struct peakSource *peakSourceLoadAll(char *fileName, int dimCount)
/* Read file, parse it line by line and return list of peakSources. */
{
struct lineFile *lf = lineFileOpen(fileName, TRUE);
int rowSize = dimCount + 6;
char *row[rowSize];
struct peakSource *sourceList = NULL, *source;
while (lineFileNextRow(lf, row, rowSize))
{
/* Allocate struct and read in fixed fields. */
AllocVar(source);
source->dataSource = cloneString(row[0]);
source->chromColIx = sqlUnsigned(row[1]);
source->startColIx = sqlUnsigned(row[2]);
source->endColIx = sqlUnsigned(row[3]);
source->scoreColIx = sqlUnsigned(row[4]);
source->normFactor = sqlDouble(row[5]);
/* Read in dimension labels. */
AllocArray(source->labels, dimCount);
int i;
for (i=0; i<dimCount; ++i)
source->labels[i] = cloneString(row[i+6]);
/* Calculate required columns. */
int minColCount = max(source->chromColIx, source->startColIx);
minColCount = max(minColCount, source->endColIx);
minColCount = max(minColCount, source->scoreColIx);
source->minColCount = minColCount + 1;
slAddHead(&sourceList, source);
}
lineFileClose(&lf);
slReverse(&sourceList);
return sourceList;
}
struct sangRead *readReads(char *fileName, struct hash *pairHash)
/* Read in read database file and hook it up to pairs in pairHash. */
{
struct sangRead *list = NULL, *el;
struct lineFile *lf = lineFileOpen(fileName, TRUE);
char *words[4];
int wordCount;
struct sangPair *pair;
printf("Reading %s\n", fileName);
while (lineFileNextRow(lf, words, 4))
{
el = sangReadLoad(words);
slAddHead(&list, el);
pair = hashMustFindVal(pairHash, el->id);
if (el->pq[0] == 'p')
{
if (pair->fRead)
warn("%s - duplicate p read line %d of %s\n", el->id, lf->lineIx, lf->fileName);
pair->fRead = el;
}
else
{
if (pair->rRead)
warn("%s - duplicate q read line %d of %s\n", el->id, lf->lineIx, lf->fileName);
pair->rRead = el;
}
}
lineFileClose(&lf);
slReverse(&list);
return list;
}
void readGbAcc(struct lineFile *gaf)
/* Read in and record all genbank accessions that have sequences */
{
struct gb *gb;
char *acc[1];
struct sts *s;
while (lineFileNextRow(gaf, acc, 1))
{
if (!hashLookup(gbAccHash, acc[0]))
{
AllocVar(gb);
gb->next = NULL;
gb->acc = cloneString(acc[0]);
gb->s = NULL;
gb->gbSeq = TRUE;
hashAdd(gbAccHash, acc[0], gb);
if (hashLookup(nameHash, acc[0]))
{
s = hashMustFindVal(nameHash, acc[0]);
addElement(acc[0], &s->si->genbank, &s->si->gbCount);
removeElement(acc[0], &s->si->otherNames, &s->si->nameCount);
}
}
else
{
gb = hashMustFindVal(gbAccHash, acc[0]);
gb->gbSeq = TRUE;
}
}
}
static void processPslFile(struct sqlConnection *conn, struct gbSelect* select,
struct gbStatusTbl* statusTbl, char* pslPath)
/* Parse a psl file looking for accessions to add to the database. */
{
char* row[PSL_NUM_COLS];
struct lineFile *pslLf = gzLineFileOpen(pslPath);
while (lineFileNextRow(pslLf, row, PSL_NUM_COLS))
{
struct psl* psl = pslLoad(row);
processPsl(conn, select, statusTbl, psl, pslLf);
pslFree(&psl);
}
gzLineFileClose(&pslLf);
}
static void processOIFile(struct sqlConnection *conn, struct gbSelect* select,
struct gbStatusTbl* statusTbl, char* oiPath)
/* Parse a psl file looking for accessions to add to the database. */
{
char *row[EST_ORIENT_INFO_NUM_COLS];
struct lineFile *oiLf = gzLineFileOpen(oiPath);
while (lineFileNextRow(oiLf, row, EST_ORIENT_INFO_NUM_COLS))
{
