int putInNameTable(struct hash *hash, FILE *f, char *name)
/* Add to name table if it isn't there already.
* Return ID of name in table. */
{
struct hashEl *hel;
if (name == NULL)
return 0;
if ((hel = hashLookup(hash, name)) != NULL)
return ptToInt(hel->val);
else
{
// It appears like this program is dead code that is no longer used.
// I don't want to make a potential bogus change to track the removal
// of hgNextId(), so a landmine is added. Code can be change to determine
// max id from table if ever needed. markd 2010-12-15
#if 1
errAbort("code hasn't been updated to work, please see markd");
return 0;
#else
int id = hgNextId();
fprintf(f, "%u\t%s\n", id, name);
hashAdd(hash, name, intToPt(id));
return id;
#endif
}
}
struct hash *optionalFieldsHash()
/* Return hash of terms we have tables for. */
{
struct hash *hash = hashNew(8);
int i;
for (i=0; i<ArraySize(expOptionalFields); ++i)
hashAdd(hash, expOptionalFields[i], intToPt(i));
return hash;
}
void addCountsToHash(struct hash *countHash, struct bed *bedList)
/* Add up the ones we find in the bed to the count hash. */
{
struct bed *bed;
for (bed = bedList; bed != NULL; bed = bed->next)
{
struct hashEl *el = hashLookup(countHash, bed->name);
int newCount = ptToInt(el->val) + 1;
el->val = intToPt(newCount);
}
}
void addFreqToHash(struct hash *freqHash, char *tag, char *id, int val)
/* Add the frequency to the end of the list in the hash. */
/* This is done at each line in the frequencies file. */
{
struct hashEl *el = hashStore(freqHash, tag);
struct slPair *newOne;
struct slPair **pList = (struct slPair **)&el->val;
AllocVar(newOne);
newOne->name = cloneString(id);
newOne->val = intToPt(val);
slAddHead(pList, newOne);
}
static void handleNoMapping(struct spMapper *sm, char *id, char reason)
/* record id that can't be mapped */
{
struct hashEl *hel = hashStore(sm->noMapTbl, id);
if (hel->val == NULL)
{
if (reason == noUnirefMapping)
sm->noUnirefMapCnt++;
else if (reason == noKGMapping)
sm->noSpIdMapCnt++;
}
hel->val = intToPt(reason);
}
struct hash *hashRowOffsets(char *line)
/* Given a space-delimited line, create a hash keyed by the words in
* line with values the position of the word (0 based) in line */
{
struct hash *hash = hashNew(0);
char *word;
int wordIx = 0;
while ((word = nextWord(&line)) != 0)
{
hashAdd(hash, word, intToPt(wordIx));
wordIx += 1;
}
return hash;
}
void loadCoverQSizes(char* coverQSizeFile)
/* load coverage query sizes */
{
struct lineFile *lf = lineFileOpen(coverQSizeFile, TRUE);
char *row[2];
coverQSizes = hashNew(0);
while (lineFileNextRowTab(lf, row, ArraySize(row)))
{
int qSize = sqlSigned(row[1]);
hashAdd(coverQSizes, row[0], intToPt(qSize));
}
lineFileClose(&lf);
}
static void addSize(char *name, unsigned size, struct hash *sizes)
/* add a name and size */
{
struct hashEl *hel = hashLookup(sizes, name);
if (hel != NULL)
{
/* size must be the same if duplicated */
if (ptToInt(hel->val) != size)
errAbort("sequence %s already specified as size %d, can't set to %d",
name, ptToInt(hel->val), size);
}
else
hashAdd(sizes, name, intToPt(size));
}
struct hash *loadNameTable(struct sqlConnection *conn,
char *tableName, int hashSize)
/* Create a hash and load it up from table. */
{
char query[128];
struct sqlResult *sr;
char **row;
struct hash *hash = newHash(hashSize);
sqlSafef(query, sizeof query, "select id,name from %s", tableName);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
hashAdd(hash, row[1], intToPt(sqlUnsigned(row[0])));
}
sqlFreeResult(&sr);
return hash;
}
struct hash *readSizes(char *fileName)
/* Read tab-separated file into hash with
* name key size value. */
{
struct lineFile *lf = lineFileOpen(fileName, TRUE);
