void mafMeFirst(char *inMaf, char *meFile, char *outMaf)
/* mafMeFirst - Move component to top if it is one of the named ones. Useful
* in conjunction with mafFrags when you don't want the one with the gene name
* to be in the middle.. */
{
struct hash *meHash = hashWordsInFile(meFile, 18);
struct mafFile *mf = mafOpen(inMaf);
FILE *f = mustOpen(outMaf, "w");
mafWriteStart(f, mf->scoring);
struct mafAli *maf;
while ((maf = mafNext(mf)) != NULL)
{
struct mafComp *comp = compInHash(maf, meHash);
if (comp == NULL)
errAbort("No components in %s in maf ending line %d of %s",
meFile, mf->lf->lineIx, mf->lf->fileName);
slRemoveEl(&maf->components, comp);
slAddHead(&maf->components, comp);
mafWrite(f, maf);
mafAliFree(&maf);
}
mafWriteEnd(f);
carefulClose(&f);
}
void weedLines(char *weedFile, char *file, char *output,
boolean invert, char *invertOutput)
/* weedLines - Selectively remove lines from file. */
{
struct hash *hash = hashWordsInFile(weedFile, 16);
struct hashEl *weedList = hashElListHash(hash);
verbose(2, "%d words in weed file %s\n", hash->elCount, weedFile);
struct lineFile *lf = lineFileOpen(file, TRUE);
char *line, *word;
FILE *f = mustOpen(output, "w");
FILE *fInvert = NULL;
boolean embedded = optionExists("embedded");
if (invertOutput != NULL)
fInvert = mustOpen(invertOutput, "w");
while (lineFileNext(lf, &line, NULL))
{
boolean doWeed = FALSE;
char *dupe = NULL;
if (embedded)
{
struct hashEl *hel;
for (hel = weedList; hel != NULL; hel = hel->next)
{
if (stringIn(hel->name, line))
doWeed = TRUE;
}
}
else
{
dupe = cloneString(line);
while ((word = nextWord(&line)) != NULL)
{
if (hashLookup(hash, word))
doWeed = TRUE;
}
line = dupe;
}
if (invert)
doWeed = !doWeed;
if (!doWeed)
fprintf(f, "%s\n", line);
else
{
if (fInvert != NULL)
fprintf(fInvert, "%s\n", line);
}
freez(&dupe);
}
}
static struct hash *processFieldHash(struct joiner *joiner, char *inName,
char *outName)
/* Read in field hash from file if inName is non-NULL,
* else read from database. If outName is non-NULL,
* save it to file. */
{
struct hash *fieldHash;
if (inName != NULL)
fieldHash = hashWordsInFile(inName, 18);
else
fieldHash = joinerAllFields(joiner);
if (outName != NULL)
{
struct hashEl *el, *list = hashElListHash(fieldHash);
FILE *f = mustOpen(outName, "w");
slSort(&list, hashElCmp);
for (el = list; el != NULL; el = el->next)
fprintf(f, "%s\n", el->name);
slFreeList(&list);
carefulClose(&f);
}
return fieldHash;
}
void txGeneBakeOff(char *database, char *refRevFile, char *refClusterFile, char *geneTrack)
/* txGeneBakeOff - Compare gene finder results to reference annotations.. */
{
hSetDb(database);
/* Make list of our clusters. */
struct refCluster *cluster, *clusterList = refClusterLoadAll(refClusterFile);
/* Make list of only refseqs in reviewed list. */
struct hash *refRevOnlyHash = hashWordsInFile(refRevFile, 16);
struct bed *refAll = bedThickOnlyList(hWholeTrackAsBedList("refGene"));
struct bed *refList = NULL, *nextRef, *ref;
struct hash *refBedHash = hashNew(18);
for (ref = refAll; ref != NULL; ref = nextRef)
{
nextRef = ref->next;
if (hashLookup(refRevOnlyHash, ref->name))
{
slAddHead(&refList, ref);
hashAdd(refBedHash, ref->name, ref);
}
}
verbose(2, "%d of %d reviewed are still in refGene track\n",
slCount(refList), refRevOnlyHash->elCount);
/* Turn this into hash. */
struct hash *refHash = bedsIntoKeeperHash(refList);
verbose(2, "Loaded %d items from %s into %d chromosomes\n",
slCount(refList), refRevFile, refHash->elCount);
struct bed *geneList = bedThickOnlyList(hWholeTrackAsBedList(geneTrack));
struct hash *geneHash = bedsIntoKeeperHash(geneList);
verbose(2, "Loaded %d items from %s into %d chromosomes\n",
slCount(geneList), geneTrack, geneHash->elCount);
int allCount = 0, allMiss = 0;
int allExact = 0, allClose = 0, allHalf = 0, allAny = 0;
