void axtAndBed(char *inAxt, char *inBed, char *outAxt)
/* axtAndBed - Intersect an axt with a bed file and output axt.. */
{
struct hash *tHash = readBed(inBed); /* target keyed, binKeeper value */
struct lineFile *lf = lineFileOpen(inAxt, TRUE);
struct axt *axt;
struct binElement *list = NULL, *el;
FILE *f = mustOpen(outAxt, "w");
struct axtScoreScheme *ss = axtScoreSchemeDefault();
while ((axt = axtRead(lf)) != NULL)
{
struct chromInfo *ci = hashFindVal(tHash, axt->tName);
if (ci != NULL)
{
list = binKeeperFind(ci->bk, axt->tStart, axt->tEnd);
if (list != NULL)
{
/* Flatten out any overlapping elements by projecting them
* onto a 0/1 valued character array and then looking for
* runs of 1 in this array. */
int tStart = axt->tStart;
int tEnd = axt->tEnd;
int tSize = tEnd - tStart;
int i, s = 0;
char c, lastC = 0;
char *merger = NULL;
AllocArray(merger, tSize+1);
for (el = list; el != NULL; el = el->next)
{
int s = el->start - tStart;
int e = el->end - tStart;
int sz;
if (s < 0) s = 0;
if (e > tSize) e = tSize;
sz = e - s;
if (sz > 0)
memset(merger + s, 1, sz);
}
for (i=0; i<=tSize; ++i)
{
c = merger[i];
if (c && !lastC)
{
s = i;
lastC = c;
}
else if (!c && lastC)
{
axtSubsetOnT(axt, s+tStart, i+tStart, ss, f);
lastC = c;
}
}
freez(&merger);
slFreeList(&list);
}
}
axtFree(&axt);
}
}
struct seqPair *readAxtBlocks(char *fileName, struct hash *pairHash, FILE *f)
/* Read in axt file and parse blocks into pairHash */
{
struct lineFile *lf = lineFileOpen(fileName, TRUE);
struct dyString *dy = newDyString(512);
struct axt *axt;
struct seqPair *spList = NULL, *sp;
lineFileSetMetaDataOutput(lf, f);
lineFileSetUniqueMetaData(lf);
while ((axt = axtRead(lf)) != NULL)
{
dyStringClear(dy);
dyStringPrintf(dy, "%s%c%s", axt->qName, axt->qStrand, axt->tName);
sp = hashFindVal(pairHash, dy->string);
if (sp == NULL)
{
AllocVar(sp);
slAddHead(&spList, sp);
hashAddSaveName(pairHash, dy->string, sp, &sp->name);
sp->qName = cloneString(axt->qName);
sp->tName = cloneString(axt->tName);
sp->qStrand = axt->qStrand;
}
axtAddBlocksToBoxInList(&sp->blockList, axt);
sp->axtCount += 1;
axtFree(&axt);
}
lineFileClose(&lf);
dyStringFree(&dy);
slSort(&spList, seqPairCmp);
return spList;
}
void axtToPsl(char *inName, char *tSizeFile, char *qSizeFile, char *outName)
/* axtToPsl - Convert axt to psl format. */
{
struct hash *tSizeHash = readSizes(tSizeFile);
struct hash *qSizeHash = readSizes(qSizeFile);
struct lineFile *lf = lineFileOpen(inName, TRUE);
char strand[2];
FILE *f = mustOpen(outName, "w");
struct psl* psl;
struct axt *axt;
strand[1] = '\0';
while ((axt = axtRead(lf)) != NULL)
{
int qSize = findSize(qSizeHash, axt->qName);
int qStart = axt->qStart;
int qEnd = axt->qEnd;
if (axt->qStrand == '-')
reverseIntRange(&qStart, &qEnd, qSize);
strand[0] = axt->qStrand;
psl = pslFromAlign(axt->qName, qSize, qStart, qEnd, axt->qSym,
axt->tName, findSize(tSizeHash, axt->tName),
axt->tStart, axt->tEnd, axt->tSym, strand,
PSL_IS_SOFTMASK);
if (psl != NULL)
{
pslTabOut(psl, f);
pslFree(&psl);
}
axtFree(&axt);
}
lineFileClose(&lf);
carefulClose(&f);
}
void predict(struct c1Counts cKozak[10], struct c1Counts *cAll,
char *axtFile, char *outFile, struct hash *rsiHash)
/* Predict location of initial ATG */
{
struct lineFile *lf = lineFileOpen(axtFile, TRUE);
FILE *f = mustOpen(outFile, "w");
struct oddsMatrix kozak[10];
int i;
int bestPos, firstPos, actualPos;
double bestScore, firstScore, actualScore;
struct axt *axt;
for (i=0; i<10; ++i)
countToOdds(&cKozak[i], cAll, &kozak[i]);
while ((axt = axtRead(lf)) != NULL)
{
struct refSeqInfo *rsi = hashFindVal(rsiHash, axt->tName);
if (rsi != NULL && rsi->cdsStart >= 5)
{
findBestHit(axt, kozak, 10, &bestPos, &bestScore, &firstPos,
&firstScore);
actualPos = tIxToSymIx(axt, rsi->cdsStart - 5);
actualScore = scoreMotif(kozak, 10,
axt->tSym+actualPos, axt->qSym + actualPos);
/* Score motif at position. */
fprintf(f, "%s\t%d\t%f\t%d\t%f\t%d\t%f\n", axt->tName,
rsi->cdsStart, actualScore,
tIxFromSymIx(axt, bestPos) + 5, bestScore,
tIxFromSymIx(axt, firstPos) + 5, firstScore);
}
axtFree(&axt);
}
carefulClose(&f);
lineFileClose(&lf);
}
void twinOrfStats(char *axtFile, char *raFile, char *outFile)
/* twinOrfStats - Collect stats on refSeq cDNAs aligned to another species via axtForEst. */
{
struct hash *rsiHash = readRefRa(raFile);
struct lineFile *lf = lineFileOpen(axtFile, TRUE);
FILE *f = mustOpen(outFile, "w");
struct axt *axt;
static struct countMatrix kozak[10], all, utr5, utr3, cds;
static struct c2Counts c2All, c2Utr5, c2Utr3, c2Cds;
char label[64];
char *predictFile = optionVal("predict", NULL);
int i;
struct codonCounts codons;
initCounts(&codons, 1);
threshold = optionFloat("threshold", threshold);
while ((axt = axtRead(lf)) != NULL)
{
struct refSeqInfo *rsi = hashFindVal(rsiHash, axt->tName);
if (rsi != NULL && rsi->cdsStart >= 5)
{
if (checkAtg(axt, rsi->cdsStart))
{
for (i=0; i<10; ++i)
addPos(&kozak[i], axt, rsi->cdsStart - 5 + i);
addRange(&all, &c2All, axt, 0, rsi->size);
addRange(&utr5, &c2Utr5, axt, 0, rsi->cdsStart);
addRange(&cds, &c2Cds, axt, rsi->cdsStart, rsi->cdsEnd);
addRange(&utr3, &c2Utr3, axt, rsi->cdsEnd, rsi->size);
addCodons(&codons, axt, rsi->cdsStart, rsi->cdsEnd-3);
}
}
axtFree(&axt);
}
lineFileClose(&lf);
dumpCounts(f, &all, "all");
dumpCounts(f, &utr5, "utr5");
dumpCounts(f, &cds, "cds");
dumpCounts(f, &utr3, "utr3");
dumpM1(f, &c2All, "c2_all");
dumpM1(f, &c2Utr5, "c2_utr5");
dumpM1(f, &c2Cds, "c2_cds");
dumpM1(f, &c2Utr3, "c2_utr3");
for (i=0; i<10; ++i)
{
sprintf(label, "kozak[%d]", i-5);
dumpCounts(f, &kozak[i], label);
}
dumpCodon(f, &codons, "codon");
if (predictFile)
{
predict(kozak, &all, axtFile, predictFile, rsiHash);
}
}
void writeMousePartsAsMaf(FILE *f, struct hash *mouseHash,
char *ratMouseDir, char *mouseChrom,
int mouseStart, int mouseEnd, int mouseChromSize,
struct hash *rSizeHash, struct hash *dupeHash)
/* Write out mouse/rat alignments that intersect given region of mouse.
