boolean fastFind(DNA *needle, int needleSize,
struct patSpace *ps, struct ffAli **retAli, boolean *retRc, int *retScore)
/* Do fast alignment. */
{
struct patClump *clumpList, *clump;
boolean isRc;
struct aliList *aliList = NULL, *ali;
for (isRc = 0; isRc <= 1; ++isRc)
{
if (isRc)
reverseComplement(needle, needleSize);
if ((clumpList = patSpaceFindOne(ps, needle, needleSize)) != NULL)
{
for (clump = clumpList; clump != NULL; clump = clump->next)
{
struct dnaSeq *haySeq = clump->seq;
DNA *haystack = haySeq->dna;
int start = clump->start;
struct ffAli *ffAli = ffFind(needle, needle+needleSize,
haystack+start, haystack+start+clump->size, ffCdna);
if (ffAli != NULL)
{
AllocVar(ali);
ali->ali = ffAli;
ali->score = ffScoreCdna(ffAli);
ali->isRc = isRc;
slAddHead(&aliList, ali);
}
}
slFreeList(&clumpList);
}
if (isRc)
reverseComplement(needle, needleSize);
}
if (aliList != NULL)
{
slSort(&aliList, cmpAliList);
*retAli = aliList->ali;
aliList->ali = NULL;
*retRc = aliList->isRc;
*retScore = aliList->score;
for (ali = aliList->next; ali != NULL; ali = ali->next)
ffFreeAli(&ali->ali);
slFreeList(&aliList);
return TRUE;
}
else
return FALSE;
}
void refineAlis(struct cdnaInfo *ci, struct dnaSeq *cdnaSeq)
/* Turn ci->roughAli into ci->fineAli. Refine alignment. */
{
struct roughAli *ra;
struct fineAli *fa;
struct ffAli *ffAli = NULL;
DNA *unpacked;
int outerStart, outerEnd;
int score;
boolean isRc;
boolean leftCruddyCount;
boolean rightCruddyCount;
DNA *hayStart;
int hayLen;
DNA *hayEnd;
int gStart, gEnd;
boolean badFind;
sortRoughAlis(&ci->roughAli);
flagDupeRoughAlis(ci->roughAli);
for (ra = ci->roughAli; ra != NULL; ra = ra->next)
{
int bestScore = -0x7fffffff;
int oldBestScore = -0x7fffffff;
int oldScore;
struct ffAli *bestAli = NULL;
boolean bestIsRc = FALSE;
if (ra->isDupe)
continue;
/* If score is less than 1/8 of cdna size, don't bother
* with further processing. */
if (ra->score < ci->baseCount/8)
{
continue;
}
gStart = ra->gStart - 16;
gEnd = ra->gEnd + 16;
/* Unpack dna, including extra at either end. */
fetchUnpacked(ra->chromIx, ra->gStart, ra->gEnd, 15250,
&unpacked, &outerStart, &outerEnd);
badFind = FALSE;
for (;;)
{
clipEnds(outerStart, &gStart, &gEnd, outerEnd);
hayStart = unpacked + gStart-outerStart;
hayLen = gEnd - gStart;
hayEnd = hayStart + hayLen;
if (!ffFindEitherStrandN(cdnaSeq->dna, cdnaSeq->size, hayStart, hayLen,
ffCdna, &ffAli, &isRc))
{
if (ra->score > 20 && ra->score > oldBestScore + 5 && ra == ci->roughAli)
{
if (badFind)
{
warn("%s - still couldn't ffFind after expansion",
ci->name);
break;
}
warn("%s Couldn't ffFind %s (%d bases %d score %d bestScore) in chromosome %s %d-%d",
ci->name, ci->name, ci->baseCount, ra->score, oldBestScore, chromNames[ra->chromIx], gStart, gEnd);
addRedoHash(ci, "ffFind");
}
else
break;
badFind = TRUE;
gStart -= 500;
gEnd += 500;
continue;
}
if (isRc)
reverseComplement(cdnaSeq->dna, cdnaSeq->size);
score = scoreExonAli(ffAli);
oldScore = ffScoreCdna(ffAli);
leftCruddyCount = leftFlakySize(ffAli, cdnaSeq->dna, cdnaSeq->size);
rightCruddyCount = rightFlakySize(ffAli, cdnaSeq->dna, cdnaSeq->size) -
polyaSize(cdnaSeq->dna, cdnaSeq->size);
if (isRc)
reverseComplement(cdnaSeq->dna, cdnaSeq->size);
if (score <= bestScore)
{
ffFreeAli(&ffAli);
break;
}
bestScore = score;
oldBestScore = oldScore;
ffFreeAli(&bestAli);
bestAli = ffAli;
bestIsRc = isRc;
if (leftCruddyCount <= 0 && rightCruddyCount <= 0)
break;
if (gStart == outerStart || gEnd == outerEnd)
break;
if (leftCruddyCount < 16)
gStart -= 2*leftCruddyCount;
else
gStart -= 5000;
if (rightCruddyCount > 0)
{
if (rightCruddyCount < 16)
gEnd += 2*rightCruddyCount;
