void readFa(char *fileName, struct rnaCover **retList, struct hash **retHash)
/* Read in an FA file and store name and size of every record in hash/list. */
{
struct rnaCover *list = NULL, *rc;
struct hash *hash = newHash(18);
struct lineFile *lf = lineFileOpen(fileName, TRUE);
DNA *dna;
int size;
char *name;
while (faSpeedReadNext(lf, &dna, &size, &name))
{
if (size >= minSize)
{
AllocVar(rc);
slAddHead(&list, rc);
if (hashLookup(hash, name))
{
warn("Duplicate %s line %d of %s, skipping", name, lf->lineIx, lf->fileName);
continue;
}
hashAddSaveName(hash, name, rc, &rc->name);
rc->qSize = size;
}
}
slReverse(&list);
*retList = list;
*retHash = hash;
}
void splitNcbiFa(char *ncbiIn, char *outDir)
/* splitNcbiFa - Split up NCBI format fa file into UCSC formatted ones.. */
{
struct lineFile *lf = lineFileOpen(ncbiIn, TRUE);
static struct dnaSeq seq;
ZeroVar(&seq);
makeDir(outDir);
while (faSpeedReadNext(lf, &seq.dna, &seq.size, &seq.name))
{
FILE *f;
char fileName[512];
char *row[5];
int wordCount;
char ourName[129];
char cloneName[128];
wordCount = chopByChar(seq.name, '|', row, ArraySize(row));
if (wordCount != 5)
errAbort("Expecting 5 | separated fields line %d of %s", lf->lineIx, lf->fileName);
strcpy(cloneName, row[3]);
chopSuffix(cloneName);
sprintf(fileName, "%s/%s.fa", outDir, cloneName);
sprintf(ourName, "%s_1", row[3]);
faWrite(fileName, ourName, seq.dna, seq.size);
}
}
void polyInfo(char *pslFile, char *genoFile, char *estFile, char *outputFile)
/* polyInfo - Collect info on polyAdenylation signals etc. */
{
struct hash *pslHash = NULL;
struct hash *genoHash = loadGeno(genoFile);
static struct dnaSeq est;
struct lineFile *lf = NULL;
FILE *f = NULL;
pslHash = pslIntoHash(pslFile);
lf = lineFileOpen(estFile, TRUE);
f = mustOpen(outputFile, "w");
while (faSpeedReadNext(lf, &est.dna, &est.size, &est.name))
{
struct pslList *pl;
struct psl *psl;
struct estOrientInfo ei;
if ((pl = hashFindVal(pslHash, est.name)) != NULL)
{
for (psl = pl->list; psl != NULL; psl = psl->next)
{
struct dnaSeq *geno = hashMustFindVal(genoHash, psl->tName);
if (psl->tSize != geno->size)
errAbort("psl generated on a different version of the genome");
ZeroVar(&ei);
fillInEstInfo(&ei, &est, geno, psl);
estOrientInfoTabOut(&ei, f);
}
}
}
}
struct frag *readFragList(char *fileName)
/* Read list of frags from file. */
{
struct frag *list = NULL, *frag;
struct lineFile *lf = lineFileOpen(fileName, TRUE);
struct dnaSeq seq;
char *s;
int fragIx;
struct hash *chromHash = newHash(5);
ZeroVar(&seq);
printf("Reading %s\n", fileName);
while (faSpeedReadNext(lf, &seq.dna, &seq.size, &seq.name))
{
AllocVar(frag);
frag->name = cloneString(seq.name);
s = strrchr(seq.name, '_');
if (s == NULL || !isdigit(s[1]))
errAbort("Expecting _ and number in %s", seq.name);
fragIx = atoi(s+1);
frag->chrom = "chr14";
frag->start = fragIx*1000;
frag->end = frag->start + 1000;
slAddHead(&list, frag);
}
lineFileClose(&lf);
printf("Read %d fragments from %s\n", slCount(list), fileName);
slReverse(&list);
return list;
}
void countSeq(char *fileName, int *retSeqCount, int *retBaseCount)
/* Count bases and sequences in fa file. */
{
int seqCount = 0, baseCount = 0, oneSize;