struct hash *hash = newHash(0);
char *row[2];
while (lineFileRow(lf, row))
{
char *name = row[0];
int size = lineFileNeedNum(lf, row, 1);
/* trust the user to not have duplicated names in the lengths file */
hashAdd(hash, name, intToPt(size));
}
lineFileClose(&lf);
return hash;
}
static char *findUniqueName(struct hash *dupeHash, char *root)
/* If root name is already in hash, return root_1, root_2
* or something like that. */
{
struct hashEl *hel;
if ((hel = hashLookup(dupeHash, root)) == NULL)
{
hashAddInt(dupeHash, root, 1);
return root;
}
else
{
static char buf[256];
int val = ptToInt(hel->val) + 1;
hel->val = intToPt(val);
safef(buf, sizeof(buf), "%s_%d", root, val);
return buf;
}
}
struct hash *readSizes(char *fileName)
/* Read tab-separated file into hash with
* name key size value. */
{
struct lineFile *lf = lineFileOpen(fileName, TRUE);
struct hash *hash = newHash(0);
char *row[2];
while (lineFileRow(lf, row))
{
char *name = row[0];
int size = lineFileNeedNum(lf, row, 1);
if (hashLookup(hash, name) != NULL)
warn("Duplicate %s, ignoring all but first\n", name);
else
hashAdd(hash, name, intToPt(size));
}
lineFileClose(&lf);
return hash;
}
void consolidateTheCounts(char *inputFile, char *outputFile)
/* Read the cat'ed file in, and either make a new hash item for each enzyme */
/* encountered on each line, or add to an existing one. Then output the hash. */
{
struct lineFile *lf = lineFileOpen(inputFile, TRUE);
struct hash *countHash = newHash(12);
char *words[2];
while (lineFileRow(lf, words))
{
char *name = words[0];
int count = lineFileNeedFullNum(lf, words, 1);
struct hashEl *el = hashLookup(countHash, name);
if (!el)
hashAddInt(countHash, name, count);
else
el->val = intToPt(ptToInt(el->val) + count);
}
writeHashToFile(countHash, outputFile);
freeHash(&countHash);
}
int oneHubTrackSettings(char *hubUrl, struct hash *totals)
/* Read hub trackDb files, noting settings used */
{
struct trackHub *hub = NULL;
struct errCatch *errCatch = errCatchNew();
if (errCatchStart(errCatch))
hub = trackHubOpen(hubUrl, "hub_0");
errCatchEnd(errCatch);
errCatchFree(&errCatch);
if (hub == NULL)
return 1;
printf("%s (%s)\n", hubUrl, hub->shortLabel);
struct trackHubGenome *genome;
struct hash *counts;
if (totals)
counts = totals;
else
counts = newHash(0);
struct hashEl *el;
for (genome = hub->genomeList; genome != NULL; genome = genome->next)
{
struct trackDb *tdb, *tdbs = trackHubTracksForGenome(hub, genome);
for (tdb = tdbs; tdb != NULL; tdb = tdb->next)
{
struct hashCookie cookie = hashFirst(trackDbHashSettings(tdb));
verbose(2, " track: %s\n", tdb->shortLabel);
while ((el = hashNext(&cookie)) != NULL)
{
int count = hashIntValDefault(counts, el->name, 0);
count++;
hashReplace(counts, el->name, intToPt(count));
}
}
}
if (!totals)
printCounts(counts);
trackHubClose(&hub);
return 0;
}
struct hash *posHashFromTable(struct sqlConnection *conn, char *table)
/* Store name, chrom, chromStart in a hash of slPairs. (cheap) */
{
struct hash *posHash = newHash(24);
struct sqlResult *sr = NULL;
char query[256];
char **row;
sqlSafef(query, sizeof(query), "select name,chrom,chromStart from %s", table);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
int chromStart = (int)sqlUnsigned(row[2]);
struct slPair *pair;
AllocVar(pair);
pair->name = cloneString(row[1]);
pair->val = intToPt(chromStart);
hashAdd(posHash, row[0], pair);
}
sqlFreeResult(&sr);
return posHash;
}
void bioImageLoad(char *setRaFile, char *itemTabFile)
/* bioImageLoad - Load data into bioImage database. */
{
struct hash *raHash = raReadSingle(setRaFile);
struct hash *rowHash;
struct lineFile *lf = lineFileOpen(itemTabFile, TRUE);
