/* @funcstatic seqwords_keysearch ********************************************
**
** Search swissprot with terms structure and writes a hitlist structure
**
** @param [r] inf [AjPFile] File pointer to swissprot database
** @param [r] terms [AjPTerms] Terms object pointer
** @param [w] hits [EmbPHitlist*] Hitlist object pointer
**
** @return [AjBool] True on success
** @@
******************************************************************************/
static AjBool seqwords_keysearch(AjPFile inf,
AjPTerms terms,
EmbPHitlist *hits)
{
AjPStr line =NULL; /* Line of text. */
AjPStr id =NULL; /* Line of text. */
AjPStr temp =NULL;
ajint s =0; /* Temp. start of hit value. */
ajint e =0; /* Temp. end of hit value. */
AjPInt start =NULL; /* Array of start of hit(s). */
AjPInt end =NULL; /* Array of end of hit(s). */
ajint nhits =0; /* Number of hits. */
ajint x =0;
AjBool foundkw =ajFalse;
AjBool foundft =ajFalse;
/* Check for valid args. */
if(!inf)
return ajFalse;
/* Allocate strings and arrays. */
line = ajStrNew();
id = ajStrNew();
start = ajIntNew();
end = ajIntNew();
/* Start of main loop. */
while((ajReadlineTrim(inf,&line)))
{
/* Parse the AC line. */
if(ajStrPrefixC(line,"AC"))
{
/* Copy accesion number and remove the ';' from the end. */
ajFmtScanS(line, "%*s %S", &id);
ajStrExchangeCC(&id, ";", "\0");
/* Reset flags & no. hits. */
foundkw=ajFalse;
foundft=ajFalse;
nhits=0;
}
/* Search the description and keyword lines with search terms. */
else if((ajStrPrefixC(line,"DE") || (ajStrPrefixC(line,"KW"))))
{
/*
** Search terms have a leading and trailing space to prevent
** them being found as substrings within other words. To
** catch cases where a DE or KW line begins with a search
** term, we must add a leading and trailing space to line.
** We must first remove punctation from the line to be parsed.
*/
ajStrExchangeSetCC(&line, ".,;:", " ");
ajStrAppendK(&line, ' ');
ajStrInsertC(&line, 0, " ");
for (x = 0; x < terms->N; x++)
/* Search term is found. */
if((ajStrFindCaseS(line, terms->Keywords[x])!=-1))
{
foundkw=ajTrue;
break;
}
}
/* Search the feature table line with search terms. */
else if((ajStrPrefixC(line,"FT DOMAIN")))
{
/*
** Search terms have a leading and trailing space to prevent
** them being found as substrings within other words. To
** catch cases where a FT line ends with a search
** term, we must add a trailing space to line
** We must first remove punctation from the line to be parsed.
*/
ajStrExchangeSetCC(&line, ".,;:", " ");
ajStrAppendK(&line, ' ');
for (x = 0; x < terms->N; x++)
if((ajStrFindCaseS(line, terms->Keywords[x])!=-1))
{
/* Search term is found. */
foundft = ajTrue;
nhits++;
/* Assign start and end of hit. */
ajFmtScanS(line, "%*s %*s %d %d", &s, &e);
ajIntPut(&start, nhits-1, s);
ajIntPut(&end, nhits-1, e);
break;
}
}
/* Parse the sequence. */
else if((ajStrPrefixC(line,"SQ") && ((foundkw == ajTrue) ||
(foundft == ajTrue))))
{
/* Allocate memory for temp. sequence. */
temp = ajStrNew();
/* Read the sequence into hitlist structure. */
while((ajReadlineTrim(inf,&line)) && !ajStrPrefixC(line,"//"))
/* Read sequence line into temp. */
ajStrAppendC(&temp,ajStrGetPtr(line)+3);
/* Clean up temp. sequence. */
ajStrRemoveWhite(&temp);
/*Priority is given to domain (rather than full length) sequence.*/
if(foundft)
{
for(x=0;x<nhits;x++)
{
/* Increment counter of hits for subsequent hits*/
(*hits)->N++;
/* Reallocate memory for array of hits in hitlist
structure. */
AJCRESIZE((*hits)->hits, (*hits)->N);
(*hits)->hits[(*hits)->N-1]=embHitNew();
ajStrAssignC(&(*hits)->hits[(*hits)->N-1]->Model,
"KEYWORD");
/* Assign start and end of hit. */
(*hits)->hits[(*hits)->N-1]->Start = ajIntGet(start, x);
(*hits)->hits[(*hits)->N-1]->End = ajIntGet(end, x);
/* Extract sequence within specified range */
ajStrAssignSubS(&(*hits)->hits[(*hits)->N - 1]->Seq, temp,
(*hits)->hits[(*hits)->N - 1]->Start - 1,
(*hits)->hits[(*hits)->N - 1]->End - 1);
/* Put id into structure */
ajStrAssignRef(&(*hits)->hits[(*hits)->N - 1]->Acc, id);
}
}
else
{
/* Increment counter of hits */
(*hits)->N++;
/* Reallocate memory for array of hits in hitlist structure */
AJCRESIZE((*hits)->hits, (*hits)->N);
(*hits)->hits[(*hits)->N-1]=embHitNew();
