Transcript * copy_Transcript(Transcript * t)
{
Transcript * out;
Exon * temp;
int i;
out = Transcript_alloc();
for(i=0;i<t->ex_len;i++) {
temp = Exon_alloc();
temp->start = t->exon[i]->start;
temp->end = t->exon[i]->end;
add_ex_Transcript(out,temp);
}
for(i=0;i<t->len;i++) {
add_Transcript(out,copy_Translation(t->translation[i]));
}
return out;
}
Gene * read_EMBL_feature_Gene(char * buffer,int maxlen,FILE * ifp)
{
Gene * gene;
Transcript * tr;
Translation * ts;
Exon * exon;
char * runner;
char * base;
char * next;
int i;
int exon_start[MAX_EMBL_EXON_PARSE];
int exon_end[MAX_EMBL_EXON_PARSE];
int number;
int exon_no = 0;
int isstart = 1;
int is_complement = 0;
int is_cds = 0;
int break_at_end = 0;
if( strstartcmp(buffer,"FT") != 0 ) {
warn("passed in a bad line [%s] to be used for feature table parsing",buffer);
return NULL;
}
if( (runner=strtok(buffer+2,spacestr)) == NULL ) {
warn("Bad embl feature line [%s]",buffer);
return NULL;
}
if( strcmp(runner,"CDS") != 0 && strcmp(runner,"mRNA") != 0 ) {
warn("passed in a feature line to read_EMBL_feature_Gene with a %s tag. This only handles CDS and mRNA tags",runner);
return NULL;
}
if( strcmp(runner,"CDS") == 0 ) {
is_cds = TRUE;
}
runner = strtok(NULL,spacestr);
if( runner == NULL ) {
warn("Bad embl feature line [%s]",buffer);
return NULL;
}
if( strstartcmp(runner,"complement") == 0 ) {
runner = strchr(runner,'(');
if( runner == NULL) {
warn("Could not find bracket on EMBL feature complement line");
return NULL;
}
is_complement = 1;
runner++;
}
if( strstartcmp(runner,"join") == 0 ) {
runner = strchr(runner,'(');
runner++;
} else if( isdigit((int)*runner) || *runner == '<' ) {
/** ok - starts with the numbers. We'll cope!**/
} else {
warn("Expecting a join statement, got a [%s]",runner);
return NULL;
}
/*** ok, now the major number loop ***/
for(;;) {
base= runner;
for(;*runner && *runner != ')' && *runner != '.' && *runner != ',' && *runner != '>' && !isspace((int)*runner);runner++)
;
/*fprintf(stderr,"Got a runner of %s\n ",runner); */
if( *runner == '\0' )
next = runner;
else next = runner+1;
if( *runner == ')' ) {
break_at_end = TRUE; /* out of reading exons */
}
*runner='\0';
if( strstartcmp(base,"complement(") == 0 ) {
is_complement = TRUE;
for(;*base != '(';base++)
;
base++;
break_at_end = FALSE; /* we found an bracket too early! */
}
if( is_integer_string(base,&number) == FALSE ) {
warn("Got a non integer [%s] in the middle of a join statement in EMBL parsing",runner);
return NULL;
}
/** put this number away **/
if( isstart ) {
exon_start[exon_no] = number;
isstart = 0;
} else {
exon_end[exon_no++] = number;
isstart = 1;
}
if( break_at_end == TRUE)
break;
for(runner=next;*runner && (*runner == '.' || isspace((int)*runner));runner++)
;
if( *runner == '\0' ) {
if( next_feature_tab_line(buffer,maxlen,ifp) == FALSE) {
warn("In the middle of getting a join statement, got a [%s]. Yuk!",buffer);
return NULL;
}
if( !isdigit((int)buffer[0]) && buffer[0] != '.' && buffer[0] != ',') {
/*** ok - sometimes people very boring end things in here ***/
/* warn("In the middle of getting a join statement, got a [%s]. Ugh!",buffer); */
break;
}
runner = buffer;
}
}
if( isstart == 0 ) {
warn("I have read an uneven number of start-end points in the exon thing. Yuk!");
return NULL;
}
/** runner should now be on bracket **/
if( is_complement == 1 ) {
/** ok . should be another bracket. Do we care? **/
}
gene = Gene_alloc_len(1);
tr = Transcript_alloc_len(exon_no);
add_Gene(gene,tr);
tr->parent = gene;
if( is_complement == 1 ) {
gene->start = exon_end[exon_no-1]-1;
gene->end = exon_start[0] -1;
for(i=exon_no -1;i >= 0;i--) {
exon = Exon_alloc();
exon->start = (gene->start+1) - exon_end[i];
exon->end = (gene->start+1) - exon_start[i] +1;
add_ex_Transcript(tr,exon);
}
} else {
gene->start = exon_start[0] -1;
gene->end = exon_end[exon_no-1] -1;
for(i=0;i<exon_no;i++) {
exon = Exon_alloc();
exon->start = exon_start[i] - (gene->start+1);
exon->end = exon_end[i] - (gene->start+1)+1;
add_ex_Transcript(tr,exon);
}
}
if( is_cds == TRUE ) {
ts = Translation_alloc();
ts->start = 0;
ts->end = length_Transcript(tr);
ts->parent = tr;
add_Transcript(tr,ts);
}
/*** read the rest of this feature ***/
while( next_feature_tab_line(buffer,maxlen,ifp) == TRUE)
;
return gene;
}