char *line, *words[256];
struct sqlConnection *conn = sqlConnect(database);
int rowSize;
int submissionSetId;
struct hash *fullDirHash = newHash(0);
struct hash *screenDirHash = newHash(0);
struct hash *thumbDirHash = newHash(0);
struct hash *treatmentHash = newHash(0);
struct hash *bodyPartHash = newHash(0);
struct hash *sliceTypeHash = newHash(0);
struct hash *imageTypeHash = newHash(0);
struct hash *sectionSetHash = newHash(0);
struct dyString *dy = dyStringNew(0);
/* Read first line of tab file, and from it get all the field names. */
if (!lineFileNext(lf, &line, NULL))
errAbort("%s appears to be empty", lf->fileName);
if (line[0] != '#')
errAbort("First line of %s needs to start with #, and then contain field names",
lf->fileName);
rowHash = hashRowOffsets(line+1);
rowSize = rowHash->elCount;
if (rowSize >= ArraySize(words))
errAbort("Too many fields in %s", lf->fileName);
/* Check that have all required fields */
{
char *fieldName;
int i;
for (i=0; i<ArraySize(requiredSetFields); ++i)
{
fieldName = requiredSetFields[i];
if (!hashLookup(raHash, fieldName))
errAbort("Field %s is not in %s", fieldName, setRaFile);
}
for (i=0; i<ArraySize(requiredItemFields); ++i)
{
fieldName = requiredItemFields[i];
if (!hashLookup(rowHash, fieldName))
errAbort("Field %s is not in %s", fieldName, itemTabFile);
}
for (i=0; i<ArraySize(requiredFields); ++i)
{
fieldName = requiredFields[i];
if (!hashLookup(rowHash, fieldName) && !hashLookup(raHash, fieldName))
errAbort("Field %s is not in %s or %s", fieldName, setRaFile, itemTabFile);
}
}
/* Create/find submission record. */
submissionSetId = saveSubmissionSet(conn, raHash);
/* Process rest of tab file. */
while (lineFileNextRowTab(lf, words, rowSize))
{
int fullDir = cachedId(conn, "location", "name",
fullDirHash, "fullDir", raHash, rowHash, words);
int screenDir = cachedId(conn, "location", "name",
screenDirHash, "screenDir", raHash, rowHash, words);
int thumbDir = cachedId(conn, "location",
"name", thumbDirHash, "thumbDir", raHash, rowHash, words);
int bodyPart = cachedId(conn, "bodyPart",
"name", bodyPartHash, "bodyPart", raHash, rowHash, words);
int sliceType = cachedId(conn, "sliceType",
"name", sliceTypeHash, "sliceType", raHash, rowHash, words);
int imageType = cachedId(conn, "imageType",
"name", imageTypeHash, "imageType", raHash, rowHash, words);
int treatment = cachedId(conn, "treatment",
"conditions", treatmentHash, "treatment", raHash, rowHash, words);
char *fileName = getVal("fileName", raHash, rowHash, words, NULL);
char *submitId = getVal("submitId", raHash, rowHash, words, NULL);
char *taxon = getVal("taxon", raHash, rowHash, words, NULL);
char *isEmbryo = getVal("isEmbryo", raHash, rowHash, words, NULL);
char *age = getVal("age", raHash, rowHash, words, NULL);
char *sectionSet = getVal("sectionSet", raHash, rowHash, words, "");
char *sectionIx = getVal("sectionIx", raHash, rowHash, words, "0");
char *gene = getVal("gene", raHash, rowHash, words, "");
char *locusLink = getVal("locusLink", raHash, rowHash, words, "");
char *refSeq = getVal("refSeq", raHash, rowHash, words, "");
char *genbank = getVal("genbank", raHash, rowHash, words, "");
char *priority = getVal("priority", raHash, rowHash, words, "200");
int sectionId = 0;
int oldId;
// char *xzy = getVal("xzy", raHash, rowHash, words, xzy);
if (sectionSet[0] != 0 && !sameString(sectionSet, "0"))
{
struct hashEl *hel = hashLookup(sectionSetHash, sectionSet);
if (hel != NULL)
sectionId = ptToInt(hel->val);
else
{
sqlUpdate(conn, "insert into sectionSet values(default)");
sectionId = sqlLastAutoId(conn);
hashAdd(sectionSetHash, sectionSet, intToPt(sectionId));
}
}
dyStringClear(dy);
dyStringAppend(dy, "select id from image ");