struct lineFile *lf = lineFileOpen(fileName, TRUE);
DNA *dna;
char *name;
while (faSpeedReadNext(lf, &dna, &oneSize, &name))
{
seqCount += 1;
baseCount += oneSize;
}
lineFileClose(&lf);
*retSeqCount = seqCount;
*retBaseCount = baseCount;
}
void correctEst(char *oldFa, char *pslFile, char *nibDir, char *outFa)
/* correctEst - Correct ESTs by passing them through genome. */
{
struct hash *pslHash = hashPsls(pslFile);
struct lineFile *lf = lineFileOpen(oldFa, FALSE);
FILE *f = mustOpen(outFa, "w");
static struct dnaSeq est;
struct hashEl *hel;
struct psl *psl;
struct hash *nibHash = newHash(8);
while (faSpeedReadNext(lf, &est.dna, &est.size, &est.name))
{
if ((psl = hashFindVal(pslHash, est.name)) != NULL)
{
correctOne(&est, psl, nibDir, nibHash, f);
}
else
{
faWriteNext(f, est.name, est.dna, est.size);
}
}
}
void gsBig(char *faName, char *gtfName,
char *suboptName,
char *transName,
char *exeName,
char *parName,
char *tmpDirName)
/* gsBig - Run Genscan on big input and produce GTF files. */
{
struct dnaSeq seq;
struct lineFile *lf = lineFileOpen(faName, TRUE);
FILE *gtfFile = mustOpen(gtfName, "w");
FILE *subFile = NULL;
FILE *transFile = NULL;
ZeroVar(&seq);
if (suboptName != NULL)
subFile = mustOpen(suboptName, "w");
if (transName != NULL)
transFile = mustOpen(transName, "w");
if (exeName != NULL)
exePath = cloneString(exeName);
if (parName != NULL)
parPath = cloneString(parName);
if (tmpDirName != NULL)
tmpDir = cloneString(tmpDirName);
if (optionExists("prerun"))
{
char *preFileName = optionVal("prerun", NULL);
char seqName[128];
struct segment *seg = parseSegment(preFileName, 0, 100000000, seqName);
writeSeg(seqName, seg, gtfFile, subFile, transFile);
}
else
{
struct dyString *dy = newDyString(1024);
char tempFa[512], tempGs[512];
char dir1[256], root1[128], ext1[64];
int myPid = (int)getpid();
splitPath(faName, dir1, root1, ext1);
while (faSpeedReadNext(lf, &seq.dna, &seq.size, &seq.name))
{
int offset, sizeOne;
struct segment *segList = NULL, *seg;
char *seqName = cloneString(seq.name);
int chunkNum = 0;
for (offset = 0; offset < seq.size; offset += stepSize)
{
boolean allN = TRUE;
int i;
safef(tempFa, sizeof(tempFa), "%s/temp_gsBig_%d_%s_%d.fa",
tmpDir, myPid, seqName, chunkNum);
safef(tempGs, sizeof(tempGs), "%s/temp_gsBig_%d_%s_%d.genscan",
tmpDir, myPid, seqName, chunkNum);
sizeOne = seq.size - offset;
if (sizeOne > winSize) sizeOne = winSize;
/* Genscan hangs forever if a chunk is all-N's... if so,
* then skip this chunk. */
for (i=offset; i < (offset+sizeOne); i++)
{
if (seq.dna[i] != 'N' && seq.dna[i] != 'n')
{
allN = FALSE;
break;
}
}
if (allN)
{
printf("\ngsBig: skipping %s[%d:%d] -- it's all N's.\n\n",
seqName, offset, (offset+sizeOne-1));
}
else
{
faWrite(tempFa, "split", seq.dna + offset, sizeOne);
dyStringClear(dy);
dyStringPrintf(dy, "%s %s %s", exePath, parPath, tempFa);
if (suboptName != NULL)
dyStringPrintf(dy, " -subopt");
dyStringPrintf(dy, " > %s", tempGs);
verbose(3, "%s\n", dy->string);
mustSystem(dy->string);
seg = parseSegment(tempGs, offset, offset+sizeOne, NULL);
slAddHead(&segList, seg);
}
chunkNum++;
}
slReverse(&segList);
seg = mergeSegs(segList);
writeSeg(seqName, seg, gtfFile, subFile, transFile);
