exon->start,exon->end,tr->exon[i]->start,tr->exon[i]->end);
add_ex_Transcript(new_tr,exon);
}
free_Transcript(tr);
tr = new_tr;
}
add_Gene(out,tr);
ts->parent = tr;
add_Transcript(tr,ts);
tr->parent = out;
} else {
if( trace )
fprintf(stderr,"Skipping %s before codon\n",alc->alu[1]->text_label);
/* do nothing if not a codon - march on */
}
}
/* free_AlnBlock(coll);*/
return 1;
}
%func
helper function for new system
%%
boolean is_exon_AlnColumn_new(AlnColumn * alc)
{
if( strstr(alc->alu[1]->text_label,"CODON") != NULL ) {
return TRUE;
} else {
return FALSE;
}
}
%func
helper function for the new system
%%
boolean is_splice_site_AlnColumn(AlnColumn * alc,int * type,int * phase)
{
if( strstr(alc->alu[1]->text_label,"SS") != NULL ) {
if( strstr(alc->alu[1]->text_label,"5SS") != NULL ) {
*type = 5;
} else {
*type = 3;
}
if( strstr(alc->alu[1]->text_label,"0") != NULL ) {
*phase = 0;
} else if ( strstr(alc->alu[1]->text_label,"1") != NULL ) {
*phase = 1;
} else if ( strstr(alc->alu[1]->text_label,"2") != NULL ) {
*phase = 2;
}
return TRUE;
} else {
return FALSE;
}
}
%func
A new hope for building genes
%%
Gene * Gene_from_AlnColumn_new(AlnColumn * alc,AlnColumn ** end)
{
Gene * out;
Transcript * tr;
Translation * ts;
Exon * ex;
int exon_start;
int exon_end;
int phase_start;
int phase_end;
int is_reversed;
int is_3ss;
int phase;
int type;
int tmp;
AlnColumn * prev;
boolean end_gene = 0;
while(alc != NULL && is_exon_AlnColumn_new(alc) == FALSE )
alc = alc->next;
if( alc == NULL ) {
*end = NULL;
return NULL;
}
if( strstr(alc->alu[1]->text_label,"CODON") == NULL ) {
warn("Bad news... exited from random columns, but not in a codon column, in a %s",alc->alu[1]->text_label);
* end = NULL;
return NULL;
}
/* we should have either a forward or reversed gene */
if( strstr(alc->alu[1]->text_label,"REV") != NULL ) {
is_reversed = 1;
} else {
is_reversed = 0;
}
out = Gene_alloc_len(1);
tr = Transcript_alloc_std();
add_Gene(out,tr);
out->start = alc->alu[1]->start +1;
phase_start = 0;
exon_start = 0; /* by definition, the first exon is at the start*/
is_3ss = 0;
for(;;) {
if( strstr(alc->alu[1]->text_label,"GENE_EXIT") != NULL ) {
break;
}
exon_start = alc->alu[1]->start+1 - out->start;
if( is_3ss ) {
if( phase_start == 0 ) {
exon_start -= 3;
} else if ( phase_start == 1 ) {
exon_start -= 2;
} else if ( phase_start == 2 ) {
exon_start -= 1;
}
}
/* this is at the start of exon */
/* go to the end of the exon */
for(; alc != NULL && is_exon_AlnColumn_new(alc);alc=alc->next) {
fprintf(stdout,"Exonifying past %d %s\n",alc->alu[1]->start,alc->alu[1]->text_label);
prev = alc;
}
/* irregardless of the fate of this exon, we now can put it
* in, as if it was phase0-phase0 */
exon_end = prev->alu[1]->end +1 - out->start;
ex = Exon_alloc_std();
fprintf(stdout,"Adding exon with %d-%d\n",ex->start,ex->end);
add_ex_Transcript(tr,ex);
ex->start = exon_start;
ex->end = exon_end;
if( alc != NULL && is_splice_site_AlnColumn(alc,&type,&phase) ) {
phase_end = phase;
} else {
is_3ss = 0;
phase_end = 0;
end_gene = 1;
}
/* jigging the splice sites for the phases */
if( phase_end == 0 ) {
ex->end = ex->end;
} else if( phase_end == 1 ) {
ex->end = ex->end +1;
} else if( phase_end == 2 ) {
ex->end = ex->end +2;
}
ex->phase = phase_start;