dyStringPrintf(dy, "where fileName = '%s' ", fileName);
dyStringPrintf(dy, "and fullLocation = %d", fullDir);
oldId = sqlQuickNum(conn, dy->string);
if (oldId != 0)
{
if (replace)
{
dyStringClear(dy);
dyStringPrintf(dy, "delete from image where id = %d", oldId);
sqlUpdate(conn, dy->string);
}
else
errAbort("%s is already in database line %d of %s",
fileName, lf->lineIx, lf->fileName);
}
dyStringClear(dy);
dyStringAppend(dy, "insert into image set\n");
dyStringPrintf(dy, " id = default,\n");
dyStringPrintf(dy, " fileName = '%s',\n", fileName);
dyStringPrintf(dy, " fullLocation = %d,\n", fullDir);
dyStringPrintf(dy, " screenLocation = %d,\n", screenDir);
dyStringPrintf(dy, " thumbLocation = %d,\n", thumbDir);
dyStringPrintf(dy, " submissionSet = %d,\n", submissionSetId);
dyStringPrintf(dy, " sectionSet = %d,\n", sectionId);
dyStringPrintf(dy, " sectionIx = %s,\n", sectionIx);
dyStringPrintf(dy, " submitId = '%s',\n", submitId);
dyStringPrintf(dy, " gene = '%s',\n", gene);
dyStringPrintf(dy, " locusLink = '%s',\n", locusLink);
dyStringPrintf(dy, " refSeq = '%s',\n", refSeq);
dyStringPrintf(dy, " genbank = '%s',\n", genbank);
dyStringPrintf(dy, " priority = %s,\n", priority);
dyStringPrintf(dy, " taxon = %s,\n", taxon);
dyStringPrintf(dy, " isEmbryo = %s,\n", isEmbryo);
dyStringPrintf(dy, " age = %s,\n", age);
dyStringPrintf(dy, " bodyPart = %d,\n", bodyPart);
dyStringPrintf(dy, " sliceType = %d,\n", sliceType);
dyStringPrintf(dy, " imageType = %d,\n", imageType);
dyStringPrintf(dy, " treatment = %d\n", treatment);
sqlUpdate(conn, dy->string);
}
}
void processRefSeq(char *database, char *faFile, char *raFile, char *pslFile, char *loc2refFile,
char *pepFile, char *mim2locFile)
/* hgRefSeqMrna - Load refSeq mRNA alignments and other info into
* refSeqGene table. */
{
struct lineFile *lf;
struct hash *raHash, *rsiHash = newHash(0);
struct hash *loc2mimHash = newHash(0);
struct refSeqInfo *rsiList = NULL, *rsi;
char *s, *line, *row[5];
int wordCount, dotMod = 0;
int noLocCount = 0;
int rsiCount = 0;
int noProtCount = 0;
struct psl *psl;
struct sqlConnection *conn = hgStartUpdate(database);
struct hash *productHash = loadNameTable(conn, "productName", 16);
struct hash *geneHash = loadNameTable(conn, "geneName", 16);
char *kgName = "refGene";
FILE *kgTab = hgCreateTabFile(".", kgName);
FILE *productTab = hgCreateTabFile(".", "productName");
FILE *geneTab = hgCreateTabFile(".", "geneName");
FILE *refLinkTab = hgCreateTabFile(".", "refLink");
FILE *refPepTab = hgCreateTabFile(".", "refPep");
FILE *refMrnaTab = hgCreateTabFile(".", "refMrna");
struct exon *exonList = NULL, *exon;
char *answer;
char cond_str[200];
/* Make refLink and other tables table if they don't exist already. */
sqlMaybeMakeTable(conn, "refLink", refLinkTableDef);
sqlUpdate(conn, "NOSQLINJ delete from refLink");
sqlMaybeMakeTable(conn, "refGene", refGeneTableDef);
sqlUpdate(conn, "NOSQLINJ delete from refGene");
sqlMaybeMakeTable(conn, "refPep", refPepTableDef);
sqlUpdate(conn, "NOSQLINJ delete from refPep");
sqlMaybeMakeTable(conn, "refMrna", refMrnaTableDef);
sqlUpdate(conn, "NOSQLINJ delete from refMrna");
/* Scan through locus link to omim ID file and put in hash. */
{
char *row[2];
printf("Scanning %s\n", mim2locFile);
lf = lineFileOpen(mim2locFile, TRUE);
while (lineFileRow(lf, row))
{
hashAdd(loc2mimHash, row[1], intToPt(atoi(row[0])));
}
lineFileClose(&lf);
}
/* Scan through .ra file and make up start of refSeqInfo
* objects in hash and list. */
printf("Scanning %s\n", raFile);
lf = lineFileOpen(raFile, TRUE);
while ((raHash = hashNextRa(lf)) != NULL)
{
if (clDots > 0 && ++dotMod == clDots )
{
dotMod = 0;
dotOut();
}