* This gets a little involved because we need to do random access on
* the mouse/rat alignment files, which are too big to fit into memory.
* On disk we have a mouse/rat alignment file for each mouse chromosome,
* and an index of it. When we first access a mouse chromosome we load
* the index for that chromosome into memory, and open the alignment file.
* We then do a seek and read to load a particular alignment. */
{
struct mouseChromCache *mcc = NULL;
struct binElement *list = NULL, *el;
char aliName[512];
/* Get cache for this mouse chromosome */
mcc = hashFindVal(mouseHash, mouseChrom);
if (mcc == NULL)
{
mcc = newMouseChromCache(mouseChrom, mouseChromSize, ratMouseDir);
hashAdd(mouseHash, mouseChrom, mcc);
}
if (mcc->lf == NULL)
return;
/* Get list of positions and process one axt into a maf for each */
list = binKeeperFindSorted(mcc->bk, mouseStart, mouseEnd);
for (el = list; el != NULL; el = el->next)
{
struct axt *axt;
struct mafAli temp;
long long *pPos, pos;
pPos = el->val;
pos = *pPos;
sprintf(aliName, "%s.%lld", mouseChrom, pos);
if (!hashLookup(dupeHash, aliName))
{
int rChromSize;
hashAdd(dupeHash, aliName, NULL);
lineFileSeek(mcc->lf, pos, SEEK_SET);
axt = axtRead(mcc->lf);
rChromSize = hashIntVal(rSizeHash, axt->qName);
prefixAxt(axt, rPrefix, mPrefix);
mafFromAxtTemp(axt, mouseChromSize, rChromSize, &temp);
mafWriteGood(f, &temp);
axtFree(&axt);
}
}
slFreeList(&list);
}
void axtPretty(char *inName, char *outName)
/* axtPretty - Convert axt to more human readable format.. */
{
struct lineFile *lf = lineFileOpen(inName, TRUE);
FILE *f = mustOpen(outName, "w");
struct axt *axt;
int lineSize = optionInt("line", 70);
while ((axt = axtRead(lf)) != NULL)
{
axtOutPretty(axt, lineSize, f);
axtFree(&axt);
}
}
void axtSwapFile(char *source, char *targetSizes, char *querySizes, char *dest)
/* axtSwapFile - Swap source and query in an axt file. */
{
struct hash *tHash = loadIntHash(targetSizes);
struct hash *qHash = loadIntHash(querySizes);
struct lineFile *lf = lineFileOpen(source, TRUE);
FILE *f = mustOpen(dest, "w");
struct axt *axt;
while ((axt = axtRead(lf)) != NULL)
{
axtSwap(axt, hashIntVal(tHash, axt->tName), hashIntVal(qHash, axt->qName));
axtWrite(axt, f);
axtFree(&axt);
}
}
void axtDropSelf(char *inFile, char *outFile)
/* axtDropSelf - Drop alignments that just align same thing to itself. */
{
FILE *f = mustOpen(outFile, "w");
struct lineFile *lf = lineFileOpen(inFile, TRUE);
struct axt *axt;
while ((axt = axtRead(lf)) != NULL)
{
if (axt->qStart != axt->tStart || axt->qEnd != axt->tEnd ||
axt->qStrand != axt->tStrand || !sameString(axt->qName, axt->tName))
{
axtWrite(axt,f);
}
axtFree(&axt);
}
}
void axtSplitByTarget(char *inName, char *outDir)
/* axtSplitByTarget - Split a single axt file into one file per target. */
{
struct hash *outHash = newHash(8); /* FILE valued hash */
struct lineFile *lf = lineFileOpen(inName, TRUE);
struct axt *axt;
makeDir(outDir);
while ((axt = axtRead(lf)) != NULL)
{
FILE *f = getSplitFile(outHash, outDir, axt->tName, axt->tStart);
axtWrite(axt, f);
totalWritten += strlen(axt->tName) + strlen(axt->qName) + 40 + strlen(axt->qSym)+ strlen(axt->tSym);
axtFree(&axt);
}
}
void subsetAxt(char *inName, char *outName, char *scoreFile, int threshold)
/* subsetAxt - Rescore alignments and output those over threshold. */
{
struct axtScoreScheme *ss = axtScoreSchemeRead(scoreFile);
struct lineFile *lf = lineFileOpen(inName, TRUE);
FILE *f = mustOpen(outName, "w");
struct axt *axt;
if (threshold <= 0)
errAbort("Threshold must be a positive number");
while ((axt = axtRead(lf)) != NULL)
{
subsetOne(axt, ss, threshold, f);
axtFree(&axt);
axt = NULL;
}
}
struct binKeeper *loadAxtsIntoRange(char *fileName, char *tPrefix, char *qPrefix)
/* Read in an axt file and shove it into a bin-keeper. */
{
struct lineFile *lf = lineFileOpen(fileName, TRUE);
struct binKeeper *bk = binKeeperNew(0, maxChromSize);
struct axt *axt;
int count = 0;
while ((axt = axtRead(lf)) != NULL)
{
binKeeperAdd(bk, axt->tStart, axt->tEnd, axt);
++count;
}
uglyf("LOaded %d from %s\n", count, fileName);
lineFileClose(&lf);
return bk;
}
void axtIndex(char *in, char *out)
/* axtIndex - Create summary file for axt. */
{
struct lineFile *lf = lineFileOpen(in, TRUE);
FILE *f = mustOpen(out, "w");
struct axt *axt;
for (;;)
{
off_t pos = lineFileTell(lf);
axt = axtRead(lf);
if (axt == NULL)
break;
fprintf(f, "%d %d %lld\n", axt->tStart, axt->tEnd - axt->tStart, (unsigned long long) pos);
axtFree(&axt);
}
carefulClose(&f);
}
void newStitch3(char *axtFile, char *output)
/* newStitch3 - Another stitching experiment - with kd-trees.. */
{
struct hash *pairHash = newHash(0); /* Hash keyed by qSeq<strand>tSeq */
struct dyString *dy = newDyString(512);
struct lineFile *lf = lineFileOpen(axtFile, TRUE);
struct axt *axt;
struct seqPair *spList = NULL, *sp;
FILE *f = mustOpen(output, "w");
/* Read input file and divide alignments into various parts. */
