void relPairs(char *allPairName, char *inPslName, char *outPairName, char *dirs[], int dirCount)
/* extract relevant pairs that could apply to a .psl file in each dir. */
{
struct hash *pairHash;
struct pair *pairList;
char inPslPath[512];
char outPairPath[512];
char *dir;
int i;
makePairHash(allPairName, &pairHash, &pairList);
for (i=0; i<dirCount; ++i)
{
dir = dirs[i];
sprintf(inPslPath, "%s/%s", dir, inPslName);
sprintf(outPairPath, "%s/%s", dir, outPairName);
if (fileExists(inPslPath))
extractUsedPairs(pairHash, inPslPath, outPairPath);
}
freeHash(&pairHash);
slFreeList(&pairList);
}
int main(int argc, char *argv[])
{
char *genoListName;
char *cdnaListName;
char *oocFileName;
char *pairFileName;
struct patSpace *patSpace;
long startTime, endTime;
char **genoList;
int genoListSize;
char *genoListBuf;
char **cdnaList;
int cdnaListSize;
char *cdnaListBuf;
char *genoName;
int i;
int estIx = 0;
struct dnaSeq **seqListList = NULL, *seq;
static char hitFileName[512], mergerFileName[512], okFileName[512];
char *outRoot;
struct hash *pairHash;
if (dumpMe)
{
bigHtmlFile = mustOpen("C:\\inetpub\\wwwroot\\test\\patAli.html", "w");
littleHtmlFile = mustOpen("C:\\inetpub\\wwwroot\\test\\patSpace.html", "w");
htmStart(bigHtmlFile, "PatSpace Alignments");
htmStart(littleHtmlFile, "PatSpace Index");
}
if ((hostName = getenv("HOST")) == NULL)
hostName = "";
if (argc != 6)
usage();
pushWarnHandler(patSpaceWarnHandler);
startTime = clock1000();
dnaUtilOpen();
makePolys();
genoListName = argv[1];
cdnaListName = argv[2];
oocFileName = argv[3];
pairFileName = argv[4];
outRoot = argv[5];
sprintf(hitFileName, "%s.hit", outRoot);
sprintf(mergerFileName, "%s.glu", outRoot);
sprintf(okFileName, "%s.ok", outRoot);
readAllWords(genoListName, &genoList, &genoListSize, &genoListBuf);
readAllWords(cdnaListName, &cdnaList, &cdnaListSize, &cdnaListBuf);
pairHash = makePairHash(pairFileName);
hitOut = mustOpen(hitFileName, "w");
mergerOut = mustOpen(mergerFileName, "w");
dumpOut = mustOpen("dump.out", "w");
seqListList = needMem(genoListSize*sizeof(seqListList[0]) );
fprintf(hitOut, "Pattern space 0.2 cDNA matcher\n");
fprintf(hitOut, "cDNA files: ", cdnaListSize);
for (i=0; i<cdnaListSize; ++i)
fprintf(hitOut, " %s", cdnaList[i]);
fprintf(hitOut, "\n");
fprintf(hitOut, "%d genomic files\n", genoListSize);
for (i=0; i<genoListSize; ++i)
{
genoName = genoList[i];
if (!startsWith("//", genoName) )
{
seqListList[i] = seq = faReadAllDna(genoName);
fprintf(hitOut, "%d els in %s ", slCount(seq), genoList[i]);
for (; seq != NULL; seq = seq->next)
fprintf(hitOut, "%d ", seq->size);
fprintf(hitOut, "\n");
}
}
patSpace = makePatSpace(seqListList, genoListSize, oocFileName);
for (i=0; i<cdnaListSize; ++i)
{
FILE *f;
char *estFileName;
DNA *dna;
char *estName;
int size;
int c;
int maxSizeForFuzzyFind = 20000;
int dotCount = 0;
estFileName = cdnaList[i];
if (startsWith("//", estFileName) )
continue;
f = mustOpen(estFileName, "rb");
while ((c = fgetc(f)) != EOF)
if (c == '>')
break;
printf("%s", cdnaList[i]);
fflush(stdout);
while (fastFaReadNext(f, &dna, &size, &estName))
{
aliSeqName = estName;
if (size < maxSizeForFuzzyFind) /* Some day need to fix this somehow... */
{
struct hashEl *hel;
struct cdnaAliList *calList = NULL;
hel = hashLookup(pairHash, estName);
if (hel != NULL) /* Do pair processing. */
{
struct estPair *ep;
struct seq *thisSeq, *otherSeq;
ep = hel->val;
if (hel->name == ep->name3)
{
thisSeq = &ep->seq3;
otherSeq = &ep->seq5;
}
else
{
thisSeq = &ep->seq5;
otherSeq = &ep->seq3;
}
if (otherSeq->dna == NULL) /* First in pair - need to save sequence. */
{
thisSeq->size = size;
thisSeq->dna = needMem(size);
memcpy(thisSeq->dna, dna, size);
}
else /* Second in pair - do gluing and free partner. */
{
char mergedName[64];
thisSeq->dna = dna;
thisSeq->size = size;
sprintf(mergedName, "%s_AND_%s", ep->name5, ep->name3);
patSpaceFindOne(patSpace, ep->seq5.dna, ep->seq5.size,
'+', '5', ep->name5, &calList);
reverseComplement(ep->seq5.dna, ep->seq5.size);
patSpaceFindOne(patSpace, ep->seq5.dna, ep->seq5.size,
'-', '5', ep->name5, &calList);
patSpaceFindOne(patSpace, ep->seq3.dna, ep->seq3.size,
'+', '3', ep->name3, &calList);
reverseComplement(ep->seq3.dna, ep->seq3.size);
patSpaceFindOne(patSpace, ep->seq3.dna, ep->seq3.size,
'-', '3', ep->name3, &calList);
slReverse(&calList);
writeMergers(calList, mergedName, genoList);
freez(&otherSeq->dna);
thisSeq->dna = NULL;
thisSeq->size =otherSeq->size = 0;
}
}
else
{
patSpaceFindOne(patSpace, dna, size, '+', '5', estName, &calList);
reverseComplement(dna, size);
patSpaceFindOne(patSpace, dna, size, '-', '5', estName, &calList);
slReverse(&calList);
writeMergers(calList, estName, genoList);
}
++estIx;
if ((estIx & 0xfff) == 0)
{
printf(".");
++dotCount;
fflush(stdout);
}
}
}
printf("\n");
}
aliSeqName = "";
printf("ffSubmitted %3d ffAccepted %3d ffOkScore %3d ffSolidMatch %2d\n",
ffSubmitted, ffAccepted, ffOkScore, ffSolidMatch);
endTime = clock1000();
printf("Total time is %4.2f\n", 0.001*(endTime-startTime));
/* Write out file who's presense say's we succeeded */
{
FILE *f = mustOpen(okFileName, "w");
fputs("ok", f);
fclose(f);
}
if (dumpMe)
{
htmEnd(bigHtmlFile);
htmEnd(littleHtmlFile);
}
return 0;
}