AllocVar(rsi);
slAddHead(&rsiList, rsi);
if ((s = hashFindVal(raHash, "acc")) == NULL)
errAbort("No acc near line %d of %s", lf->lineIx, lf->fileName);
rsi->mrnaAcc = cloneString(s);
if ((s = hashFindVal(raHash, "siz")) == NULL)
errAbort("No siz near line %d of %s", lf->lineIx, lf->fileName);
rsi->size = atoi(s);
if ((s = hashFindVal(raHash, "gen")) != NULL)
rsi->geneName = cloneString(s);
//!!!else
//!!! warn("No gene name for %s", rsi->mrnaAcc);
if ((s = hashFindVal(raHash, "cds")) != NULL)
parseCds(s, 0, rsi->size, &rsi->cdsStart, &rsi->cdsEnd);
else
rsi->cdsEnd = rsi->size;
if ((s = hashFindVal(raHash, "ngi")) != NULL)
rsi->ngi = atoi(s);
rsi->geneNameId = putInNameTable(geneHash, geneTab, rsi->geneName);
s = hashFindVal(raHash, "pro");
if (s != NULL)
rsi->productName = cloneString(s);
rsi->productNameId = putInNameTable(productHash, productTab, s);
hashAdd(rsiHash, rsi->mrnaAcc, rsi);
freeHashAndVals(&raHash);
}
lineFileClose(&lf);
if (clDots) printf("\n");
/* Scan through loc2ref filling in some gaps in rsi. */
printf("Scanning %s\n", loc2refFile);
lf = lineFileOpen(loc2refFile, TRUE);
while (lineFileNext(lf, &line, NULL))
{
char *mrnaAcc;
if (line[0] == '#')
continue;
wordCount = chopTabs(line, row);
if (wordCount < 5)
errAbort("Expecting at least 5 tab-separated words line %d of %s",
lf->lineIx, lf->fileName);
mrnaAcc = row[1];
mrnaAcc = accWithoutSuffix(mrnaAcc);
if (mrnaAcc[2] != '_')
warn("%s is and odd name %d of %s",
mrnaAcc, lf->lineIx, lf->fileName);
if ((rsi = hashFindVal(rsiHash, mrnaAcc)) != NULL)
{
rsi->locusLinkId = lineFileNeedNum(lf, row, 0);
rsi->omimId = ptToInt(hashFindVal(loc2mimHash, row[0]));
rsi->proteinAcc = cloneString(accWithoutSuffix(row[4]));
}
}
lineFileClose(&lf);
/* Report how many seem to be missing from loc2ref file.
* Write out knownInfo file. */
printf("Writing %s\n", "refLink.tab");
for (rsi = rsiList; rsi != NULL; rsi = rsi->next)
{
++rsiCount;
if (rsi->locusLinkId == 0)
++noLocCount;
if (rsi->proteinAcc == NULL)
++noProtCount;
fprintf(refLinkTab, "%s\t%s\t%s\t%s\t%u\t%u\t%u\t%u\n",
emptyForNull(rsi->geneName),
emptyForNull(rsi->productName),
emptyForNull(rsi->mrnaAcc),
emptyForNull(rsi->proteinAcc),
rsi->geneNameId, rsi->productNameId,
rsi->locusLinkId, rsi->omimId);
}
if (noLocCount)
printf("Missing locusLinkIds for %d of %d\n", noLocCount, rsiCount);
if (noProtCount)
printf("Missing protein accessions for %d of %d\n", noProtCount, rsiCount);
/* Process alignments and write them out as genes. */
lf = pslFileOpen(pslFile);
dotMod = 0;
while ((psl = pslNext(lf)) != NULL)
{
if (hashFindVal(rsiHash, psl->qName) != NULL)
{
if (clDots > 0 && ++dotMod == clDots )
{
dotMod = 0;
dotOut();
}
sqlSafefFrag(cond_str, sizeof cond_str, "extAC='%s'", psl->qName);
answer = sqlGetField(proteinDB, "spXref2", "displayID", cond_str);
if (answer == NULL)
{
fprintf(stderr, "%s NOT FOUND.\n", psl->qName);
fflush(stderr);
}
if (answer != NULL)
{
struct genePred *gp = NULL;
exonList = pslToExonList(psl);
fprintf(kgTab, "%s\t%s\t%c\t%d\t%d\t",
psl->qName, psl->tName, psl->strand[0], psl->tStart, psl->tEnd);
rsi = hashMustFindVal(rsiHash, psl->qName);
gp = genePredFromPsl(psl, rsi->cdsStart, rsi->cdsEnd, genePredStdInsertMergeSize);
if (!gp)
errAbort("Cannot convert psl (%s) to genePred.\n", psl->qName);
fprintf(kgTab, "%d\t%d\t", gp->cdsStart, gp->cdsEnd);
fprintf(kgTab, "%d\t", slCount(exonList));
fflush(kgTab);
for (exon = exonList; exon != NULL; exon = exon->next)
fprintf(kgTab, "%d,", exon->start);
fprintf(kgTab, "\t");
for (exon = exonList; exon != NULL; exon = exon->next)
fprintf(kgTab, "%d,", exon->end);
fprintf(kgTab, "\n");
slFreeList(&exonList);
}
}
else
{