while ((axt = axtRead(lf)) != NULL)
{
struct cBlock *block;
if (axt->score < 500)
{
axtFree(&axt);
continue;
}
dyStringClear(dy);
dyStringPrintf(dy, "%s%c%s", axt->qName, axt->qStrand, axt->tName);
sp = hashFindVal(pairHash, dy->string);
if (sp == NULL)
{
AllocVar(sp);
slAddHead(&spList, sp);
hashAddSaveName(pairHash, dy->string, sp, &sp->name);
}
AllocVar(block);
block->qStart = axt->qStart;
block->qEnd = axt->qEnd;
block->tStart = axt->tStart;
block->tEnd = axt->tEnd;
block->score = axt->score;
slAddHead(&sp->blockList, block);
axtFree(&axt);
}
for (sp = spList; sp != NULL; sp = sp->next)
{
slReverse(&sp->blockList);
chainPair(sp, f);
}
dyStringFree(&dy);
}
void axtRescore(char *in, char *out)
/* axtRescore - Recalculate scores in axt. */
{
struct lineFile *lf = lineFileOpen(in, TRUE);
FILE *f = mustOpen(out, "w");
struct axt *axt;
lineFileSetMetaDataOutput(lf, f);
axtScoreSchemeDnaWrite(scoreScheme, f, "axtRescore");
for (;;)
{
axt = axtRead(lf);
if (axt == NULL)
break;
axt->score = axtScore(axt, scoreScheme);
axtWrite(axt, f);
axtFree(&axt);
}
}
void axtDropOverlap(char *inName, char *tSizeFile, char *qSizeFile, char *outName)
/* used for cleaning up self alignments - deletes all overlapping self alignments */
{
struct hash *qSizeHash = readSizes(qSizeFile);
struct lineFile *lf = lineFileOpen(inName, TRUE);
FILE *f = mustOpen(outName, "w");
struct axt *axt;
int totMatch = 0;
int totSkip = 0;
int totLines = 0;
while ((axt = axtRead(lf)) != NULL)
{
totLines++;
totMatch += axt->score;
if (sameString(axt->qName, axt->tName))
{
int qs = axt->qStart;
int qe = axt->qEnd;
if (axt->qStrand == '-')
reverseIntRange(&qs, &qe, findSize(qSizeHash, axt->qName));
if (axt->tStart == qs && axt->tEnd == qe)
{
/*
printf( "skip %c\t%s\t%d\t%d\t%d\t%s\t%d\t%d\t%d\n",
axt->qStrand,
axt->qName, axt->symCount, axt->qStart, axt->qEnd,
axt->tName, axt->symCount, axt->tStart, axt->tEnd
);
*/
totSkip++;
continue;
}
}
axtWrite(axt, f);
axtFree(&axt);
}
fclose(f);
lineFileClose(&lf);
}
void setAliBits(char *axtBestDir, char *chrom, int chromSize,
Bits *aliBits, Bits *matchBits)
/* Set bits where there are alignments and matches. */
{
char axtFileName[512];
struct axt *axt;
struct lineFile *lf;
sprintf(axtFileName, "%s/%s.axt", axtBestDir, chrom);
if ((lf = lineFileMayOpen(axtFileName, TRUE)) == NULL)
{
warn("Couldn't open %s", axtFileName);
return;
}
while ((axt = axtRead(lf)) != NULL)
{
axtSetBits(axt, chromSize, aliBits, matchBits);
axtFree(&axt);
}
lineFileClose(&lf);
}
struct mafAli *axtLoadAsMafInRegion(struct sqlConnection *conn, char *table,
char *chrom, int start, int end,
char *tPrefix, char *qPrefix, int tSize, struct hash *qSizeHash)
/* Return list of alignments in region from axt external file as a maf. */
{
char **row;
unsigned int extFileId = 0;
struct lineFile *lf = NULL;
struct mafAli *maf, *mafList = NULL;
struct axt *axt;
int rowOffset;
struct sqlResult *sr = hRangeQuery(conn, table, chrom,
start, end, NULL, &rowOffset);
while ((row = sqlNextRow(sr)) != NULL)
{
struct scoredRef ref;
scoredRefStaticLoad(row + rowOffset, &ref);
if (ref.extFile != extFileId)
{
char *path = hExtFileName(sqlGetDatabase(conn),"extFile", ref.extFile);
lf = lineFileOpen(path, TRUE);
extFileId = ref.extFile;
}
lineFileSeek(lf, ref.offset, SEEK_SET);
axt = axtRead(lf);
if (axt == NULL)
internalErr();
maf = mafFromAxt(axt, tSize, tPrefix, hashIntVal(qSizeHash, axt->qName), qPrefix);
axtFree(&axt);
slAddHead(&mafList, maf);
}
sqlFreeResult(&sr);
lineFileClose(&lf);
slReverse(&mafList);
return mafList;
}
void axtQueryCount(char *fileName)
/* axtQueryCount - Count bases covered on each query sequence. */
{
struct lineFile *lf = lineFileOpen(fileName, TRUE);
struct hash *hash = newHash(0);
struct axt *axt;
struct qInfo *qList = NULL, *q;
while ((axt = axtRead(lf)) != NULL)
{
char *qName = axt->qName;
if ((q = hashFindVal(hash, qName)) == NULL)
{
AllocVar(q);
slAddHead(&qList, q);
hashAddSaveName(hash, qName, q, &q->name);
}
q->covered += axt->qEnd - axt->qStart;
axtFree(&axt);
}
slSort(&qList, qInfoCmpName);
for (q = qList; q != NULL; q = q->next)
printf("%s\t%d\n", q->name, q->covered);
}
void ggcChrom(struct chromGenes *chrom, char *axtFile,
struct ggcInfo *g, struct hash *restrictHash,
FILE *fParts)
/* Tabulate matches on chromosome. */
{
struct lineFile *lf = lineFileOpen(axtFile, TRUE);
bool *hits, *covers;
int hitCount = 0, coverCount = 0;
struct axt *axt;
struct genePred *gp;
int closeSize = g->closeSize;
int closeHalf = closeSize/2;
/* Build up array of booleans - one per base - which are
* 1's where mouse/human align and bases match, zero
* elsewhere. */
AllocArray(hits, chrom->size);
AllocArray(covers, chrom->size);
printf("%s (%d bases)\n", chrom->name, chrom->size);
while ((axt = axtRead(lf)) != NULL)
{
int tPos = axt->tStart;
int symCount = axt->symCount, i;
char t, q, *tSym = axt->tSym, *qSym = axt->qSym;
if (axt->tEnd > chrom->size)
