int main(int argc, char *argv[])
{
char *genoListName;
char *otherListName;
char *oocFileName;
char *typeName;
char *outName;
struct patSpace *patSpace;
long startTime, endTime;
char **genoList;
int genoListSize;
char *genoListBuf;
char **otherList;
int otherListSize;
char *otherListBuf;
char *genoName;
int i;
int blockCount = 0;
struct dnaSeq **seqListList = NULL, *seq = NULL;
char *outRoot;
struct sqlConnection *conn;
enum ffStringency stringency = ffCdna;
int seedSize = 10;
FILE *out;
boolean noHead = FALSE;
struct repeatTracker *rt;
struct hash *repeatHash = newHash(10);
hostName = getenv("HOST");
pushWarnHandler(warnHandler);
startTime = clock1();
cgiSpoof(&argc, argv);
minMatch = cgiOptionalInt("minMatch", minMatch);
maxBad = cgiOptionalInt("maxBad", maxBad);
minBases = cgiOptionalInt("minBases", minBases);
dnaUtilOpen();
#ifdef DEBUG
/* Hard wire command line input so don't have to type it in each
* time run the stupid Gnu debugger. */
genoListName = "pFoo/geno.lst";
otherListName = "pFoo/bacend.lst";
typeName = "genomic";
oocFileName = "/d/biodata/human/10.ooc";
outName = "pFoo/pFoo.psl";
#else
if (argc != 6 && argc != 7)
usage();
genoListName = argv[1];
otherListName = argv[2];
typeName = argv[3];
oocFileName = argv[4];
if (sameWord(oocFileName, "none"))
oocFileName = NULL;
outName = argv[5];
if (argc == 7)
{
if (sameWord("noHead", argv[6]))
noHead = TRUE;
else
usage();
}
#endif
if (sameWord(typeName, "mRNA") || sameWord(typeName, "cDNA"))
{
stringency = ffCdna;
}
else if (sameWord(typeName, "genomic"))
{
stringency = ffTight;
}
else if (sameWord(typeName, "g2g"))
{
stringency = ffTight;
veryTight = TRUE;
seedSize = 11;
}
else if (sameString(typeName, "asm"))
{
stringency = ffTight;
avoidSelfSelf = TRUE;
}
else
{
warn("Unrecognized otherType %s\n", typeName);
usage();
}
readAllWordsOrFa(genoListName, &genoList, &genoListSize, &genoListBuf);
filterMissingFiles(genoList, &genoListSize);
if (genoListSize <= 0)
errAbort("There are no files that exist in %s\n", genoListName);
readAllWordsOrFa(otherListName, &otherList, &otherListSize, &otherListBuf);
if (otherListSize <= 0)
errAbort("There are no files that exist in %s\n", otherListName);
filterMissingFiles(otherList, &otherListSize);
out = mustOpen(outName, "w");
if (!noHead)
pslWriteHead(out);
AllocArray(seqListList, genoListSize);
for (i=0; i<genoListSize; ++i)
{
genoName = genoList[i];
if (!startsWith("#", genoName) )
seqListList[i] = seq = faReadAllDna(genoName);
for (;seq != NULL; seq = seq->next)
{
int size = seq->size;
char *name = seq->name;
struct hashEl *hel;
AllocVar(rt);
AllocArray(rt->repBytes, size);
rt->seq = seq;
if ((hel = hashLookup(repeatHash, name)) != NULL)
errAbort("Duplicate %s in %s\n", name, genoName);
hashAdd(repeatHash, name, rt);
}
storeMasked(repeatHash, genoName);
}
patSpace = makePatSpace(seqListList, genoListSize, seedSize, oocFileName, minMatch, 2000);
endTime = clock1();
printf("Made index in %ld seconds\n", (endTime-startTime));
startTime = endTime;
for (i=0; i<otherListSize; ++i)
{
FILE *f;
char *otherName;
int c;
int dotCount = 0;
struct dnaSeq otherSeq;
ZeroVar(&otherSeq);
otherName = otherList[i];
if (startsWith("#", otherName) )
continue;
f = mustOpen(otherName, "r");
while ((c = fgetc(f)) != EOF)
if (c == '>')
break;
printf("%s\n", otherName);
fflush(stdout);
while (faFastReadNext(f, &otherSeq.dna, &otherSeq.size, &otherSeq.name))
{
aliSeqName = otherSeq.name;
oneStrand(patSpace, repeatHash, &otherSeq, FALSE, stringency, out);
reverseComplement(otherSeq.dna, otherSeq.size);
oneStrand(patSpace, repeatHash, &otherSeq, TRUE, stringency, out);
aliSeqName = NULL;
}
fclose(f);
}
freePatSpace(&patSpace);
endTime = clock1();
printf("Alignment time is %ld sec\n", (endTime-startTime));
startTime = endTime;
fclose(out);
return 0;
}
void firstPass(char *aList, char *bList, char *outName)
/* Do first pass - find areas of homology between a and b,
* save to outName. */
{
char *aNameBuf, **aNames;
char *bNameBuf, **bNames;
int aCount, bCount;
struct nt4Seq **bNts, *bNt, *bNtList = NULL;
int bNtCount;
int i;
FILE *out = mustOpen(outName, "w");
/* Read in fa file lists . */
readAllWordsOrFa(aList, &aNames, &aCount, &aNameBuf);
readAllWordsOrFa(bList, &bNames, &bCount, &bNameBuf);
/* Convert second list to nt4 (packed) format in memory. */
printf("Loading and packing dna in %s\n", bList);
for (i=0; i<bCount; ++i)
{
char *bName = bNames[i];
struct dnaSeq *seqList, *seq;
seqList = faReadAllDna(bName);
for (seq = seqList; seq != NULL; seq = seq->next)
{
char uniqName[512];
sprintf(uniqName, "%s@%s", seq->name, bName);
bNt = newNt4(seq->dna, seq->size, uniqName);
slAddHead(&bNtList, bNt);
}
freeDnaSeqList(&seqList);
}
slReverse(&bNtList);
bNtCount = slCount(bNtList);
AllocArray(bNts, bNtCount);
for (i=0, bNt=bNtList; i<bNtCount; ++i, bNt=bNt->next)
bNts[i] = bNt;
printf("Loaded %d contigs from %d files\n", bNtCount, bCount);
/* Align elements of A list one at a time against B list. */
for (i=0; i<aCount; ++i)
{
char *aName = aNames[i];
struct dnaSeq *seqList, *seq;
printf("Aligning %s against %s\n", aName, bList);
seqList = faReadAllDna(aName);
for (seq = seqList; seq != NULL; seq = seq->next)
{
doCrude(aName, seq, bNts, bNtCount, out);
}
printf("\n");
freeDnaSeqList(&seqList);
}
/* Cleanup time. */
for (i=0; i<bNtCount; ++i)
freeNt4(&bNts[i]);
freeMem(bNts);
freeMem(aNames);
freeMem(bNames);
freeMem(aNameBuf);
freeMem(bNameBuf);
fclose(out);
}