fprintf(stderr, "%s found in psl, but not in .fa or .ra data files.\n", psl->qName);
fflush(stderr);
}
}
if (clDots) printf("\n");
if (!clTest)
{
writeSeqTable(pepFile, refPepTab, FALSE, TRUE);
writeSeqTable(faFile, refMrnaTab, FALSE, FALSE);
}
carefulClose(&kgTab);
carefulClose(&productTab);
carefulClose(&geneTab);
carefulClose(&refLinkTab);
carefulClose(&refPepTab);
carefulClose(&refMrnaTab);
if (!clTest)
{
printf("Loading database with %s\n", kgName);
fflush(stdout);
hgLoadTabFile(conn, ".", kgName, NULL);
printf("Loading database with %s\n", "productName");
fflush(stdout);
hgLoadTabFile(conn, ".", "productName", NULL);
printf("Loading database with %s\n", "geneName");
fflush(stdout);
hgLoadTabFile(conn, ".", "geneName", NULL);
printf("Loading database with %s\n", "refLink");
fflush(stdout);
hgLoadTabFile(conn, ".", "refLink", NULL);
printf("Loading database with %s\n", "refPep");
fflush(stdout);
hgLoadTabFile(conn, ".", "refPep", NULL);
printf("Loading database with %s\n", "refMrna");
fflush(stdout);
hgLoadTabFile(conn, ".", "refMrna", NULL);
}
}
void rangeTreeAddToCoverageDepth(struct rbTree *tree, int start, int end)
/* Add area from start to end to a tree that is being built up to store the
* depth of coverage. Recover coverage back out by looking at ptToInt(range->val)
* on tree elements. */
{
struct range q;
q.start = start;
q.end = end;
struct range *r, *existing = rbTreeFind(tree, &q);
if (existing == NULL)
{
lmAllocVar(tree->lm, r);
r->start = start;
r->end = end;
r->val = intToPt(1);
rbTreeAdd(tree, r);
}
else
{
if (existing->start <= start && existing->end >= end)
/* The existing one completely encompasses us */
{
/* Make a new section for the bit before start. */
if (existing->start < start)
{
lmAllocVar(tree->lm, r);
r->start = existing->start;
r->end = start;
r->val = existing->val;
existing->start = start;
rbTreeAdd(tree, r);
}
/* Make a new section for the bit after end. */
if (existing->end > end)
{
lmAllocVar(tree->lm, r);
r->start = end;
r->end = existing->end;
r->val = existing->val;
existing->end = end;
rbTreeAdd(tree, r);
}
/* Increment existing section in overlapping area. */
existing->val = (char *)(existing->val) + 1;
}
else
/* In general case fetch list of regions that overlap us.
Remaining cases to handle are:
r >> e rrrrrrrrrrrrrrrrrrrr
eeeeeeeeee
e < r rrrrrrrrrrrrrrr
eeeeeeeeeeee
r < e rrrrrrrrrrrr
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*/
{
struct range *existingList = rangeTreeAllOverlapping(tree, start, end);
#ifdef DEBUG
/* Make sure that list is really sorted for debugging... */
int lastStart = existingList->start;
for (r = existingList; r != NULL; r = r->next)
{
int start = r->start;
if (start < lastStart)
internalErr();
}
#endif /* DEBUG */
int s = start, e = end;
for (existing = existingList; existing != NULL; existing = existing->next)
{
/* Deal with start of new range that comes before existing */
if (s < existing->start)
{
lmAllocVar(tree->lm, r);
r->start = s;
r->end = existing->start;
r->val = intToPt(1);
s = existing->start;
rbTreeAdd(tree, r);
}
else if (s > existing->start)
{
lmAllocVar(tree->lm, r);
r->start = existing->start;
r->end = s;
r->val = existing->val;
existing->start = s;
rbTreeAdd(tree, r);
}
existing->val = (char *)(existing->val) + 1;
s = existing->end;
}
if (s < e)
/* Deal with end of new range that doesn't overlap with anything. */
{
lmAllocVar(tree->lm, r);
r->start = s;
r->end = e;
r->val = intToPt(1);
rbTreeAdd(tree, r);
}
}
}
}
static int bedToGffLines(struct bed *bedList, struct slName *exonFramesList, struct hTableInfo *hti,
int fieldCount, char *source, boolean gtf2StopCodons)
/* Translate a (list of) bed into gff and print out.