errAbort("tEnd %d, chrom size %d in %s",
axt->tEnd, chrom->size, axtFile);
if (axt->tStrand == '-')
errAbort("Can't handle minus strand on target in %s", axtFile);
for (i=0; i<symCount; ++i)
{
t = tSym[i];
if (t != '-')
{
q = qSym[i];
if (toupper(t) == toupper(q))
{
hits[tPos] = TRUE;
++hitCount;
}
if (q == '-')
covers[tPos] = 1;
else
covers[tPos] = 2;
++tPos;
}
}
axtFree(&axt);
}
for (gp = chrom->geneList; gp != NULL; gp = gp->next)
{
int exonIx;
int utr3Size = 0, utr5Size = 0, cdsAllSize = 0;
int utr3Pos = 0, utr5Pos = 0, cdsAllPos = 0;
bool *utr3Hits = NULL, *utr3Covers = NULL;
bool *utr5Hits = NULL, *utr5Covers = NULL;
bool *cdsAllHits = NULL, *cdsAllCovers = NULL;
bool isRev = (gp->strand[0] == '-');
/* Filter out genes not in restrict hash if any. */
++totalGenes;
if (restrictHash != NULL)
if (!hashLookup(restrictHash, gp->name))
continue;
++reviewedGenes;
/* Filter out genes without meaningful UTRs */
if (gp->cdsStart - gp->txStart < g->closeSize/2 ||
gp->txEnd - gp->cdsEnd < g->closeSize/2)
continue;
++genesUsed;
/* Total up UTR and CDS sizes. */
for (exonIx=0; exonIx<gp->exonCount; ++exonIx)
{
int eStart = gp->exonStarts[exonIx];
int eEnd = gp->exonEnds[exonIx];
int eSize = eEnd - eStart;
int oneUtr, oneCds;
oneCds = rangeIntersection(gp->cdsStart, gp->cdsEnd, eStart, eEnd);
if (oneCds > 0)
{
cdsAllSize += oneCds;
}
if (eStart < gp->cdsStart)
{
int utrStart = eStart;
int utrEnd = min(gp->cdsStart, eEnd);
int utrSize = utrEnd - utrStart;
if (isRev)
utr3Size += utrSize;
else
utr5Size += utrSize;
}
if (eEnd > gp->cdsEnd)
{
int utrStart = max(gp->cdsEnd, eStart);
int utrEnd = eEnd;
int utrSize = utrEnd - utrStart;
if (isRev)
utr5Size += utrSize;
else
utr3Size += utrSize;
}
}
/* Condense hits from UTRs and CDSs */
if (utr5Size > 0)
{
AllocArray(utr5Hits, utr5Size);
AllocArray(utr5Covers, utr5Size);
}
if (utr3Size > 0)
{
AllocArray(utr3Hits, utr3Size);
AllocArray(utr3Covers, utr3Size);
}
if (cdsAllSize > 0)
{
AllocArray(cdsAllHits, cdsAllSize);
AllocArray(cdsAllCovers, cdsAllSize);
}
for (exonIx=0; exonIx<gp->exonCount; ++exonIx)
{
int eStart = gp->exonStarts[exonIx];
int eEnd = gp->exonEnds[exonIx];
int eSize = eEnd - eStart;
int oneUtr, oneCds;
oneCds = rangeIntersection(gp->cdsStart, gp->cdsEnd, eStart, eEnd);
if (oneCds > 0)
{
int cdsStart = eStart;
int cdsEnd = gp->cdsEnd;
if (cdsStart < gp->cdsStart)
cdsStart = gp->cdsStart;
memcpy(cdsAllHits + cdsAllPos, hits + cdsStart, oneCds * sizeof(*hits));
memcpy(cdsAllCovers + cdsAllPos, covers + cdsStart, oneCds * sizeof(*covers));
cdsAllPos += oneCds;
}
if (eStart < gp->cdsStart)
{
int utrStart = eStart;
int utrEnd = min(gp->cdsStart, eEnd);
int utrSize = utrEnd - utrStart;
if (isRev)
{
memcpy(utr3Hits + utr3Pos, hits + utrStart, utrSize * sizeof(*hits));
memcpy(utr3Covers + utr3Pos, covers + utrStart, utrSize * sizeof(*covers));
utr3Pos += utrSize;
}
else
{
memcpy(utr5Hits + utr5Pos, hits + utrStart, utrSize * sizeof(*hits));
memcpy(utr5Covers + utr5Pos, covers + utrStart, utrSize * sizeof(*covers));
utr5Pos += utrSize;
}
}
if (eEnd > gp->cdsEnd)
{
int utrStart = max(gp->cdsEnd, eStart);
int utrEnd = eEnd;
int utrSize = utrEnd - utrStart;
if (isRev)
{
memcpy(utr5Hits + utr5Pos, hits + utrStart, utrSize * sizeof(*hits));
memcpy(utr5Covers + utr5Pos, covers + utrStart, utrSize * sizeof(*covers));
utr5Pos += utrSize;
}
else
{
memcpy(utr3Hits + utr3Pos, hits + utrStart, utrSize * sizeof(*hits));
memcpy(utr3Covers + utr3Pos, covers + utrStart, utrSize * sizeof(*covers));
utr3Pos += utrSize;
}
}
}
assert(utr3Pos == utr3Size);
assert(utr5Pos == utr5Size);
assert(cdsAllPos == cdsAllSize);
tallyHits(&g->utr5, utr5Hits, utr5Covers, utr5Size, isRev);
tallyHits(&g->utr3, utr3Hits, utr3Covers, utr3Size, isRev);
tallyHits(&g->cdsAll, cdsAllHits, cdsAllCovers, cdsAllSize, isRev);
/* Optionally write out file with gene by gene info. */
if (fParts != NULL)
{
/* Write header line first time through. */
static boolean firstTime = TRUE;
if (firstTime)
{
firstTime = FALSE;
fprintf(fParts, "#accession\tsize_5\tali_5\tmatch_5\tsize_c\tali_c\tmatch_c\tsize_3\tali_3\tmatch_3\n");
}
fprintf(fParts, "%s\t", gp->name);
fprintf(fParts, "%d\t%d\t%d\t", utr5Size,
countBools(utr5Covers, utr5Size),
countBools(utr5Hits, utr5Size));
fprintf(fParts, "%d\t%d\t%d\t", cdsAllSize,
countBools(cdsAllCovers, cdsAllSize),
countBools(cdsAllHits, cdsAllSize));
fprintf(fParts, "%d\t%d\t%d\n", utr3Size,
countBools(utr3Covers, utr3Size),
countBools(utr3Hits, utr3Size));
}
/* Tally upstream/downstream hits. */
{
int s1 = gp->txStart - closeHalf;
int e1 = s1 + closeSize;
int s2 = gp->txEnd - closeHalf;
int e2 = s2 + closeSize;
if (isRev)
{
tallyInRange(&g->down, hits, covers, chrom->size, gp->txStart - g->baseDown,
gp->txStart, isRev);
tallyInRange(&g->up, hits, covers, chrom->size, gp->txEnd,
gp->txEnd + g->baseUp, isRev);
tallyInRange(&g->txEnd, hits, covers, chrom->size, s1, e1, isRev);