else
gEnd += 5000;
}
}
if (bestAli != NULL)
{
AllocVar(fa);
fa->chromIx = ra->chromIx;
fa->isRc = bestIsRc;
fa->score = bestScore;
fa->blocks = bestAli;
fa->virtNeedle = cdnaSeq->dna;
fa->virtHaystack = unpacked - outerStart;
findAliEnds(fa->blocks, fa->virtNeedle, fa->virtHaystack,
&fa->nStart, &fa->nEnd, &fa->hStart, &fa->hEnd);
findClosestGene(chromNames[fa->chromIx], fa->hStart, fa->hEnd,
(fa->isRc ? '-' : '+'), &fa->geneName, &fa->geneStart, &fa->geneEnd);
fa->isBackwards = correctIsBackwards(ci->isBackwards, fa->isRc, fa->blocks, cdnaSeq->name);
fa->next = ci->fineAli;
ci->fineAli = fa;
}
freez(&unpacked);
}
slReverse(&ci->fineAli);
sortFineAlis(&ci->fineAli);
flagDupeFineAlis(ci->fineAli);
if (weAreWeb())
hyperReportAlis(ci);
else
printf("%d %s\n", ci->ix, ci->name);
slFreeList(&ci->roughAli);
}
void glueFindOne(struct patSpace *ps, DNA *cdna, int cdnaSize,
char strand, char dir, char *cdnaName, struct cdnaAliList **pList)
/* Find occurrences of DNA in patSpace and print to hitOut. */
{
struct patClump *clumpList, *clump;
clumpList = patSpaceFindOne(ps, cdna, cdnaSize);
for (clump = clumpList; clump != NULL; clump = clump->next)
{
struct ffAli *ff;
struct dnaSeq *seq = clump->seq;
DNA *tStart = seq->dna + clump->start;
char *contigName = seq->name;
int seqIx = clump->seqIx;
int bacIx = clump->bacIx;
++ffSubmitted;
ff = ffFind(cdna, cdna+cdnaSize, tStart, tStart + clump->size, ffCdna);
if (ff != NULL)
{
int ffScore = ffScoreCdna(ff);
++ffAccepted;
if (ffScore >= 22)
{
int hiStart, hiEnd;
int oldStart, oldEnd;
struct ffAli *left, *right;
ffFindEnds(ff, &left, &right);
hiStart = oldStart = left->nStart - cdna;
hiEnd = oldEnd = right->nEnd - cdna;
++ffOkScore;
if (solidMatch(&left, &right, cdna, &hiStart, &hiEnd))
{
int solidSize = hiEnd - hiStart;
int solidScore;
int seqStart, seqEnd;
double cookedScore;
solidScore = scoreCdna(left, right);
cookedScore = (double)solidScore/solidSize;
if (cookedScore > 0.25)
{
struct cdnaAliList *cal;
++ffSolidMatch;
seqStart = left->hStart - seq->dna;
seqEnd = right->hEnd - seq->dna;
fprintf(hitOut, "%3.1f%% %c %s:%d-%d (old %d-%d) of %d at %s.%d:%d-%d\n",
100.0 * cookedScore, strand, cdnaName,
hiStart, hiEnd, oldStart, oldEnd, cdnaSize,
contigName, seqIx, seqStart, seqEnd);
cal = newCal(bacIx, seqIx, hiStart, hiEnd, cdnaSize, strand, dir, cookedScore);
slAddHead(pList, cal);
}
}
}
ffFreeAli(&ff);
}
}
slFreeList(&clumpList);
}
void writeClump(struct blockPos *first, struct blockPos *last,
char *cdnaName, char strand, char dir, DNA *cdna, int cdnaSize, struct cdnaAliList **pList)
/* Write hitOut one clump. */
{
struct dnaSeq *seq = first->seq;
char *bacName = seq->name;
int seqIx = first->seqIx;
int start = first->offset;
int end = last->offset+last->size;
struct ffAli *ff, *left, *right;
int extraAtEnds = minMatch*patSize;
struct cdnaAliList *cal;
start -= extraAtEnds;
if (start < 0)
start = 0;
end += extraAtEnds;
if (end >seq->size)
end = seq->size;
++ffSubmitted;
if (dumpMe)
fprintf(dumpOut, "%s %d %s %d-%d\n", cdnaName, cdnaSize, bacName, start, end);
ff = ffFind(cdna, cdna+cdnaSize, seq->dna+start, seq->dna+end, ffCdna);
if (dumpMe)
{
fprintf(dumpOut, "ffFind = %x\n", ff);
}
if (ff != NULL)
{
int ffScore = ffScoreCdna(ff);
++ffAccepted;
if (dumpMe) fprintf(dumpOut, "ffScore = %d\n", ffScore);
if (ffScore >= 22)
{
int hiStart, hiEnd;
int oldStart, oldEnd;
ffFindEnds(ff, &left, &right);
hiStart = oldStart = left->nStart - cdna;
hiEnd = oldEnd = right->nEnd - cdna;
++ffOkScore;
if (solidMatch(&left, &right, cdna, &hiStart, &hiEnd))
{
int solidSize = hiEnd - hiStart;
int solidScore;
int seqStart, seqEnd;