if( end_gene == 1 ) {
break;
}
for(; alc != NULL && !is_exon_AlnColumn_new(alc);alc=alc->next) {
/* fprintf(stdout,"Moving past %d %s\n",alc->alu[1]->start,alc->alu[1]->text_label);*/
if( is_splice_site_AlnColumn(alc,&type,&phase) ) {
is_3ss = 1;
phase_start = phase;
}
if( strstr(alc->alu[1]->text_label,"GENE_EXIT") != NULL ) {
/* fprintf(stdout,"Exiting %d %s\n",alc->alu[1]->start,alc->alu[1]->text_label); */
end_gene = 1;
break;
}
}
if( end_gene == 1 ) {
break;
}
if( alc == NULL ) {
break;
}
}
*end = alc;
out->end = ex->end + out->start;
if( is_reversed == 1 ) {
tmp = out->start;
out->start = out->end;
out->end = tmp;
}
ts = Translation_alloc();
ts->start = 0;
ts->end = length_Transcript(tr);
ts->parent = tr;
add_Transcript(tr,ts);
tr->parent = out;
fprintf(stdout,"returning gene %d %d\n",out->start,out->end);
return out;
}
%func
A wrap for making a gene structure from
an AlnBlock derived from one of the genewise
methods
%arg
alc Alignment column in an AlnBlock produced by genewise
org_start offset that the genewise alignment was to the coordinate system
org_end emd that the genewise alignment was to the coordinate system
end w pointer to a AlnColumn * to say when it has finished with this gene
%%
Gene * Gene_from_AlnColumn_GeneWise(AlnColumn * alc,int org_start,int org_end,boolean predict_pseudo_for_frameshift,AlnColumn ** end)
{
Gene * out;
Transcript * tr;
Translation * ts;
Exon * ex;
AlnColumn * prev;
SupportingFeature * sf;
int score = 0;
int dosf = 0;
int phase = 0;
int frame_break = 0;
while(alc != NULL && is_random_AlnColumn_genewise(alc) == TRUE )
alc = alc->next;
while (alc != NULL && strcmp(alc->alu[1]->text_label,"CODON") != 0 )
alc = alc->next;
if( alc == NULL)
return NULL;
out = Gene_alloc_len(1);
tr = Transcript_alloc_std();
add_Gene(out,tr);
out->start = alc->alu[1]->start +1;
score += alc->alu[0]->score[0];
for(;;) {
/* fprintf(stderr,"Top loop - alc at %s %s\n",alc->alu[1]->text_label,alc->alu[0]->text_label); */
/* fprintf(stderr,"2 Score is %.2f %s %d %.2f\n",Score2Bits(score),alc->alu[1]->text_label,alc->alu[0]->score[0],Score2Bits(alc->alu[0]->score[0]));*/
ex = Exon_alloc_std();
add_ex_Transcript(tr,ex);
/*
* this is always the start of an exon
*/
dosf = 0;
if( strcmp(alc->alu[1]->text_label,"CODON") == 0 ) {
ex->start = alc->alu[1]->start+1 - out->start; /* coordinated in alignment coords */
dosf = 1;
phase = 0;
} else if ( strcmp(alc->alu[1]->text_label,"3SS_PHASE_0") == 0 ) {
ex->start = alc->alu[1]->start +4 - out->start;
dosf = 1;
phase = 0;
} else if ( strcmp(alc->alu[1]->text_label,"3SS_PHASE_1") == 0 ) {
ex->start = alc->alu[1]->start +4 - out->start;
phase = 1;
} else if ( strcmp(alc->alu[1]->text_label,"3SS_PHASE_2") == 0 ) {
ex->start = alc->alu[1]->start +4 - out->start;
phase = 2;
} else {
ex->start = alc->alu[1]->start +1 - out->start; /* coordinated in alignment coords */
phase = -1;
}
ex->phase = phase;
/*
* Exons can start in INSERTs (yuk). In which case we don't
* make a supporting feature
*/
if( dosf == 1 && strstartcmp(alc->alu[0]->text_label,"INSERT") != 0 ) {
sf = SupportingFeature_alloc();
/* we fill in start and end from the exon at the moment. Not pretty */
sf->hstart = alc->alu[0]->start+1;