tallyInRange(&g->txStart, hits, covers, chrom->size, s2, e2, isRev);
}
else
{
tallyInRange(&g->up, hits, covers, chrom->size, gp->txStart - g->baseUp,
gp->txStart, isRev);
tallyInRange(&g->down, hits, covers, chrom->size, gp->txEnd,
gp->txEnd + g->baseDown, isRev);
tallyInRange(&g->txStart, hits, covers, chrom->size, s1, e1, isRev);
tallyInRange(&g->txEnd, hits, covers, chrom->size, s2, e2, isRev);
}
}
/* Tally hits in coding exons */
for (exonIx=0; exonIx < gp->exonCount; ++exonIx)
{
int eStart = gp->exonStarts[exonIx];
int eEnd = gp->exonEnds[exonIx];
/* Single coding exon. */
if (eStart <= gp->cdsStart && eEnd >= gp->cdsEnd)
{
eStart = gp->cdsStart;
eEnd = gp->cdsEnd;
tallyInRange(&g->cdsSingle, hits, covers, chrom->size,
eStart, eEnd, isRev);
}
/* Initial coding exon */
else if (eStart < gp->cdsStart && eEnd > gp->cdsStart)
{
int cs = gp->cdsStart - closeHalf;
int ce = cs + closeSize;
eStart = gp->cdsStart;
if (isRev)
{
tallyInRange(&g->tlEnd, hits, covers, chrom->size, cs, ce, isRev);
tallyInRange(&g->cdsLast, hits, covers, chrom->size,
eStart, eEnd, isRev);
}
else
{
tallyInRange(&g->tlStart, hits, covers, chrom->size, cs, ce, isRev);
tallyInRange(&g->cdsFirst, hits, covers, chrom->size,
eStart, eEnd, isRev);
}
}
/* Final coding exon */
else if (eStart < gp->cdsEnd && eEnd > gp->cdsEnd)
{
int cs = gp->cdsEnd - closeHalf;
int ce = cs + closeSize;
eEnd = gp->cdsEnd;
if (isRev)
{
tallyInRange(&g->tlStart, hits, covers, chrom->size, cs, ce, isRev);
tallyInRange(&g->cdsFirst, hits, covers, chrom->size,
eStart, eEnd, isRev);
}
else
{
tallyInRange(&g->tlEnd, hits, covers, chrom->size, cs, ce, isRev);
tallyInRange(&g->cdsLast, hits, covers, chrom->size,
eStart, eEnd, isRev);
}
}
/* Middle (but not only) coding exon */
else if (eStart >= gp->cdsStart && eEnd <= gp->cdsEnd)
{
tallyInRange(&g->cdsMiddle, hits, covers, chrom->size, eStart, eEnd, isRev);
}
else
{
}
}
/* Tally hits in introns and splice sites. */
for (exonIx=1; exonIx<gp->exonCount; ++exonIx)
{
int iStart = gp->exonEnds[exonIx-1];
int iEnd = gp->exonStarts[exonIx];
int s1 = iStart - closeHalf;
int e1 = s1 + closeSize;
int s2 = iEnd - closeHalf;
int e2 = s2 + closeSize;
if (isRev)
{
tallyInRange(&g->splice3, hits, covers, chrom->size,
s1, e1, isRev);
tallyInRange(&g->splice5, hits, covers, chrom->size,
s2, e2, isRev);
}
else
{
tallyInRange(&g->splice5, hits, covers, chrom->size,
s1, e1, isRev);
tallyInRange(&g->splice3, hits, covers, chrom->size,
s2, e2, isRev);
}
tallyInRange(&g->intron, hits, covers, chrom->size, iStart, iEnd, isRev);
}
freez(&utr5Hits);
freez(&utr3Hits);
freez(&cdsAllHits);
freez(&utr5Covers);
freez(&utr3Covers);
freez(&cdsAllCovers);
}
freez(&hits);
freez(&covers);
lineFileClose(&lf);
}
void twinOrfStats(char *axtFile, char *raFile, char *outFile)
/* twinOrfStats - Collect stats on refSeq cDNAs aligned to another species via axtForEst. */
{
struct hash *rsiHash = readRefRa(raFile);
struct lineFile *lf = lineFileOpen(axtFile, TRUE);
FILE *f = mustOpen(outFile, "w");
struct axt *axt;
static struct c1Counts c1Kozak[10], c1all, c1utr5, c1utr3, c1cds;
static struct c2Counts c2Kozak[10], c2All, c2Utr5, c2Utr3, c2Cds;
static struct c3Counts c3All, c3Utr5, c3Utr3, c3Cds;
char label[64];
char *predictFile = optionVal("predict", NULL);
int i;
static struct c3Counts cod1, cod2, cod3, stop, earlyCod1, earlyCod2, earlyCod3;
int earlySize;
initC3Counts(&cod1, 0);
initC3Counts(&cod2, 0);
initC3Counts(&cod3, 0);
initC3Counts(&earlyCod1, 0);
initC3Counts(&earlyCod2, 0);
initC3Counts(&earlyCod3, 0);
initC3Counts(&c3Utr3, 0);
initC3Counts(&c3Utr5, 0);
initC3Counts(&stop, 0);
threshold = optionFloat("threshold", threshold);
earlyAaSize = optionInt("earlyAaSize", earlyAaSize);
earlySize = 3*earlyAaSize;
while ((axt = axtRead(lf)) != NULL)
{
struct refSeqInfo *rsi = hashFindVal(rsiHash, axt->tName);
if (rsi != NULL && rsi->cdsStart >= 6)
{
if (checkAtg(axt, rsi->cdsStart))
{
for (i=0; i<10; ++i)
addPos(&c1Kozak[i], &c2Kozak[i], axt, rsi->cdsStart - 5 + i);
addRange(&c1all, &c2All, &c3All, axt, 0, rsi->size);
addRange(&c1utr5, &c2Utr5, &c3Utr5, axt, 0, rsi->cdsStart);
addRange(&c1cds, &c2Cds, &c3Cds, axt, rsi->cdsStart, rsi->cdsEnd);
addRange(&c1utr3, &c2Utr3, &c3Utr3, axt, rsi->cdsEnd, rsi->size);
/* The +3+1 in the expression below breaks down as so: the
* +3 is to move past the first 'ATG' codon, which is part of
* the Kozak consensus model, not the coding model. The +1
* is so that we look at the 2nd and 3rd bases of the previous
* codon, and the first base of the current codon. */
addCodons(&earlyCod1, axt, rsi->cdsStart+3+1, rsi->cdsStart+1+earlySize);
addCodons(&earlyCod2, axt, rsi->cdsStart+3+2, rsi->cdsStart+2+earlySize);
addCodons(&earlyCod3, axt, rsi->cdsStart+3+3, rsi->cdsStart+3+earlySize);
addCodons(&cod1, axt, rsi->cdsStart+3+1+earlySize, rsi->cdsEnd-5);
addCodons(&cod2, axt, rsi->cdsStart+3+2+earlySize, rsi->cdsEnd-4);
addCodons(&cod3, axt, rsi->cdsStart+3+3+earlySize, rsi->cdsEnd-3);