double cookedScore;
solidScore = scoreCdna(left, right);
cookedScore = (double)solidScore/solidSize;
if (cookedScore > 0.25)
{
++ffSolidMatch;
seqStart = left->hStart - seq->dna;
seqEnd = right->hEnd - seq->dna;
fprintf(hitOut, "%3.1f%% %c %s:%d-%d (old %d-%d) of %d at %s.%d:%d-%d\n",
100.0 * cookedScore, strand, cdnaName,
hiStart, hiEnd, oldStart, oldEnd, cdnaSize,
bacName, seqIx, seqStart, seqEnd);
if (dumpMe)
{
fprintf(bigHtmlFile, "<A NAME=i%d>", htmlIx);
fprintf(bigHtmlFile, "<H2>%4.1f%% %4d %4d %c %s:%d-%d of %d at %s.%d:%d-%d</H2><BR>",
100.0 * cookedScore, solidScore, ffScore, strand, cdnaName,
hiStart, hiEnd, cdnaSize,
bacName, seqIx, seqStart, seqEnd);
fprintf(bigHtmlFile, "</A>");
ffShAli(bigHtmlFile, ff, cdnaName, cdna, cdnaSize, 0,
bacName, seq->dna+start, end-start, start, FALSE);
fprintf(bigHtmlFile, "<BR><BR>\n");
fprintf(littleHtmlFile, "<A HREF=\"patAli.html#i%d\">", htmlIx);
fprintf(littleHtmlFile, "%4.1f%% %4d %4d %c %s:%d-%d of %d at %s.%d:%d-%d\n",
100.0 * cookedScore, solidScore, ffScore, strand, cdnaName,
hiStart, hiEnd, cdnaSize,
bacName, seqIx, seqStart, seqEnd);
fprintf(littleHtmlFile, "</A><BR>");
++htmlIx;
}
cal = newCal(first->bacIx, seqIx, hiStart, hiEnd, cdnaSize, strand, dir, cookedScore);
slAddHead(pList, cal);
}
}
}
ffFreeAli(&ff);
}
}
int main(int argc, char *argv[])
{
char *estName, *targetName, *oocName;
FILE *estFile;
struct dnaSeq *target;
struct dnaSeq *est;
struct patSpace *ps;
struct patClump *clumpList, *clump;
int estIx = 0;
/* Check command line arguments and assign to local variables. */
if (argc != 4)
usage();
estName = argv[1];
estFile = mustOpen(estName, "rb");
targetName = argv[2];
oocName = argv[3];
/* Read in target DNA from fasta files and check not too big. */
fprintf(stderr, "Reading %s\n", targetName);
target = faReadAllDna(targetName);
if (totalSequenceSize(target) > 8000000)
{
errAbort("Can only handle 8000000 bases of genomic sequence at once, %s has %d.",
targetName, totalSequenceSize(target));
}
/* Make a pattern space index structure. */
fprintf(stderr, "Making Pattern Space index\n");
ps = makePatSpace(&target, 1, oocName, 4, 32000);
/* Loop through each EST in query list. */
printf("Searching for hits\n\n");
while (faReadNext(estFile, NULL, TRUE, NULL, &est))
{
boolean isRc; /* Reverse complemented? */
if (++estIx % 5000 == 0)
fprintf(stderr, "Processing EST %d\n", estIx);
if (est->size > 20000)
{
warn("Very large EST sequence %s.\n"
"Maybe you mixed up the EST and genomic parameters?", est->name);
usage();
}
for (isRc = 0; isRc <= 1; ++isRc) /* Search both strands. */
{
if (isRc)
reverseComplement(est->dna, est->size);
clumpList = patSpaceFindOne(ps, est->dna, est->size);
/* For each homology clump patSpace finds, do a fuzzyFinder
* alignment of it and print the results. */
for (clump = clumpList; clump != NULL; clump = clump->next)
{
struct ffAli *ali, *a;
boolean isRc;
int score;
struct dnaSeq *t = clump->seq;
DNA *tStart = t->dna + clump->start;
ali = ffFind(est->dna, est->dna+est->size, tStart, tStart + clump->size, ffCdna);
if (ali != NULL)
{
score = ffScoreCdna(ali);
printf("%s hits %s strand %c score %d\n",
est->name, t->name, (isRc ? '+' : '-'), score);
for (a = ali; a != NULL; a = a->right)
{
printf(" Q %4d - %4d\t T %4d -%4d\n",
a->nStart - est->dna, a->nEnd - est->dna,
a->hStart - t->dna, a->hEnd - t->dna);
}
printf("\n");
ffFreeAli(&ali);
}
else
{
printf("Couldn't align clump at %s %d-%d\n",
t->name, clump->start, clump->start + clump->size);
}
}
slFreeList(&clumpList);
}
freeDnaSeq(&est);
}
/* Clean up time. */
freePatSpace(&ps);
freeSeqList(&target);
return 0;
}