* Note that field count (perhaps reduced by bitwise intersection)
* can in effect override hti. */
{
if (! bedList)
return 0;
struct hash *nameHash = newHash(20);
struct bed *bed;
struct slName *exonFrames = exonFramesList;
int i, exonStart, exonEnd;
char txName[256];
int itemCount = 0;
static int namelessIx = 0;
for (bed = bedList; bed != NULL; bed = bed->next)
{
/* Enforce unique transcript_ids. */
if (bed->name != NULL)
{
struct hashEl *hel = hashLookup(nameHash, bed->name);
int dupCount = (hel != NULL ? ptToInt(hel->val) : 0);
if (dupCount > 0)
{
safef(txName, sizeof(txName), "%s_dup%d", bed->name, dupCount);
hel->val = intToPt(dupCount + 1);
}
else
{
safef(txName, sizeof(txName), "%s", bed->name);
hashAddInt(nameHash, bed->name, 1);
}
}
else
safef(txName, sizeof(txName), "tx%d", ++namelessIx);
if (hti->hasBlocks && hti->hasCDS && fieldCount > 4)
{
/* first pass: compute frames, in order dictated by strand. */
int startIndx = 0, stopIndx = 0;
char *frames = NULL;
char *ef = NULL;
if (exonFramesList)
ef = exonFrames->name;
frames = computeFrames(bed, ef, &startIndx, &stopIndx);
/* second pass: one exon (possibly CDS, start/stop_codon) per block. */
for (i=0; i < bed->blockCount; i++)
{
exonStart = bed->chromStart + bed->chromStarts[i];
exonEnd = exonStart + bed->blockSizes[i];
if ((exonStart < bed->thickEnd) && (exonEnd > bed->thickStart))
{
int exonCdsStart = max(exonStart, bed->thickStart);
int exonCdsEnd = min(exonEnd, bed->thickEnd);
addCdsStartStop(bed, source, exonCdsStart, exonCdsEnd,
frames, i, startIndx, stopIndx, gtf2StopCodons, txName);
}
addGffLineFromBed(bed, source, "exon", exonStart, exonEnd, '.', txName);
}
freeMem(frames);
}
else if (hti->hasBlocks && fieldCount > 4)
{
for (i=0; i < bed->blockCount; i++)
{
exonStart = bed->chromStart + bed->chromStarts[i];
exonEnd = exonStart + bed->blockSizes[i];
addGffLineFromBed(bed, source, "exon", exonStart, exonEnd, '.', txName);
}
}
else if (hti->hasCDS && fieldCount > 4)
{
if (bed->thickStart == 0 && bed->thickEnd == 0)
bed->thickStart = bed->thickEnd = bed->chromStart;
if (bed->thickStart > bed->chromStart)
{
addGffLineFromBed(bed, source, "exon", bed->chromStart, bed->thickStart, '.', txName);
}
if (bed->thickEnd > bed->thickStart)
addGffLineFromBed(bed, source, "CDS", bed->thickStart, bed->thickEnd, '0', txName);
if (bed->thickEnd < bed->chromEnd)
{
addGffLineFromBed(bed, source, "exon", bed->thickEnd, bed->chromEnd, '.', txName);
}
}
else
{
addGffLineFromBed(bed, source, "exon", bed->chromStart, bed->chromEnd, '.', txName);
}
itemCount++;
if (exonFrames)
exonFrames = exonFrames->next;
}
hashFree(&nameHash);
return itemCount;
}
static void clusterClone(int argc, char *argv[])
{
int i;
for (i=1; i < argc; ++i)
{
struct lineFile *lf;
struct psl *psl;
unsigned tSize;
char *prevAccPart = (char *)NULL;
char *prevAccName = (char *)NULL;
char *prevTargetName = (char *)NULL;
struct hashEl *el;
struct hash *chrHash = newHash(0);
struct hash *coordHash = newHash(0);
struct coordEl *coord;
struct coordEl **coordListPt = (struct coordEl **) NULL;
unsigned querySize = 0;
int partCount = 0;
int partsConsidered = 0;