addCodons(&stop, axt, rsi->cdsEnd-3, rsi->cdsEnd);
}
}
axtFree(&axt);
}
lineFileClose(&lf);
dumpC1(f, &c1all, "c1_all");
dumpC2(f, &c2All, "c2_all");
dumpC3(f, &c3All, "c3_all");
dumpC1(f, &c1utr5, "c1_utr5");
dumpC2(f, &c2Utr5, "c2_utr5");
dumpC3(f, &c3Utr5, "c3_utr5");
dumpC1(f, &c1cds, "c1_cds");
dumpC2(f, &c2Cds, "c2_cds");
dumpC3(f, &c3Cds, "c3_cds");
dumpC1(f, &c1utr3, "c1_utr3");
dumpC2(f, &c2Utr3, "c2_utr3");
dumpC3(f, &c3Utr3, "c3_utr3");
for (i=0; i<10; ++i)
{
sprintf(label, "c1_kozak[%d]", i-5);
dumpC1(f, &c1Kozak[i], label);
sprintf(label, "c2_kozak[%d]", i-5);
dumpC2(f, &c2Kozak[i], label);
}
dumpC3(f, &earlyCod1, "earlyCod1");
dumpC3(f, &earlyCod2, "earlyCod2");
dumpC3(f, &earlyCod3, "earlyCod3");
dumpC3(f, &cod1, "cod1");
dumpC3(f, &cod2, "cod2");
dumpC3(f, &cod3, "cod3");
dumpC3(f, &stop, "stop");
if (predictFile)
{
predict(c1Kozak, &c1all, axtFile, predictFile, rsiHash);
}
}
void checkExp(char *bedFileName, char *tNibDir, char *nibList)
{
struct lineFile *bf = lineFileOpen(bedFileName , TRUE), *af = NULL;
char *row[PSEUDOGENELINK_NUM_COLS] ;
struct pseudoGeneLink *ps;
char *tmpName[512], cmd[512];
struct axt *axtList = NULL, *axt, *mAxt = NULL;
struct dnaSeq *qSeq = NULL, *tSeq = NULL, *seqList = NULL;
struct nibInfo *qNib = NULL, *tNib = NULL;
FILE *op;
int ret;
if (nibHash == NULL)
nibHash = hashNew(0);
while (lineFileNextRow(bf, row, ArraySize(row)))
{
struct misMatch *misMatchList = NULL;
struct binKeeper *bk = NULL;
struct binElement *el, *elist = NULL;
struct psl *mPsl = NULL, *rPsl = NULL, *pPsl = NULL, *psl ;
struct misMatch *mf = NULL;
ps = pseudoGeneLinkLoad(row);
tmpName[0] = cloneString(ps->name);
chopByChar(tmpName[0], '.', tmpName, sizeof(tmpName));
verbose(2,"name %s %s:%d-%d\n",
ps->name, ps->chrom, ps->chromStart,ps->chromEnd);
/* get expressed retro from hash */
bk = hashFindVal(mrnaHash, ps->chrom);
elist = binKeeperFindSorted(bk, ps->chromStart, ps->chromEnd ) ;
for (el = elist; el != NULL ; el = el->next)
{
rPsl = el->val;
verbose(2,"retroGene %s %s:%d-%d\n",rPsl->qName, ps->chrom, ps->chromStart,ps->chromEnd);
}
/* find mrnas that overlap parent gene */
bk = hashFindVal(mrnaHash, ps->gChrom);
elist = binKeeperFindSorted(bk, ps->gStart , ps->gEnd ) ;
for (el = elist; el != NULL ; el = el->next)
{
pPsl = el->val;
verbose(2,"parent %s %s:%d %d,%d\n",
pPsl->qName, pPsl->tName,pPsl->tStart,
pPsl->match, pPsl->misMatch);
}
/* find self chain */
bk = hashFindVal(chainHash, ps->chrom);
elist = binKeeperFind(bk, ps->chromStart , ps->chromEnd ) ;
slSort(&elist, chainCmpScoreDesc);
for (el = elist; el != NULL ; el = el->next)
{
struct chain *chain = el->val, *subChain, *retChainToFree, *retChainToFree2;
int qs = chain->qStart;
int qe = chain->qEnd;
int id = chain->id;
if (chain->qStrand == '-')
{
qs = chain->qSize - chain->qEnd;
qe = chain->qSize - chain->qStart;
}
if (!sameString(chain->qName , ps->gChrom) ||
!positiveRangeIntersection(qs, qe, ps->gStart, ps->gEnd))
{
verbose(2," wrong chain %s:%d-%d %s:%d-%d parent %s:%d-%d\n",
chain->qName, qs, qe,
chain->tName,chain->tStart,chain->tEnd,
ps->gChrom,ps->gStart,ps->gEnd);
continue;
}
verbose(2,"chain id %d %4.0f",chain->id, chain->score);
chainSubsetOnT(chain, ps->chromStart+7, ps->chromEnd-7,
&subChain, &retChainToFree);
if (subChain != NULL)
chain = subChain;
chainSubsetOnQ(chain, ps->gStart, ps->gEnd,
&subChain, &retChainToFree2);
if (subChain != NULL)
chain = subChain;
if (chain->qStrand == '-')
{
qs = chain->qSize - chain->qEnd;
qe = chain->qSize - chain->qStart;
}
verbose(2," %s:%d-%d %s:%d-%d ",
chain->qName, qs, qe,
chain->tName,chain->tStart,chain->tEnd);
if (subChain != NULL)
verbose(2,"subChain %s:%d-%d %s:%d-%d\n",
subChain->qName, subChain->qStart, subChain->qEnd,
subChain->tName,subChain->tStart,subChain->tEnd);
qNib = nibInfoFromCache(nibHash, tNibDir, chain->qName);
tNib = nibInfoFromCache(nibHash, tNibDir, chain->tName);
tSeq = nibInfoLoadStrand(tNib, chain->tStart, chain->tEnd, '+');
qSeq = nibInfoLoadStrand(qNib, chain->qStart, chain->qEnd, chain->qStrand);
axtList = chainToAxt(chain, qSeq, chain->qStart, tSeq, chain->tStart,
maxGap, BIGNUM);
verbose(2,"axt count %d misMatch cnt %d\n",slCount(axtList), slCount(misMatchList));
for (axt = axtList; axt != NULL ; axt = axt->next)
{
addMisMatch(&misMatchList, axt, chain->qSize);
}
verbose(2,"%d in mismatch list %s id %d \n",slCount(misMatchList), chain->qName, id);
chainFree(&retChainToFree);
chainFree(&retChainToFree2);
break;
}
/* create axt of each expressed retroGene to parent gene */
/* get alignment for each mrna overlapping retroGene */
bk = hashFindVal(mrnaHash, ps->chrom);
elist = binKeeperFindSorted(bk, ps->chromStart , ps->chromEnd ) ;
{
char queryName[512];
char axtName[512];
char pslName[512];
safef(queryName, sizeof(queryName), "/tmp/query.%s.fa", ps->chrom);
safef(axtName, sizeof(axtName), "/tmp/tmp.%s.axt", ps->chrom);