struct estOrientInfo* oi = estOrientInfoLoad(row);
processOI(conn, select, statusTbl, oi, oiLf);
estOrientInfoFree(&oi);
}
gzLineFileClose(&oiLf);
}
void initKillList()
/* Load up a hash of the accessions to avoid. */
{
struct lineFile *lf = NULL;
char *killFile = optionVal("killList", NULL);
char *words[1];
assert(killFile);
killHash = newHash(10);
lf = lineFileOpen(killFile, TRUE);
while(lineFileNextRow(lf, words, ArraySize(words)))
{
hashAddInt(killHash, words[0], 1);
}
lineFileClose(&lf);
}
void readTissueLibraryIntoCache(char *fileName)
/* Read in the tissue and library information from fileName. */
{
struct lineFile *lf = lineFileOpen(fileName, TRUE);
char *words[3];
struct slInt *tissue = NULL, *library = NULL;
tissLibHash = newHash(12);
while(lineFileNextRow(lf, words, ArraySize(words)))
{
library = newSlInt(sqlSigned(words[1]));
tissue = newSlInt(sqlSigned(words[2]));
slAddTail(&library, tissue);
hashAdd(tissLibHash, words[0], library);
}
lineFileClose(&lf);
}
void protDat(char *protName, char *blatName, char *aliasFile, char *outName)
{
FILE *outFile = mustOpen(outName, "w");
struct hash *protHash = newHash(10);
struct hash *blatHash = newHash(10);
struct hash *aliasHash = newHash(10);
struct psl *psls, *pslPtr, *protPsls, *blatPsl;
struct lineFile *lf = lineFileOpen(aliasFile, TRUE);
struct alias *alPtr;
char buffer[1024];
char *words[3];
int numWords = optionExists("fb") ? 2 : 3;
while (lineFileNextRow(lf, words, numWords))
{
AllocVar(alPtr);
alPtr->kgName = cloneString(words[1]);
if (numWords == 3)
alPtr->spName = cloneString(words[2]);
hashAdd(aliasHash, cloneString(words[0]), alPtr);
}
protPsls = pslLoadAll(protName);
pslPtr = psls = pslLoadAll(blatName);
for(; pslPtr; pslPtr = pslPtr->next)
hashAdd(blatHash, pslPtr->qName, pslPtr);
for(pslPtr = protPsls; pslPtr; pslPtr = pslPtr->next)
{
if ((blatPsl = hashFindVal(blatHash, pslPtr->qName)) != NULL)
{
if ((alPtr = hashFindVal(aliasHash, pslPtr->qName)) != NULL)
{
if (numWords == 3)
sprintf(buffer,"%s.%s:%d-%d.%s.%s",pslPtr->qName,blatPsl->tName,
blatPsl->tStart, blatPsl->tEnd,alPtr->kgName, alPtr->spName);
else
sprintf(buffer,"%s.%s:%d-%d.%s",pslPtr->qName,blatPsl->tName,
blatPsl->tStart, blatPsl->tEnd,alPtr->kgName);
pslPtr->qName = buffer;
pslTabOut(pslPtr, outFile);
}
}
}
}
static struct hash *readLift(char *liftAcross)
/* read in liftAcross file, create hash of srcName as hash key,
* hash elements are simple lists of coordinate relationships
* return them all sorted by start position
*/
{
char *row[6];
struct hash *result = newHash(8);
struct hashEl *hel = NULL;
struct lineFile *lf = lineFileOpen(liftAcross, TRUE);
while (lineFileNextRow(lf, row, ArraySize(row)))
{
struct liftSpec *liftSpec;
hel = hashStore(result, row[0]); /* srcName hash */
AllocVar(liftSpec);
liftSpec->start = sqlUnsigned(row[1]); /* src start */
liftSpec->end = sqlUnsigned(row[2]); /* src end */
liftSpec->dstName = cloneString(row[3]); /* dstName */
liftSpec->dstStart = sqlUnsigned(row[4]); /* dst start */
liftSpec->strand = '+'; /* dst strand */
if ('-' == *row[5])
liftSpec->strand = '-';
/* accumulate list of lift specs under the srcName hash */
slAddHead(&(hel->val), liftSpec);
}
/* Go through each srcName in the hash, and sort the list there by
* the start coordinate of each item. The searching will expect
* them to be in order.