sf->hstrand = 1; /* currently only got proteins. Thank the lord! */
sf->start = ex->start;
} else {
sf = NULL; /* make sure we don't generate a sf here */
}
for(prev=alc,alc=alc->next;alc != NULL; ) {
/* fprintf(stderr,"Exon loop - alc at %s %s %d\n",alc->alu[1]->text_label,alc->alu[0]->text_label,sf); */
score += alc->alu[0]->score[0];
/* fprintf(stderr,"1 Score is %.2f %s\n",Score2Bits(score),alc->alu[1]->text_label); */
if( is_frameshift_AlnColumn_genewise(alc) == TRUE && predict_pseudo_for_frameshift == TRUE ) {
score += alc->alu[0]->score[0];
fprintf(stderr,"Score is %.2f\n",Score2Bits(score));
out->ispseudo = TRUE;
alc = alc->next;
continue;
}
if( is_random_AlnColumn_genewise(alc) == TRUE)
break;
if( strcmp(alc->alu[1]->text_label,"CODON") != 0 ) {
if( strstartcmp(alc->alu[0]->text_label,"DELETE") == 0 ) {
/* must add sf and start a new one */
/*fprintf(stderr,"Looking at alc at %s %s %d %d %d\n",alc->alu[1]->text_label,alc->alu[0]->text_label,prev,out,sf);*/
if( sf != NULL ) {
sf->end = prev->alu[1]->end+1 - out->start;
sf->hend = prev->alu[0]->end+1;
add_Exon(ex,sf);
sf = NULL;
}
/*
* go the end of this delete run, which are residues in the query with no
* target info
*/
while( alc->next != NULL && strstartcmp(alc->next->alu[0]->text_label,"DELETE") == 0 ) {
alc = alc->next;
}
if( alc->next != NULL && strcmp(alc->next->alu[1]->text_label,"CODON") == 0 ) {
/* the next position is the start of the new alignment */
sf = SupportingFeature_alloc();
sf->hstart = alc->next->alu[0]->start+1;
sf->start = alc->next->alu[1]->start+1 - out->start;
} else {
sf = NULL;
}
} else {
break;
}
} else {
/* it is a codon match, but it could be an insert */
if( strstartcmp(alc->alu[0]->text_label,"INSERT") == 0) {
/* break at this point, add this supporting feature */
if( sf != NULL ) {
sf->end = prev->alu[1]->end+1 - out->start;
sf->hend = prev->alu[0]->end+1;
add_Exon(ex,sf);
sf = NULL;
}
frame_break = 0;
/* go to the end of this insert run, watching for frameshifts */
while( alc->next != NULL && strstartcmp(alc->next->alu[0]->text_label,"INSERT") == 0 ) {
if( is_frameshift_AlnColumn_genewise(alc->next) == TRUE || is_random_AlnColumn_genewise(alc->next) == TRUE) {
if( is_frameshift_AlnColumn_genewise(alc->next) == TRUE && predict_pseudo_for_frameshift == TRUE ) {
out->ispseudo = TRUE;
alc = alc->next;
continue;
} else {
alc = alc->next;
frame_break = 1;
break;
}
}
alc = alc->next;
}
if( frame_break == 1 ) {
break; /* out of this gene */
}
if( alc->next != NULL && strcmp(alc->next->alu[1]->text_label,"CODON") == 0 ) {
/* the next position is the start of the new alignment */
sf = SupportingFeature_alloc();
/* do not understand why not having a +1 here is correct. Hmph */
sf->hstart = alc->next->alu[0]->start+1;
sf->start = alc->next->alu[1]->start+1 - out->start;
} else {
sf = NULL;
}
} else {
/* could be the start of a run from INSERT into match */
if( sf == NULL ) {
sf = SupportingFeature_alloc();
/* we fill in start and end from the exon at the moment. Not pretty */
sf->hstart = alc->alu[0]->start+1;
sf->hstrand = 1; /* currently only got proteins. Thank the lord! */
sf->start = alc->alu[1]->start+1 - out->start;
}
}
} /* end of else it is a codon match */
prev = alc;
alc = alc->next;
}
/*
* The exon has ended. But why?