safef(pslName, sizeof(pslName), "/tmp/tmp.%s.psl", ps->chrom);
op = fopen(pslName,"w");
for (el = elist ; el != NULL ; el = el->next)
{
psl = el->val;
pslOutput(psl, op, '\t','\n');
qSeq = twoBitReadSeqFrag(twoBitFile, psl->qName, 0, 0);
if (qSeq != NULL)
slAddHead(&seqList, qSeq);
else
errAbort("seq %s not found \n", psl->qName);
}
fclose(op);
faWriteAll(queryName, seqList);
safef(cmd,sizeof(cmd),"pslPretty -long -axt %s %s %s %s",pslName , nibList, queryName, axtName);
ret = system(cmd);
if (ret != 0)
errAbort("ret is %d %s\n",ret,cmd);
verbose(2, "ret is %d %s\n",ret,cmd);
af = lineFileOpen(axtName, TRUE);
while ((axt = axtRead(af)) != NULL)
slAddHead(&mAxt, axt);
lineFileClose(&af);
}
slReverse(&mAxt);
/* for each parent/retro pair, count bases matching retro and parent better */
for (el = elist; el != NULL ; el = el->next)
{
int i, scoreRetro=0, scoreParent=0, scoreNeither=0;
struct dyString *parentMatch = newDyString(16*1024);
struct dyString *retroMatch = newDyString(16*1024);
mPsl = el->val;
if (mAxt != NULL)
{
verbose(2,"mrna %s %s:%d %d,%d axt %s\n",
mPsl->qName, mPsl->tName,mPsl->tStart,
mPsl->match, mPsl->misMatch,
mAxt->qName);
assert(sameString(mPsl->qName, mAxt->qName));
for (i = 0 ; i< (mPsl->tEnd-mPsl->tStart) ; i++)
{
int j = mAxt->tStart - mPsl->tStart;
verbose(5, "listLen = %d\n",slCount(&misMatchList));
if ((mf = matchFound(&misMatchList, (mPsl->tStart)+i)) != NULL)
{
if (toupper(mf->retroBase) == toupper(mAxt->qSym[j+i]))
{
verbose (3,"match retro[%d] %d %c == %c parent %c %d\n",
i,mf->retroLoc, mf->retroBase, mAxt->qSym[j+i],
mf->parentBase, mf->parentLoc);
dyStringPrintf(retroMatch, "%d,", mf->retroLoc);
scoreRetro++;
}
else if (toupper(mf->parentBase) == toupper(mAxt->qSym[j+i]))
{
verbose (3,"match parent[%d] %d %c == %c retro %c %d\n",
i,mf->parentLoc, mf->parentBase, mAxt->qSym[j+i],
mf->retroBase, mf->retroLoc);
dyStringPrintf(parentMatch, "%d,", mf->parentLoc);
scoreParent++;
}
else
{
verbose (3,"match neither[%d] %d %c != %c retro %c %d\n",
i,mf->parentLoc, mf->parentBase, mAxt->tSym[j+i],
mf->retroBase, mf->retroLoc);
scoreNeither++;
}
}
}
verbose(2,"final score %s parent %d retro %d neither %d\n",
mPsl->qName, scoreParent, scoreRetro, scoreNeither);
fprintf(outFile,"%s\t%d\t%d\t%s\t%d\t%s\t%d\t%d\t%s\t%d\t%d\t%d\t%s\t%s\n",
ps->chrom, ps->chromStart, ps->chromEnd, ps->name, ps->score,
mPsl->tName, mPsl->tStart, mPsl->tEnd, mPsl->qName,
scoreParent, scoreRetro, scoreNeither, parentMatch->string, retroMatch->string);
mAxt = mAxt->next;
}
dyStringFree(&parentMatch);
dyStringFree(&retroMatch);
}
}
}
void liftAxt(char *destFile, struct hash *liftHash,
int sourceCount, char *sources[], boolean querySide)
/* Lift up coordinates in .axt file. */
{
FILE *f = mustOpen(destFile, "w");
int sourceIx;
int dotMod = dots;
for (sourceIx = 0; sourceIx < sourceCount; ++sourceIx)
{
char *source = sources[sourceIx];
struct lineFile *lf = lineFileOpen(source, TRUE);
struct axt *axt;
lineFileSetMetaDataOutput(lf, f);
verbose(1, "Lifting %s\n", source);
while ((axt = axtRead(lf)) != NULL)
{
struct liftSpec *spec;
struct axt a = *axt;
char *seqName;
if (querySide)
seqName = a.qName;
else
seqName = a.tName;
spec = findLift(liftHash, seqName, lf);
if (spec == NULL)
{
if (how != carryMissing)
{
axtFree(&axt);
continue;
}
}
else
{
int offset;
char strand = (querySide ? a.qStrand : a.tStrand);
cantHandleSpecRevStrand(spec);
if (strand == '-')
{
int ctgEnd = spec->offset + spec->oldSize;
offset = spec->newSize - ctgEnd;
}
else
offset = spec->offset;
if (querySide)
{
a.qStart += offset;
a.qEnd += offset;
a.qName = spec->newName;
}
else
{
a.tStart += offset;
a.tEnd += offset;
a.tName = spec->newName;
if (strand == '-')
warn("Target minus strand, please double check results.");
}
}
axtWrite(&a, f);
axtFree(&axt);
doDots(&dotMod);
}
lineFileClose(&lf);
if (dots)
verbose(1, "\n");
}
}
void axtHiQualDiffs(char *axtFile, struct hash *qacHash, FILE *f)
/* Write out high quality diffs in axtFile to f. */
{
char *qName = cloneString("");
UBYTE *qQuals = NULL;
UBYTE *quals = NULL;
struct qac *qac = NULL;
struct axt *axt = NULL;
struct lineFile *lf = lineFileOpen(axtFile, TRUE);
int qStart, qDir, qPos, qWinStart, qWinEnd, tPos;
int qWinSize = optionInt("winSize", 11);
int qQualMin = optionInt("diffQualMin", 30);
int qWinQualMin = optionInt("winQualMin", 25);
int qWinMaxDiff = optionInt("winMaxDiff", 2);
boolean qIndelOk = optionExists("indelOk");
boolean qIgnore98 = optionExists("ignore98");
boolean chimpPos = optionExists("chimpPos");
int qHalfWinSize = qWinSize/2;
while ((axt = axtRead(lf)) != NULL)
{
char *qSym = axt->qSym, *tSym = axt->tSym;
int symIx, symCount = axt->symCount;
char qc,tc;
toUpperN(qSym, symCount);
toUpperN(tSym, symCount);
if (!sameString(axt->qName, qName))
{
freez(&qName);
qName = cloneString(axt->qName);
qac = hashMustFindVal(qacHash, qName);
freez(&qQuals);
qQuals = needHugeMem(qac->uncSize);