verbose(2,"#\tprocess: %s\n", argv[i]);
lf=pslFileOpen(argv[i]);
while ((struct psl *)NULL != (psl = pslNext(lf)) )
{
char *accName = (char *)NULL;
char *targetName = (char *)NULL;
int chrCount = 0;
double percentCoverage;
accName = cloneString(psl->qName);
if ((char *)NULL == prevAccPart)
{
prevAccPart = cloneString(psl->qName); /* first time */
querySize = psl->qSize;
++partsConsidered;
}
chopSuffixAt(accName,'_');
if ((char *)NULL == prevAccName)
prevAccName = cloneString(accName); /* first time */
if ((char *)NULL == prevTargetName)
prevTargetName = cloneString(psl->tName); /* first time */
/* encountered a new accession name, process the one we
* were working on
*/
if (differentWord(accName, prevAccName))
{
if (partCount > 0)
processResult(chrHash, coordHash, prevAccName, querySize,
partsConsidered);
else
verbose(1,"# ERROR %s %s - no coordinates found in %d parts considered\n",
prevTargetName, prevAccName, partsConsidered);
freeMem(prevAccName);
prevAccName = cloneString(accName);
freeHash(&chrHash);
freeHash(&coordHash);
chrHash = newHash(0);
coordHash = newHash(0);
querySize = 0;
partCount = 0;
partsConsidered = 0;
}
tSize = psl->tEnd - psl->tStart;
percentCoverage = 100.0*((double)(tSize+1)/(psl->qSize + 1));
if (differentWord(psl->qName, prevAccPart))
{
++partsConsidered;
querySize += psl->qSize;
freeMem(prevAccPart);
prevAccPart = cloneString(psl->qName);
}
targetName = cloneString(psl->tName);
if (differentWord(targetName, prevTargetName))
{
freeMem(prevTargetName);
prevTargetName = cloneString(targetName);
}
/* keep a hash of chrom names encountered */
el = hashLookup(chrHash, targetName);
if (el == NULL)
{
if (percentCoverage > minCover)
{
hashAddInt(chrHash, targetName, 1);
chrCount = 1;
}
else
{
hashAddInt(chrHash, targetName, 0);
chrCount = 0;
}
}
else
{
if (percentCoverage > minCover)
{
chrCount = ptToInt(el->val) + 1;
el->val=intToPt(chrCount);
}
}
AllocVar(coord);
coord->start = psl->tStart;
coord->end = psl->tEnd;
coord->qSize = psl->qSize;
coord->strand = sameWord(psl->strand,"+") ? 1 : 0;
/* when coverage is sufficient */
if (percentCoverage > minCover)
{
++partCount;
coord->name = cloneString(psl->qName);
/* for each chrom name, accumulate a list of coordinates */
el = hashLookup(coordHash, targetName);
if (el == NULL)
{
AllocVar(coordListPt);
hashAdd(coordHash, targetName, coordListPt);
}
else
{
coordListPt = el->val;
}
slAddHead(coordListPt,coord);
verbose(2,"# %s\t%u\t%u\t%u\t%.4f\t%d %s:%d-%d %s\n",
psl->qName, psl->qSize, tSize, tSize - psl->qSize,
percentCoverage, chrCount, psl->tName, psl->tStart, psl->tEnd,
psl->strand);
}
else
{
verbose(3,"# %s\t%u\t%u\t%u\t%.4f\t%d %s:%d-%d %s\n",
psl->qName, psl->qSize, tSize, tSize - psl->qSize,
percentCoverage, chrCount, psl->tName, psl->tStart, psl->tEnd,
psl->strand);
}
freeMem(accName);
freeMem(targetName);
pslFree(&psl);
}
if (partCount > 0)
processResult(chrHash, coordHash, prevAccName, querySize,
partsConsidered);
else
verbose(1,"# ERROR %s %s - no coordinates found\n",
prevTargetName, prevAccName);
freeMem(prevAccName);
freeHash(&chrHash);
freeHash(&coordHash);
lineFileClose(&lf);
}
} /* static void clusterClone() */