// struct hash *uniqHash = hashNew(0);
for (ref = refList; ref != NULL; ref = ref->next)
{
double ratio;
struct bed *gene = mostOverlappingBed(ref, geneHash, &ratio);
if (gene != NULL)
{
++allAny;
if (ratio == 1.0)
++allExact;
else if (ratio >= 0.80)
++allClose;
else if (ratio >= 0.50)
++allHalf;
}
else
++allMiss;
++allCount;
}
printf("Exact match: %d (%4.2f%%)\n", allExact, 100.0 * allExact/allCount);
printf("80%% match: %d (%4.2f%%)\n", allClose, 100.0 * allClose/allCount);
//printf("50%% match: %d (%4.2f%%)\n", allHalf, 100.0 * allHalf/allCount);
//printf("any match: %d (%4.2f%%)\n", allAny, 100.0 * allAny/allCount);
//printf("Clean miss: %d (%4.2f%%)\n", allMiss, 100.0 * allMiss/allCount);
int anyCount = 0, anyMiss = 0;
int anyExact = 0, anyClose = 0, anyHalf = 0, anyAny = 0;
for (cluster = clusterList; cluster != NULL; cluster = cluster->next)
{
struct bed *gene, *ref;
double ratio;
if (findMostOverlappingInCluster(cluster, geneHash, refBedHash, &gene, &ref, &ratio))
{
++anyAny;
if (ratio == 1.0)
++anyExact;
else if (ratio >= 0.80)
++anyClose;
else if (ratio >= 0.50)
++anyHalf;
}
else
++anyMiss;
++anyCount;
}
// printf("Total reviewed clusters: %d\n", anyCount);
printf("Exact match any: %d (%4.2f%%)\n", anyExact, 100.0 * anyExact/anyCount);
printf("80%% match any: %d (%4.2f%%)\n", anyClose, 100.0 * anyClose/anyCount);
// printf("50%% match any: %d (%4.2f%%)\n", anyHalf, 100.0 * anyHalf/anyCount);
// printf("any match any: %d (%4.2f%%)\n", anyAny, 100.0 * anyAny/anyCount);
// printf("Clean miss any: %d (%4.2f%%)\n", anyMiss, 100.0 * anyMiss/anyCount);
printf("Base coverage: (%4.2f%%)\n", 100.0*calcBaseCoverage(refHash, geneHash));
}
void txInfoAssemble(char *txBedFile, char *cdsEvFile, char *txCdsPredictFile, char *altSpliceFile,
char *exceptionFile, char *sizePolyAFile, char *pslFile, char *flipFile, char *outFile)
/* txInfoAssemble - Assemble information from various sources into txInfo table.. */
{
/* Build up hash of evidence keyed by transcript name. */
struct hash *cdsEvHash = hashNew(18);
struct cdsEvidence *cdsEv, *cdsEvList = cdsEvidenceLoadAll(cdsEvFile);
for (cdsEv = cdsEvList; cdsEv != NULL; cdsEv = cdsEv->next)
hashAddUnique(cdsEvHash, cdsEv->name, cdsEv);
verbose(2, "Loaded %d elements from %s\n", cdsEvHash->elCount, cdsEvFile);
/* Build up hash of bestorf structures keyed by transcript name */
struct hash *predictHash = hashNew(18);
struct cdsEvidence *predict, *predictList = cdsEvidenceLoadAll(txCdsPredictFile);
for (predict = predictList; predict != NULL; predict = predict->next)
hashAddUnique(predictHash, predict->name, predict);
verbose(2, "Loaded %d predicts from %s\n", predictHash->elCount, txCdsPredictFile);
/* Build up structure for random access of retained introns */
struct bed *altSpliceList = bedLoadNAll(altSpliceFile, 6);
verbose(2, "Loaded %d alts from %s\n", slCount(altSpliceList), altSpliceFile);
struct hash *altSpliceHash = bedsIntoHashOfKeepers(altSpliceList);
/* Read in exception info. */
struct hash *selenocysteineHash, *altStartHash;
genbankExceptionsHash(exceptionFile, &selenocysteineHash, &altStartHash);
/* Read in polyA sizes */
struct hash *sizePolyAHash = hashNameIntFile(sizePolyAFile);
verbose(2, "Loaded %d from %s\n", sizePolyAHash->elCount, sizePolyAFile);
/* Read in psls */
struct hash *pslHash = hashNew(20);
struct psl *psl, *pslList = pslLoadAll(pslFile);
for (psl = pslList; psl != NULL; psl = psl->next)
hashAdd(pslHash, psl->qName, psl);
verbose(2, "Loaded %d from %s\n", pslHash->elCount, pslFile);
/* Read in accessions that we flipped for better splice sites. */
struct hash *flipHash = hashWordsInFile(flipFile, 0);
/* Open primary gene input and output. */
struct lineFile *lf = lineFileOpen(txBedFile, TRUE);
FILE *f = mustOpen(outFile, "w");
/* Main loop - process each gene */