ajStrAssignC(&(*hits)->hits[(*hits)->N-1]->Model, "KEYWORD");
/* Extract whole sequence */
ajStrAssignRef(&(*hits)->hits[(*hits)->N - 1]->Seq, temp);
(*hits)->hits[(*hits)->N - 1]->Start = 1;
(*hits)->hits[(*hits)->N - 1]->End =
ajStrGetLen((*hits)->hits[(*hits)->N - 1]->Seq);
/* Put id into structure */
ajStrAssignRef(&(*hits)->hits[(*hits)->N - 1]->Acc, id);
}
/* Free temp. sequence */
ajStrDel(&temp);
}
}
/* Clean up */
ajStrDel(&line);
ajStrDel(&id);
ajIntDel(&start);
ajIntDel(&end);
return ajTrue;
}
int main(int argc, char **argv)
{
AjPSeqall nucseq; /* input nucleic sequences */
AjPSeqset protseq; /* input aligned protein sequences */
AjPSeqout seqout;
AjPSeq nseq; /* next nucleic sequence to align */
const AjPSeq pseq; /* next protein sequence use in alignment */
AjPTrn trnTable;
AjPSeq pep; /* translation of nseq */
AjPStr tablelist;
ajint table;
AjPSeqset outseqset; /* set of aligned nucleic sequences */
ajint proteinseqcount = 0;
AjPStr degapstr = NULL;
/* used to check if it matches with START removed */
AjPStr degapstr2 = NULL;
AjPStr codon = NULL; /* holds temporary codon to check if is START */
char aa; /* translated putative START codon */
ajint type; /* returned type of the putative START codon */
/* start position of guide protein in translation */
ajlong pos = 0;
AjPSeq newseq = NULL; /* output aligned nucleic sequence */
ajint frame;
embInit("tranalign", argc, argv);
nucseq = ajAcdGetSeqall("asequence");
protseq = ajAcdGetSeqset("bsequence");
tablelist = ajAcdGetListSingle("table");
seqout = ajAcdGetSeqoutset("outseq");
outseqset = ajSeqsetNew();
degapstr = ajStrNew();
/* initialise the translation table */
ajStrToInt(tablelist, &table);
trnTable = ajTrnNewI(table);
ajSeqsetFill(protseq);
while(ajSeqallNext(nucseq, &nseq))
{
if((pseq = ajSeqsetGetseqSeq(protseq, proteinseqcount++)) == NULL)
ajErr("No guide protein sequence available for "
"nucleic sequence %S",
ajSeqGetNameS(nseq));
ajDebug("Aligning %S and %S\n",
ajSeqGetNameS(nseq), ajSeqGetNameS(pseq));
/* get copy of pseq string with no gaps */
ajStrAssignS(°apstr, ajSeqGetSeqS(pseq));
ajStrRemoveGap(°apstr);
/*
** for each translation frame look for subset of pep that
** matches pseq
*/
for(frame = 1; frame <4; frame++)
{
ajDebug("trying frame %d\n", frame);
pep = ajTrnSeqOrig(trnTable, nseq, frame);
degapstr2 = ajStrNew();
ajStrAssignRef(°apstr2, degapstr);
pos = ajStrFindCaseS(ajSeqGetSeqS(pep), degapstr);
/*
** we might have a START codon that should be translated as 'M'
** we need to check if there is a match after a possible START
** codon
*/
if(pos == -1 && ajStrGetLen(degapstr) > 1 &&
(ajStrGetPtr(degapstr)[0] == 'M' ||
ajStrGetPtr(degapstr)[0] == 'm'))
{
/* see if pep minus the first character is a match */
ajStrCutStart(°apstr2, 1);
pos = ajStrFindCaseS(ajSeqGetSeqS(pep), degapstr2);
/*
** pos is >= 1 if we have a match that is after the first
** residue
*/
if(pos >= 1)
{
/* point back at the putative START Methionine */
pos--;
/* test if first codon is a START */
codon = ajStrNew();
ajStrAssignSubS(&codon, ajSeqGetSeqS(nseq),
(pos*3)+frame-1, (pos*3)+frame+2);
type = ajTrnCodonstrTypeS(trnTable, codon, &aa);
if(type != 1)
{
/* first codon is not a valid START, force a mismatch */
pos = -1;
}
ajStrDel(&codon);
}
else
{
/* force 'pos == 0' to be treated as a mismatch */
pos = -1;
}
}
ajStrDel(°apstr2);
ajSeqDel(&pep);
if(pos != -1)
break;
}
if(pos == -1)
ajErr("Guide protein sequence %S not found in nucleic sequence %S",
ajSeqGetNameS(pseq), ajSeqGetNameS(nseq));
else
{
ajDebug("got a match with frame=%d\n", frame);
/* extract the coding region of nseq with gaps */
newseq = ajSeqNew();
ajSeqSetNuc(newseq);
ajSeqAssignNameS(newseq, ajSeqGetNameS(nseq));
ajSeqAssignDescS(newseq, ajSeqGetDescS(nseq));
tranalign_AddGaps(newseq, nseq, pseq, (pos*3)+frame-1);
/* output the gapped nucleic sequence */
ajSeqsetApp(outseqset, newseq);
ajSeqDel(&newseq);
}
ajStrRemoveWhiteExcess(°apstr);
}
ajSeqoutWriteSet(seqout, outseqset);
ajSeqoutClose(seqout);
ajTrnDel(&trnTable);
ajSeqsetDel(&outseqset);
ajStrDel(°apstr);
ajStrDel(°apstr2);
ajSeqallDel(&nucseq);
ajSeqDel(&nseq);
ajSeqoutDel(&seqout);
ajSeqsetDel(&protseq);
ajStrDel(&tablelist);
embExit();
return 0;
}