freez(&seqName);
}
if (! optionExists("noRemove"))
{
remove(tempFa);
remove(tempGs);
}
}
}
void faCount(char *faFiles[], int faCount)
/* faCount - count bases. */
{
int f, i, j, k;
struct dnaSeq seq;
unsigned long long totalLength = 0;
unsigned long long totalBaseCount[5];
unsigned long long totalDinucleotideCount[5][5];
unsigned long long totalCpgCount = 0;
struct lineFile *lf;
ZeroVar(&seq);
for (i = 0; i < ArraySize(totalBaseCount); i++)
totalBaseCount[i] = 0;
for (i = 0; i < ArraySize(totalDinucleotideCount); i++)
for (j = 0; j < ArraySize(totalDinucleotideCount[i]); j++)
totalDinucleotideCount[i][j] = 0;
printf("#seq\tlen\tA\tC\tG\tT\tN\tcpg");
if (dinuc)
printf("\tAA\tAC\tAG\tAT\tCA\tCC\tCG\tCT\tGA\tGC\tGG\tGT\tTA\tTC\tTG\tTT");
printf("\n");
dnaUtilOpen();
for (f = 0; f<faCount; ++f)
{
lf = lineFileOpen(faFiles[f], FALSE);
while (faSpeedReadNext(lf, &seq.dna, &seq.size, &seq.name))
{
int prevBase = -1;
int prevRcBase = -1;
unsigned long long length = 0;
unsigned long long baseCount[5];
unsigned long long dinucleotideCount[5][5];
unsigned long long cpgCount = 0;
for (i = 0; i < ArraySize(baseCount); i++)
baseCount[i] = 0;
for (i = 0; i < ArraySize(dinucleotideCount); i++)
for (j = 0; j < ArraySize(dinucleotideCount[i]); j++)
dinucleotideCount[i][j] = 0;
for (j=0; j<seq.size; ++j)
{
int baseVal = ntVal5[(int)(seq.dna[j])];
int rcBaseVal;
assert(baseVal != -1);
assert(baseVal <= 4);
length++;
switch(baseVal)
{
case A_BASE_VAL: rcBaseVal = T_BASE_VAL; break;
case C_BASE_VAL: rcBaseVal = G_BASE_VAL; break;
case G_BASE_VAL: rcBaseVal = C_BASE_VAL; break;
case T_BASE_VAL: rcBaseVal = A_BASE_VAL; break;
default: rcBaseVal = N_BASE_VAL; break;
}
baseCount[baseVal]++;
if ((prevBase == C_BASE_VAL) && (baseVal == G_BASE_VAL))
cpgCount++;
if (prevBase != -1)
dinucleotideCount[prevBase][baseVal]++;
if (strands)
{
length++;
baseCount[rcBaseVal]++;
if ((prevRcBase == G_BASE_VAL) && (rcBaseVal == C_BASE_VAL))
cpgCount++;
if (prevRcBase != -1)
dinucleotideCount[rcBaseVal][prevRcBase]++;
}
prevBase = baseVal;
prevRcBase = rcBaseVal;
}
if (!summary)
{
printf("%s\t%llu\t%llu\t%llu\t%llu\t%llu\t%llu\t%llu",
seq.name, length,
baseCount[A_BASE_VAL], baseCount[C_BASE_VAL],
baseCount[G_BASE_VAL], baseCount[T_BASE_VAL],
baseCount[N_BASE_VAL], cpgCount);
if (dinuc)
printf("\t%llu\t%llu\t%llu\t%llu\t%llu\t%llu\t%llu\t%llu\t%llu\t%llu\t%llu\t%llu\t%llu\t%llu\t%llu\t%llu",
dinucleotideCount[A_BASE_VAL][A_BASE_VAL], dinucleotideCount[A_BASE_VAL][C_BASE_VAL],
dinucleotideCount[A_BASE_VAL][G_BASE_VAL], dinucleotideCount[A_BASE_VAL][T_BASE_VAL],
dinucleotideCount[C_BASE_VAL][A_BASE_VAL], dinucleotideCount[C_BASE_VAL][C_BASE_VAL],
dinucleotideCount[C_BASE_VAL][G_BASE_VAL], dinucleotideCount[C_BASE_VAL][T_BASE_VAL],
dinucleotideCount[G_BASE_VAL][A_BASE_VAL], dinucleotideCount[G_BASE_VAL][C_BASE_VAL],
dinucleotideCount[G_BASE_VAL][G_BASE_VAL], dinucleotideCount[G_BASE_VAL][T_BASE_VAL],
dinucleotideCount[T_BASE_VAL][A_BASE_VAL], dinucleotideCount[T_BASE_VAL][C_BASE_VAL],
dinucleotideCount[T_BASE_VAL][G_BASE_VAL], dinucleotideCount[T_BASE_VAL][T_BASE_VAL]);
printf("\n");
}
totalLength += length;
totalCpgCount += cpgCount;