rleUncompress(qac->data, qac->compSize, qQuals, qac->uncSize);
}
if (axt->qStrand == '+')
{
qStart = axt->qStart;
qDir = 1;
}
else
{
qStart = qac->uncSize - axt->qStart - 1;
qDir = -1;
}
qPos = qStart;
tPos = axt->tStart;
for (symIx = 0; symIx < symCount; ++symIx)
{
qc = qSym[symIx];
tc = tSym[symIx];
if (qc == '-')
tPos += 1;
else if (tc == '-')
qPos += qDir;
else
{
if (qc != tc)
{
qWinStart = qPos - qHalfWinSize;
qWinEnd = qWinStart + qWinSize;
if (qWinStart >= 0 && qWinEnd < qac->uncSize)
{
if (qQuals[qPos] >= qQualMin)
{
int i;
boolean ok = TRUE;
for (i = qWinStart; i<qWinEnd; ++i)
if (qQuals[i] < qWinQualMin)
{
ok = FALSE;
break;
}
if (ok)
{
int diffCount = 0;
int symWinStart = symIx - qHalfWinSize;
int symWinEnd = symWinStart + qWinSize;
for (i=symWinStart; i < symWinEnd; ++i)
{
qc = qSym[i];
tc = tSym[i];
if (qc == '-' || tc == '-')
{
ok = FALSE;
break;
}
if (qc != tc)
++diffCount;
}
if (ok && diffCount <= qWinMaxDiff && (!qIgnore98 || qQuals[qPos] != 98) )
{
if (chimpPos)
fprintf(f, "%s\t%d\t%d\t%c\t%c\t%s\t%d\t%d\n",
axt->tName, tPos, tPos+1, tSym[symIx], qSym[symIx], axt->qName, qPos, qPos+1);
else
fprintf(f, "%s\t%d\t%d\t%c\t%c\n",
axt->tName, tPos, tPos+1, tSym[symIx], qSym[symIx]);
}
}
}
}
}
qPos += qDir;
tPos += 1;
}
}
axtFree(&axt);
}
lineFileClose(&lf);
}
void axtCalcMatrix(int fileCount, char *files[])
/* axtCalcMatrix - Calculate substitution matrix and make indel histogram. */
{
int *histIns, *histDel, *histPerfect, *histGapless, *histT, *histQ;
int maxInDel = optionInt("maxInsert", 21);
static int matrix[4][4];
static char bestGapless[256], bestPerfect[256];
int i, j, total = 0;
double scale;
int fileIx;
struct axt *axt;
static int trans[4] = {A_BASE_VAL, C_BASE_VAL, G_BASE_VAL, T_BASE_VAL};
static char *bases[4] = {"A", "C", "G", "T"};
int totalT = 0, totalMatch = 0, totalMismatch = 0,
tGapStart = 0, tGapExt=0, qGapStart = 0, qGapExt = 0;
AllocArray(histIns, maxInDel+1);
AllocArray(histDel, maxInDel+1);
AllocArray(histPerfect, maxPerfect+1);
AllocArray(histGapless, maxPerfect+1);
AllocArray(histT, maxInDel+1);
AllocArray(histQ, maxInDel+1);
for (fileIx = 0; fileIx < fileCount; ++fileIx)
{
char *fileName = files[fileIx];
struct lineFile *lf = lineFileOpen(fileName, TRUE);
while ((axt = axtRead(lf)) != NULL)
{
totalT += axt->tEnd - axt->tStart;
addMatrix(matrix, axt->tSym, axt->qSym, axt->symCount);
addInsert(histIns, maxInDel, axt->tSym, axt->symCount,
&tGapStart, &tGapExt);
addInsert(histDel, maxInDel, axt->qSym, axt->symCount,
&qGapStart, &qGapExt);
addPerfect(axt, histPerfect, maxPerfect,
axt->qSym, axt->tSym, axt->symCount, bestPerfect);
addGapless(axt, histGapless, maxPerfect,
axt->qSym, axt->tSym, axt->symCount, bestGapless);
axtFree(&axt);
}
lineFileClose(&lf);
}
printf(" ");
for (i=0; i<4; ++i)
printf("%5s ", bases[i]);
printf("\n");
for (i=0; i<4; ++i)
{
for (j=0; j<4; ++j)
{
int one = matrix[i][j];
total += matrix[i][j];
if (i == j)
totalMatch += one;
else
totalMismatch += one;
}
}
scale = 1.0 / total;
for (i=0; i<4; ++i)
{
int it = trans[i];
printf(" %s", bases[i]);
for (j=0; j<4; ++j)
{
int jt = trans[j];
printf(" %5.4f", matrix[it][jt] * scale);
}
printf("\n");
}
printf("\n");
for (i=1; i<21; ++i)
{
if (i == 20)
printf(">=");
printf("%2d %6.4f%% %6.4f%%\n", i, 100.0*histIns[i]/totalT,
100.0*histDel[i]/totalT);
}
#ifdef OLD
for (i=0; i<100; i += 10)
{
int delSum = 0, insSum=0, perfectSum = 0, perfectBaseSum = 0;
for (j=0; j<10; ++j)
{
int ix = i+j;
insSum += histIns[ix];
delSum += histDel[ix];
perfectSum += histPerfect[ix];
perfectBaseSum += histPerfect[ix] * ix;
}
printf("%2d to %2d: %6.4f%% %6.4f%% %6d %7d\n", i, i+9,
100.0*insSum/totalT, 100.0*delSum/totalT, perfectSum, perfectBaseSum);
}
for (i=0; i<1000; i += 100)
{
int delSum = 0, insSum=0, perfectSum = 0, perfectBaseSum = 0;
for (j=0; j<100; ++j)
{
int ix = i+j;
int ins = histIns[ix];
int del = histDel[ix];
both = ins + del;
insSum += ins;
delSum += del;
perfectSum += histPerfect[ix];
perfectBaseSum += histPerfect[ix] * ix;
}
printf("%3d to %3d: %6.4f%% %6.4f%% %6d %7d\n", i, i+99,
100.0*insSum/totalT, 100.0*delSum/totalT, perfectSum, perfectBaseSum);
}
printf(">1000 %6.4f%% %6.4f%% %6d %7d\n",
100.0*histIns[1000]/totalT, 100.0*histDel[1000]/totalT, histPerfect[1000],
histPerfect[1000]*1000);
both = histIns[1000] + histDel[1000];
#endif /* OLD */
printf("\n");
printMedianEtc("perfect", histPerfect, maxPerfect, bestPerfect);
printMedianEtc("gapless", histGapless, maxPerfect, bestGapless);
printf("\n");
printLabeledPercent("totalT: ", totalT, totalT);
printLabeledPercent("matches: ", totalMatch, totalT);
printLabeledPercent("mismatches:", totalMismatch, totalT);
printLabeledPercent("tGapStart: ", tGapStart, totalT);
printLabeledPercent("qGapStart: ", qGapStart, totalT);
printLabeledPercent("tGapExt: ", tGapExt, totalT);
printLabeledPercent("qGapExt: ", qGapExt, totalT);
printLabeledPercent("baseId: ", totalMatch, totalMatch+totalMismatch);
}