void biolib_getorf(AjPSeq seq, AjPTrn table, unsigned int minsize) {
ORFrec record;
/* ORF number to append to name of sequence to create unique name */
ajint orf_no;
AjBool sense; /* ajTrue = forward sense */
ajint len;
orf_no = 1; /* number of the next ORF */
sense = ajTrue; /* forward sense initially */
/* get the length of the sequence */
len = ajSeqGetLen(seq);
/* find the ORFs */
getorf_FindORFs(seq, len, trnTable, minsize/3, 10000, seqout, sense,
circular, find, &orf_no, methionine, around, &record);
/* now reverse complement the sequence and do it again */
sense = ajFalse;
ajSeqReverseForce(seq);
// getorf_FindORFs(seq, len, trnTable, minsize, maxsize, seqout, sense,
// circular, find, &orf_no, methionine,
// around);
}
int main(int argc, char **argv)
{
AjPSeqall seqall;
AjPSeqout seqout;
AjPSeq seq = NULL;
AjPStr str = NULL;
AjPStr desc = NULL;
ajint tail3;
ajint tail5 = 0;
ajint minlength;
ajint mismatches;
AjBool reverse;
AjBool fiveprime;
AjBool cvttolower;
embInit("trimest", argc, argv);
seqall = ajAcdGetSeqall("sequence");
seqout = ajAcdGetSeqoutall("outseq");
minlength = ajAcdGetInt("minlength");
mismatches = ajAcdGetInt("mismatches");
reverse = ajAcdGetBoolean("reverse");
fiveprime = ajAcdGetBoolean("fiveprime");
cvttolower = ajAcdGetToggle("tolower");
str = ajStrNew();
while(ajSeqallNext(seqall, &seq))
{
/* get sequence description */
ajStrAssignS(&desc, ajSeqGetDescS(seq));
/* get positions to cut in 5' poly-T and 3' poly-A tails */
if(fiveprime)
tail5 = trimest_get_tail(seq, 5, minlength, mismatches);
tail3 = trimest_get_tail(seq, 3, minlength, mismatches);
/* get a COPY of the sequence string */
ajStrAssignS(&str, ajSeqGetSeqS(seq));
/* cut off longest of 3' or 5' tail */
if(tail5 > tail3)
{
/* if 5' poly-T tail, then reverse the sequence */
ajDebug("Tail=%d\n", tail5);
if(cvttolower)
trimest_tolower(&str, 0, tail5-1);
else
ajStrKeepRange(&str, tail5, ajSeqGetLen(seq)-1);
ajStrAppendC(&desc, " [poly-T tail removed]");
}
else if(tail3 > tail5)
{
/* remove 3' poly-A tail */
ajDebug("Tail=%d\n", tail3);
if(cvttolower)
trimest_tolower(&str, ajSeqGetLen(seq)-tail3,
ajSeqGetLen(seq));
else
ajStrKeepRange(&str, 0, ajSeqGetLen(seq)-tail3-1);
ajStrAppendC(&desc, " [poly-A tail removed]");
}
/* write sequence out */
ajSeqAssignSeqS(seq, str);
/* reverse complement if poly-T found */
if(tail5 > tail3 && reverse)
{
ajSeqReverseForce(seq);
ajStrAppendC(&desc, " [reverse complement]");
}
/* set description */
ajSeqAssignDescS(seq, desc);
ajSeqoutWriteSeq(seqout, seq);
}
ajSeqoutClose(seqout);
ajStrDel(&str);
ajStrDel(&desc);
ajSeqallDel(&seqall);
ajSeqDel(&seq);
ajSeqoutDel(&seqout);
embExit();
return 0;
}
AjPSeqout get_orf(
AjPSeqout seqout,
AjPSeqall seqall,
AjPStr tablestr,
ajuint minsize,
ajuint maxsize,
AjPStr findstr,
AjBool methionine,
AjBool circular,
AjBool reverse,
ajint around
) {
ajint table;
ajint find;
AjPSeq seq = NULL;
AjPTrn trnTable;
AjPStr sseq = NULL; /* sequence string */
/* ORF number to append to name of sequence to create unique name */
ajint orf_no;
AjBool sense; /* ajTrue = forward sense */
ajint len;
/* initialise the translation table */
ajStrToInt(tablestr, &table);
trnTable = ajTrnNewI(table);
/* what sort of ORF are we looking for */
ajStrToInt(findstr, &find);
/*
** get the minimum size converted to protein length if storing
** protein sequences
*/
if (find == P_STOP2STOP || find == P_START2STOP || find == AROUND_START) {
minsize /= 3;
maxsize /= 3;
}
while (ajSeqallNext(seqall, &seq)) {
orf_no = 1; /* number of the next ORF */
sense = ajTrue; /* forward sense initially */
/* get the length of the sequence */
len = ajSeqGetLen(seq);
/*
** if the sequence is circular, append it to itself to triple its
** length so can deal easily with wrapped ORFs, but don't update
** len
*/
if (circular) {
ajStrAssignS(&sseq, ajSeqGetSeqS(seq));
ajStrAppendS(&sseq, ajSeqGetSeqS(seq));
ajStrAppendS(&sseq, ajSeqGetSeqS(seq));
ajSeqAssignSeqS(seq, sseq);
}
/* find the ORFs */
getorf_FindORFs(seq, len, trnTable, minsize, maxsize, seqout, sense,
circular, find, &orf_no, methionine, around, &record);
/* now reverse complement the sequence and do it again */
if (reverse) {
sense = ajFalse;
ajSeqReverseForce(seq);
getorf_FindORFs(seq, len, trnTable, minsize, maxsize, seqout, sense,
circular, find, &orf_no, methionine,
around);
}
}
ajTrnDel(&trnTable);
ajSeqDel(&seq);
ajStrDel(&sseq);
}
