static struct qaSeq *qaFaRead(char *qaName, char *faName, boolean mustReadQa)
/* Read both QA(C) and FA files. */
{
FILE *f = NULL;
struct qaSeq *qaList = NULL, *qa;
struct hash *hash = newHash(0);
struct qaSeq seq;
/* Read in all the .fa files. */
f = mustOpen(faName, "r");
while (faFastReadNext(f, &seq.dna, &seq.size, &seq.name))
{
if (hashLookup(hash, seq.name) != NULL)
{
warn("Duplicate %s, ignoring all but first.", seq.name);
continue;
}
AllocVar(qa);
hashAdd(hash, seq.name, qa);
qa->name = cloneString(seq.name);
qa->dna = cloneMem(seq.dna, seq.size+1);
qa->size = seq.size;
slAddHead(&qaList, qa);
}
fclose(f);
/* Read in corresponding .qa files and make sure they correspond.
* If no file exists then fake it. */
if (qaName)
{
if (!mustReadQa && !fileExists(qaName))
{
warn("No quality file %s", qaName);
for (qa = qaList; qa != NULL; qa = qa->next)
qaMakeFake(qa);
}
else
{
if (isQacFile(qaName))
fillInQac(qaName, hash, qaList);
else
fillInQa(qaName, hash, qaList);
}
}
freeHash(&hash);
slReverse(&qaList);
return qaList;
}
int main(int argc, char *argv[])
/* Process command line. */
{
char *inName, *outName, **inNames;
FILE *in, *out;
int i, inCount;
DNA *dna;
int inSize, outSize;
int dnaOff;
char *seqName;
struct dyString *subSeqName = newDyString(512);
int maxSize = 100000;
if (argc < 3)
usage();
outName = argv[1];
inNames = &argv[2];
inCount = argc-2;
out = mustOpen(outName, "w");
for (i=0; i<inCount; ++i)
{
inName = inNames[i];
printf("processing %s", inName);
in = mustOpen(inName, "r");
while (faFastReadNext(in, &dna, &inSize, &seqName))
{
for (dnaOff = 0; dnaOff < inSize; dnaOff += outSize)
{
printf(".");
fflush(stdout);
outSize = inSize - dnaOff;
if (outSize > maxSize) outSize = maxSize;
dyStringClear(subSeqName);
dyStringPrintf(subSeqName, "%s.%d", seqName, dnaOff);
faWriteNext(out, subSeqName->string, dna+dnaOff, outSize);
}
}
fclose(in);
printf("\n");
}
}
struct hash *loadChroms(char *dir)
/* Load zipped chromosome files into memory. */
{
FILE *f;
char fastaScan[16];
safef(fastaScan, sizeof(fastaScan), "*.%s", faExtn);
struct fileInfo *chromEl, *chromList = listDirX(dir, fastaScan, TRUE);
struct hash *chromHash = newHash(0);
struct dnaSeq *seq;
char chrom[128];
char *faName;
int count = 0;
verbose(2, "# scanning '%s/%s'\n", dir, fastaScan);
for (chromEl = chromList; chromEl != NULL; chromEl = chromEl->next)
{
char *fileName = chromEl->name;
splitPath(fileName, NULL, chrom, NULL);
chopSuffix(chrom);
if (startsWith("chr0", chrom)) /* Convert chr01 to chr1, etc. */
stripChar(chrom, '0');
if (sameString(chrom, "chrmt"))
strcpy(chrom, "chr17");
f = fopen(fileName, "r");
AllocVar(seq);
seq->name = cloneString(chrom);
if (!faFastReadNext(f, &seq->dna, &seq->size, &faName))
errAbort("Couldn't load sequence from %s", fileName);
seq->dna = cloneMem(seq->dna, seq->size+1);
toUpperN(seq->dna, seq->size);
hashAdd(chromHash, chrom, seq);
verbose(3, "# loadChrom %s '%s'\n", fileName, chrom);
fclose(f);
f = NULL;
count++;
}
if (0 == count)
errAbort("not fasta files found in '%s/%s'\n", dir, fastaScan);
return chromHash;
}
void fakeOut(char *inName, char *outName)
/* fakeOut - fake a RepeatMasker .out file based on a N's in .fa file. */
{
FILE *out = mustOpen(outName, "w");
FILE *in = mustOpen(inName, "r");
DNA *dna;
int dnaSize;
char *name;
fprintf(out,
" SW perc perc perc query position in query matching repeat position in repeat\n"
"score div. del. ins. sequence begin end (left) repeat class/family begin end (left) ID\n"
"\n");
while (faFastReadNext(in, &dna, &dnaSize, &name))
{
int start = 0, end = 0;
int i;
boolean n, lastN = TRUE;
dna[dnaSize] = 'n'; /* Replace 0 with 'n' to make end condition not a special case. */
for (i=0; i<=dnaSize; ++i)
{
n = (dna[i] == 'n');
if (n != lastN)
{
if (n)
start = i;
else
{
end = i;
if (i != 0)
fprintf(out, " 1000 15.0 2.0 2.0 %-9s %7d %7d (1234567) + faked fake 1 100 1\n",
name, start+1, end);
}
lastN = n;
}
}
}
}
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;
}