*/
if( sf != NULL ) {
sf->hend = prev->alu[0]->end+1;
add_Exon(ex,sf);
}
if( alc == NULL ) {
out->end = prev->alu[1]->end +1;
ex->end = out->end - out->start;
if( sf != NULL ) {
sf->end = ex->end;
}
break;
}
if( is_random_AlnColumn_genewise(alc) == TRUE) {
out->end = prev->alu[1]->end +1;
ex->end = out->end - out->start;
if( sf != NULL ) {
sf->end = ex->end;
}
break;
}
/* fprintf(stderr,"Exiting out of exon loop...\n");*/
if( strcmp(alc->alu[1]->text_label,"5SS_PHASE_0") == 0 ) {
out->end = alc->alu[1]->start+1;
phase = 0;
} else if ( strcmp(alc->alu[1]->text_label,"5SS_PHASE_1") == 0 ) {
out->end = alc->alu[1]->start+2;
phase = 1;
} else if ( strcmp(alc->alu[1]->text_label,"5SS_PHASE_2") == 0 ) {
out->end = alc->alu[1]->start+3;
phase = 2;
} else {
phase = 0;
/* fixes from Steve, via an issue with Steve */
if ( strncmp(prev->alu[1]->text_label,"3SS_PHASE_0",11) == 0 ) {
out->end = prev->alu[1]->end + 4;
} else if ( strncmp(prev->alu[1]->text_label,"3SS_PHASE_1",11) == 0 ) {
out->end = prev->alu[1]->end + 4;
} else if ( strncmp(prev->alu[1]->text_label,"3SS_PHASE_1",11) == 0 ) {
out->end = prev->alu[1]->end + 4;
} else {
out->end = prev->alu[1]->end +1;
}
ex->end = out->end - out->start;
if( sf != NULL ) {
sf->end = ex->end;
}
break;
}
/** set end of exon to the correct size from here **/
ex->end = out->end - out->start;
/** sf is to the codon, not to the exon */
if( sf != NULL ) {
if( phase == 0 ) {
sf->end = ex->end;
} else if ( phase == 1 ) {
sf->end = ex->end-1;
} else {
sf->end = ex->end-2;
}
}
while( alc != NULL && strstartcmp(alc->alu[1]->text_label,"3SS") != 0 ) {
/* fprintf(stderr,"Intron loop - alc at %s %s %d\n",alc->alu[1]->text_label,alc->alu[0]->text_label,sf); */
alc = alc->next;
score += alc->alu[0]->score[0];
}
if( alc == NULL ) {
warn("Got to the end of an alignment inside an intron. Oooops!");
break;
}
}/* back to for(;;) */
if( end != NULL )
*end = alc;
if( org_start < org_end) {
out->start += org_start-1;
out->end += org_start-1;
} else {
/* fprintf(stderr,"was %d to %d\n",out->start,out->end); */
out->start = org_start-1 - out->start;
out->end = org_start-1 - out->end;
/* fprintf(stderr,"now %d to %d (%d)\n",out->start,out->end,org_start); */
}
if( out->ispseudo == FALSE ) {
ts = Translation_alloc();
ts->start = 0;
ts->end = length_Transcript(tr);
ts->parent = tr;
add_Transcript(tr,ts);
}
tr->parent = out;
out->bits = Score2Bits(score);
return out;
}
%func
This function is to say what is a frameshift label
%type internal
%%
boolean is_frameshift_AlnColumn_genewise(const AlnColumn * alc)
{
if( strcmp(alc->alu[1]->text_label,"SEQUENCE_INSERTION") == 0 ) {
return TRUE;
}