*/
struct hashCookie cookie = hashFirst(result);
while ((hel = hashNext(&cookie)) != NULL)
{
slSort(&(hel->val), lsStartCmp);
if (verboseLevel() > 2)
{
struct liftSpec *ls;
for (ls = hel->val; ls != NULL; ls = ls->next)
verbose(3, "# %s\t%d\t%d\t%s\t%d\t%c\n", hel->name, ls->start,
ls->end, ls->dstName, ls->dstStart, ls->strand);
}
}
return result;
}
struct sangRange *readRanges(char *fileName, struct hash *hash)
/* Read range file into list/hash. */
{
struct sangRange *list = NULL, *el;
struct lineFile *lf = lineFileOpen(fileName, TRUE);
char *words[3];
int wordCount;
printf("Reading %s\n", fileName);
while (lineFileNextRow(lf, words, 3))
{
el = sangRangeLoad(words);
slAddHead(&list, el);
hashAddUnique(hash, el->name, el);
}
lineFileClose(&lf);
slReverse(&list);
return list;
}
struct hash *readBed(char *fileName)
/* Read bed and return it as a hash keyed by chromName
* with binKeeper values. */
{
char *row[5];
struct lineFile *lf = lineFileOpen(fileName, TRUE);
struct hash *hash = newHash(0);
int expectedCols = bScore ? 5 : 3;
while (lineFileNextRow(lf, row, expectedCols))
{
struct binKeeper *bk;
struct bed5 *bed;
struct hashEl *hel = hashLookup(hash, row[0]);
if (hel == NULL)
{
bk = binKeeperNew(0, 1024*1024*1024);
hel = hashAdd(hash, row[0], bk);
}
bk = hel->val;
AllocVar(bed);
bed->chrom = hel->name;
bed->start = lineFileNeedNum(lf, row, 1);
bed->end = lineFileNeedNum(lf, row, 2);
if (bScore)
bed->score = lineFileNeedNum(lf, row, 4);
if (bed->start > bed->end)
errAbort("start after end line %d of %s", lf->lineIx, lf->fileName);
if (bed->start == bed->end)
{
if (allowStartEqualEnd)
// Note we are tweaking binKeeper coords here, so use bed->start and bed->end.
binKeeperAdd(bk, max(0, bed->start-1), bed->end+1, bed);
else
lineFileAbort(lf, "start==end (if this is legit, use -allowStartEqualEnd)");
}
else
binKeeperAdd(bk, bed->start, bed->end, bed);
}
lineFileClose(&lf);
return hash;
}
void bedFileStats(char *bedFile, int colCount, FILE *f)
/* Collect stats on sizes of things in a bed file, and scores too. */
{
struct lineFile *lf = lineFileOpen(bedFile, TRUE);
struct slDouble *sizeList=NULL, *scoreList=NULL, *el;
char *row[colCount];
while (lineFileNextRow(lf, row, colCount))
{
int size = sqlUnsigned(row[endColIx]) - sqlUnsigned(row[startColIx]);
el = slDoubleNew(size);
slAddHead(&sizeList, el);
double score = sqlDouble(row[scoreColIx]);
el = slDoubleNew(score);
slAddHead(&scoreList, el);
}
fprintf(f, "%s\t%d\tsize:", bedFile, slCount(scoreList));
printStats(f, sizeList);
fprintf(f, "\tscore:");
printStats(f, scoreList);
fprintf(f, "\n");
lineFileClose(&lf);
}
static double minOfCol(char *fileName, int colIx)
/* Return minimum value seen in given column of file. */
{
struct lineFile *lf = lineFileOpen(fileName, TRUE);
int minColCount = colIx+1;
char *row[minColCount];
boolean gotAny = FALSE;
double minVal = 0;
while (lineFileNextRow(lf, row, minColCount))
{
double val = lineFileNeedDouble(lf, row, colIx);
if (!gotAny || val < minVal)
{