for (i = 0; i < ArraySize(baseCount); i++)
totalBaseCount[i] += baseCount[i];
for (i = 0; i < ArraySize(dinucleotideCount); i++)
for (k = 0; k < ArraySize(dinucleotideCount[i]); k++)
totalDinucleotideCount[i][k] += dinucleotideCount[i][k];
}
lineFileClose(&lf);
}
printf("total\t%llu\t%llu\t%llu\t%llu\t%llu\t%llu\t%llu",
totalLength,
totalBaseCount[A_BASE_VAL], totalBaseCount[C_BASE_VAL],
totalBaseCount[G_BASE_VAL], totalBaseCount[T_BASE_VAL],
totalBaseCount[N_BASE_VAL], totalCpgCount);
if (dinuc)
printf("\t%llu\t%llu\t%llu\t%llu\t%llu\t%llu\t%llu\t%llu\t%llu\t%llu\t%llu\t%llu\t%llu\t%llu\t%llu\t%llu",
totalDinucleotideCount[A_BASE_VAL][A_BASE_VAL], totalDinucleotideCount[A_BASE_VAL][C_BASE_VAL],
totalDinucleotideCount[A_BASE_VAL][G_BASE_VAL], totalDinucleotideCount[A_BASE_VAL][T_BASE_VAL],
totalDinucleotideCount[C_BASE_VAL][A_BASE_VAL], totalDinucleotideCount[C_BASE_VAL][C_BASE_VAL],
totalDinucleotideCount[C_BASE_VAL][G_BASE_VAL], totalDinucleotideCount[C_BASE_VAL][T_BASE_VAL],
totalDinucleotideCount[G_BASE_VAL][A_BASE_VAL], totalDinucleotideCount[G_BASE_VAL][C_BASE_VAL],
totalDinucleotideCount[G_BASE_VAL][G_BASE_VAL], totalDinucleotideCount[G_BASE_VAL][T_BASE_VAL],
totalDinucleotideCount[T_BASE_VAL][A_BASE_VAL], totalDinucleotideCount[T_BASE_VAL][C_BASE_VAL],
totalDinucleotideCount[T_BASE_VAL][G_BASE_VAL], totalDinucleotideCount[T_BASE_VAL][T_BASE_VAL]);
printf("\n");
if (summary)
{
printf("prcnt\t%-5.1f\t%-5.4f\t%-5.4f\t%-5.4f\t%-5.4f\t%-5.4f\t%-5.4f",
(float)totalLength/totalLength,
((float)totalBaseCount[A_BASE_VAL])/(float)totalLength, ((float)totalBaseCount[C_BASE_VAL])/(float)totalLength,
((float)totalBaseCount[G_BASE_VAL])/(float)totalLength, ((float)totalBaseCount[T_BASE_VAL])/(float)totalLength,
((float)totalBaseCount[N_BASE_VAL])/(float)totalLength, (float)totalCpgCount/(float)totalLength);
if (dinuc)
printf("\t%-5.4f\t%-5.4f\t%-5.4f\t%-5.4f\t%-5.4f\t%-5.4f\t%-5.4f\t%-5.4f\t%-5.4f\t%-5.4f\t%-5.4f\t%-5.4f\t%-5.4f\t%-5.4f\t%-5.4f\t%-5.4f",
(float)totalDinucleotideCount[A_BASE_VAL][A_BASE_VAL]/(float)totalLength, (float)totalDinucleotideCount[A_BASE_VAL][C_BASE_VAL]/(float)totalLength,
(float)totalDinucleotideCount[A_BASE_VAL][G_BASE_VAL]/(float)totalLength, (float)totalDinucleotideCount[A_BASE_VAL][T_BASE_VAL]/(float)totalLength,
(float)totalDinucleotideCount[C_BASE_VAL][A_BASE_VAL]/(float)totalLength, (float)totalDinucleotideCount[C_BASE_VAL][C_BASE_VAL]/(float)totalLength,
(float)totalDinucleotideCount[C_BASE_VAL][G_BASE_VAL]/(float)totalLength, (float)totalDinucleotideCount[C_BASE_VAL][T_BASE_VAL]/(float)totalLength,
(float)totalDinucleotideCount[G_BASE_VAL][A_BASE_VAL]/(float)totalLength, (float)totalDinucleotideCount[G_BASE_VAL][C_BASE_VAL]/(float)totalLength,
(float)totalDinucleotideCount[G_BASE_VAL][G_BASE_VAL]/(float)totalLength, (float)totalDinucleotideCount[G_BASE_VAL][T_BASE_VAL]/(float)totalLength,
(float)totalDinucleotideCount[T_BASE_VAL][A_BASE_VAL]/(float)totalLength, (float)totalDinucleotideCount[T_BASE_VAL][C_BASE_VAL]/(float)totalLength,
(float)totalDinucleotideCount[T_BASE_VAL][G_BASE_VAL]/(float)totalLength, (float)totalDinucleotideCount[T_BASE_VAL][T_BASE_VAL]/(float)totalLength);
printf("\n");
}
}