if( strcmp(alc->alu[1]->text_label,"SEQUENCE_DELETION") == 0 ) {
return TRUE;
}
return FALSE;
}
%func
This function is to say where this should
be skipped in alignment/gene prediction problems
%type internal
%%
boolean is_random_AlnColumn_genewise(const AlnColumn * alc)
{
char * la;
la = alc->alu[1]->text_label;
if( strcmp(la,"RANDOM_SEQUENCE") == 0 )
return TRUE;
if( strcmp(la,"END") == 0 )
return TRUE;
la = alc->alu[0]->text_label;
if( strstr(la,"_RND_") != NULL )
return TRUE;
return FALSE;
}
%func
This function is to say where things are introns
%type internal
%%
boolean is_intron_AlnColumn_genewise(const AlnColumn * alc)
{
char * la;
la = alc->alu[1]->text_label;
if( strcmp(la,"CENTRAL_INTRON") == 0 )
return TRUE;
if( strcmp(la,"PYRIMIDINE_TRACT") == 0 )
return TRUE;
if( strcmp(la,"SPACER") == 0 )
return TRUE;
return FALSE;
}
#define GW_EXON_TYPE_UTR5 45
#define GW_EXON_TYPE_CDS 46
#define GW_EXON_TYPE_UTR3 47
#define GW_EXON_TYPE_NONE 48
int exon_type_AlnColumn_genomewise(AlnColumn * alc)
{
if( strcmp(alc->alu[1]->text_label,"CODON") == 0 ) {
return GW_EXON_TYPE_CDS;
}
if( strcmp(alc->alu[1]->text_label,"UTR5") == 0 ) {
return GW_EXON_TYPE_UTR5;
}
if( strcmp(alc->alu[1]->text_label,"UTR3") == 0 || strcmp(alc->alu[1]->text_label,"STOP_CODON") == 0) {
return GW_EXON_TYPE_UTR3;
}
return GW_EXON_TYPE_NONE;
}
void show_utr_exon_genomewise(AlnBlock * alb,FILE * ofp)
{
AlnColumn * alc;
int exon_start;
int exon_end;
int is_start;
int phase;
int endphase;
int is_3ss;
for(alc=alb->start;alc != NULL;) {
/* find the first exon */
for(;alc != NULL && exon_type_AlnColumn_genomewise(alc) != GW_EXON_TYPE_UTR5;alc = alc->next)
;
if( alc == NULL ) {
break;
}
fprintf(ofp,"Gene\n");
if( alc != NULL && exon_type_AlnColumn_genomewise(alc) == GW_EXON_TYPE_UTR5 ) {
is_start = 1;
while( alc != NULL ) { /* while loop goes over all 5UTRs */
exon_start = alc->alu[1]->start+ (is_start ? 2 : 3);
is_start = 0;
for(;alc != NULL && exon_type_AlnColumn_genomewise(alc) == GW_EXON_TYPE_UTR5;alc = alc->next ) {
;
}
/* fprintf(stderr,"Broken out with %s\n",alc->alu[1]->text_label); */
if( strcmp(alc->alu[1]->text_label,"UTR5_INTRON") ==0 ) {
/* ntron. should be +2-1 at the end of this, goes to 1*/
fprintf(ofp," utr5 %d %d\n",exon_start,alc->alu[1]->start+1);
/* now loop through the intron */
for(;alc != NULL && strcmp(alc->alu[1]->text_label,"UTR5_INTRON") == 0;alc = alc->next ) {
;
}
if( alc == NULL || exon_type_AlnColumn_genomewise(alc) != GW_EXON_TYPE_UTR5 ) {
break; /* while loop */
} else{
continue; /* another utr5 exon */
}
} else {
/* print this guy and break */
fprintf(ofp," utr5 %d %d\n",exon_start,alc->alu[1]->start+1);
break;
}
}
}