char *row[12];
while (lineFileRow(lf, row))
{
struct bed *bed = bedLoad12(row);
verbose(3, "Processing %s\n", bed->name);
/* Initialize info to zero */
struct txInfo info;
ZeroVar(&info);
/* Figure out name, sourceAcc, and isRefSeq from bed->name */
info.name = bed->name;
info.category = "n/a";
if (isRfam(bed->name) || stringIn("tRNA", bed->name) != NULL)
{
info.sourceAcc = cloneString(bed->name);
}
else
{
info.sourceAcc = txAccFromTempName(bed->name);
}
info.isRefSeq = startsWith("NM_", info.sourceAcc);
if (startsWith("antibody.", info.sourceAcc)
|| startsWith("CCDS", info.sourceAcc) || isRfam(info.sourceAcc)
|| stringIn("tRNA", info.sourceAcc) != NULL)
{
/* Fake up some things for antibody frag and CCDS that don't have alignments. */
info.sourceSize = bedTotalBlockSize(bed);
info.aliCoverage = 1.0;
info.aliIdRatio = 1.0;
info. genoMapCount = 1;
}
else
{
/* Loop through all psl's associated with our RNA. Figure out
* our overlap with each, and pick best one. */
struct hashEl *hel, *firstPslHel = hashLookup(pslHash, info.sourceAcc);
if (firstPslHel == NULL)
errAbort("%s is not in %s", info.sourceAcc, pslFile);
int mapCount = 0;
struct psl *psl, *bestPsl = NULL;
int coverage, bestCoverage = 0;
boolean isFlipped = (hashLookup(flipHash, info.sourceAcc) != NULL);
for (hel = firstPslHel; hel != NULL; hel = hashLookupNext(hel))
{
psl = hel->val;
mapCount += 1;
coverage = pslBedOverlap(psl, bed);
if (coverage > bestCoverage)
{
bestCoverage = coverage;
bestPsl = psl;
}
/* If we flipped it, try it on the opposite strand too. */
if (isFlipped)
{
psl->strand[0] = (psl->strand[0] == '+' ? '-' : '+');
coverage = pslBedOverlap(psl, bed);
if (coverage > bestCoverage)
{
bestCoverage = coverage;
bestPsl = psl;
}
psl->strand[0] = (psl->strand[0] == '+' ? '-' : '+');
}
}
if (bestPsl == NULL)
errAbort("%s has no overlapping alignments with %s in %s",
bed->name, info.sourceAcc, pslFile);
/* Figure out and save alignment statistics. */
int polyA = hashIntValDefault(sizePolyAHash, bed->name, 0);
info.sourceSize = bestPsl->qSize - polyA;
info.aliCoverage = (double)bestCoverage / info.sourceSize;
info.aliIdRatio = (double)(bestPsl->match + bestPsl->repMatch)/
(bestPsl->match + bestPsl->misMatch + bestPsl->repMatch);
info. genoMapCount = mapCount;
}
/* Get orf size and start/end complete from cdsEv. */
if (bed->thickStart < bed->thickEnd)
{
cdsEv = hashFindVal(cdsEvHash, bed->name);
if (cdsEv != NULL)
{
info.orfSize = cdsEv->end - cdsEv->start;
info.startComplete = cdsEv->startComplete;
info.endComplete = cdsEv->endComplete;
}
}
/* Get score from prediction. */
predict = hashFindVal(predictHash, bed->name);
if (predict != NULL)
info.cdsScore = predict->score;
/* Figure out nonsense-mediated-decay from bed itself. */
info.nonsenseMediatedDecay = isNonsenseMediatedDecayTarget(bed);
/* Figure out if retained intron from bed and alt-splice keeper hash */
info.retainedIntron = hasRetainedIntron(bed, altSpliceHash);
info.strangeSplice = countStrangeSplices(bed, altSpliceHash);
info.atacIntrons = countAtacIntrons(bed, altSpliceHash);
info.bleedIntoIntron = addIntronBleed(bed, altSpliceHash);
/* Look up selenocysteine info. */
info.selenocysteine = (hashLookup(selenocysteineHash, bed->name) != NULL);
/* Loop through bed looking for small gaps indicative of frame shift/stop */
int i, lastBlock = bed->blockCount-1;
int exonCount = 1;
for (i=0; i < lastBlock; ++i)
{
int gapStart = bed->chromStarts[i] + bed->blockSizes[i];
int gapEnd = bed->chromStarts[i+1];
int gapSize = gapEnd - gapStart;
switch (gapSize)
{
case 1:
case 2:
info.genomicFrameShift = TRUE;
break;
case 3:
info.genomicStop = TRUE;
break;
default:
exonCount += 1;
break;
}
}
info.exonCount = exonCount;
/* Write info, free bed. */
txInfoTabOut(&info, f);
bedFree(&bed);
}
/* Clean up and go home. */
carefulClose(&f);
}