/* we now should be at a CDS column */
if( alc != NULL && exon_type_AlnColumn_genomewise(alc) == GW_EXON_TYPE_CDS ) {
is_start = 1;
while( alc != NULL ) { /* while loop goes over all coding Exons */
/* fprintf(stderr,"Entering codoing loop with %s\n",alc->alu[1]->text_label); */
exon_start = alc->alu[1]->start+2;
if( strstr(alc->alu[1]->text_label,"3SS") != NULL ) {
is_3ss = 1;
if( strstr(alc->alu[1]->text_label,"1") != NULL ) {
phase = 1;
} else if ( strstr(alc->alu[1]->text_label,"2") != NULL ) {
phase = 2;
} else {
phase = 0;
}
alc = alc->next;
} else {
is_3ss = 0;
phase = 0;
}
if( phase == 1 ) {
exon_start += 3;
} else if ( phase == 2) {
exon_start += 3;
} else if ( is_3ss ) {
/* phase 0 and spliced needs adjusting */
exon_start += 3;
}
for(;alc != NULL && exon_type_AlnColumn_genomewise(alc) == GW_EXON_TYPE_CDS ;alc = alc->next ) {
;
}
if( strstr(alc->alu[1]->text_label,"5SS") != NULL ) {
exon_end = alc->alu[1]->start+1;
if( strstr(alc->alu[1]->text_label,"1") != NULL ) {
endphase = 1;
} else if ( strstr(alc->alu[1]->text_label,"2") != NULL ) {
endphase = 2;
} else {
endphase = 0;
}
if( endphase == 1 ) {
exon_end += 1;
} else if( endphase == 2 ) {
exon_end += 2;
} /* no change for phase 0 */
/* intron. should be +1-1 at the end of this, goes to 0*/
fprintf(ofp," cds %d %d phase %d\n",exon_start,exon_end,phase);
/* now loop through the intron */
for(alc= alc->next;alc != NULL && strstr(alc->alu[1]->text_label,"3SS") == NULL;alc = alc->next ) {
;
}
if( alc == NULL || strstr(alc->alu[1]->text_label,"3SS") == NULL ) {
break; /* while loop */
} else{
continue; /* another cds exon */
}
} else {
fprintf(ofp," cds %d %d phase %d\n",exon_start,alc->alu[1]->start+1,phase);
break;
}
}
}
if( alc != NULL && exon_type_AlnColumn_genomewise(alc) == GW_EXON_TYPE_UTR3 ) {
is_start = 1;
while( alc != NULL ) { /* while loop goes over all 3UTRs */
exon_start = alc->alu[1]->start+ (is_start ? 2 : 3);
is_start = 0;
for(;alc != NULL && exon_type_AlnColumn_genomewise(alc) == GW_EXON_TYPE_UTR3 ;alc = alc->next ) {
;
}
if( strstr(alc->alu[1]->text_label,"INTRON") != NULL ) {
/* intron. should be +2-1 at the end of this, goes to 1*/
fprintf(ofp," utr3 %d %d\n",exon_start,alc->alu[1]->start+1);
/* now loop through the intron */
for(;alc != NULL && strstr(alc->alu[1]->text_label,"INTRON") != NULL;alc = alc->next ) {
;
}
if( alc == NULL || exon_type_AlnColumn_genomewise(alc) != GW_EXON_TYPE_UTR3 ) {
break; /* while loop */
} else{
continue; /* another utr3 exon */
}
} else {
fprintf(ofp," utr3 %d %d\n",exon_start,alc->alu[1]->start+1);
break;
}
}
}
fprintf(ofp,"End\n");
/* back to next gene */
}
}
%}
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