gotAny = TRUE;
minVal = val;
}
}
lineFileClose(&lf);
if (!gotAny)
errAbort("No data in %s", fileName);
return minVal;
}
struct sage *loadSageTags(char *fileName, int numExps)
{
struct sage *sgList=NULL, *sg=NULL;
char *words[3];
struct lineFile *lf = lineFileOpen(fileName, TRUE);
while(lineFileNextRow(lf, words,3))
{
if(sg == NULL || sg->uni != atoi(words[0]))
{
if(sg != NULL)
slSafeAddHead(&sgList,sg);
sg = createNewSage(numExps);
sg->uni = atoi(words[0]);
snprintf(sg->gb, sizeof(sg->gb), "unknown");
snprintf(sg->gi, sizeof(sg->gb), "unknown");
sg->description = cloneString(words[1]);
sg->numTags =1;
assert(strlen(words[2]) <= 10);
sg->tags = needMem(sizeof(char*) * 1);
sg->tags[0] = needMem(sizeof(char) * 11);
strcpy(sg->tags[0],words[2]);
}
else
{
sg->tags = needMoreMem(sg->tags, (sg->numTags*sizeof(char*)), ((sg->numTags+1)*sizeof(char*)));
sg->tags[sg->numTags] = needMem(sizeof(char) * 11);
strcpy(sg->tags[sg->numTags],words[2]);
sg->numTags++;
}
}
return(sgList);
/*for(sg=sgList; sg != NULL; sg = sg->next)
{
sageTabOut(sg,stdout);
}*/
}
struct sangPair *readPairs(char *fileName, struct hash *pairHash, struct hash *rangeHash)
/* Read in pair file and connect pairs to relevant range. */
{
struct sangPair *list = NULL, *el;
struct hashEl *hel;
struct sangInsert si;
struct lineFile *lf = lineFileOpen(fileName, TRUE);
char *words[2];
int wordCount;
printf("Reading %s\n", fileName);
while (lineFileNextRow(lf, words, 2))
{
sangInsertStaticLoad(words, &si);
AllocVar(el);
hel = hashAddUnique(pairHash, si.id, el);
el->name = hel->name;
el->range = hashMustFindVal(rangeHash, si.name);
slAddHead(&list, el);
}
slReverse(&list);
lineFileClose(&lf);
return list;
}
int *readInConservationVals(char *fileName)
/* Open up the file and read in the conservation scores.
return an array indexed by base position with the conservation
scores. Free with freez() */
{
struct lineFile *lf = NULL;
int *scores = NULL;
int chromSize = optionInt("chromSize", 0);
int i = 0;
char *words[2];
if(chromSize == 0)
errAbort("Can't have chromSize set to 0.");
warn("Reading in conservation");
setMaxAlloc(sizeof(*scores)*chromSize+1);
AllocArray(scores, chromSize);
/* Make empty data be -1, a not possible score. */
for(i = 0; i < chromSize; i++)
scores[i] = -1;
/* Open up our conservation file. */
if(sameString(fileName, "stdin"))
lf = lineFileStdin(TRUE);
else
lf = lineFileOpen(fileName, TRUE);
dotForUserInit( chromSize/10 > 1 ? chromSize/10 : 1);
while(lineFileNextRow(lf, words, ArraySize(words)))
{
scores[atoi(words[0])] = round(atof(words[1]) * FLOAT_CHEAT);
dotForUser();
}
lineFileClose(&lf);
warn("Done");
return scores;
}
void ctgToChromFa(char *chromName, char *insertFile, char *chromDir,
char *orderLst, char *outName, struct hash *liftHash)
/* ctgToChromFa - convert contig level fa files to chromosome level. */
{
struct hash *uniq = newHash(0);
struct bigInsert *bi;
struct chromInserts *chromInserts;
struct hash *insertHash = newHash(9);
struct lineFile *lf = lineFileOpen(orderLst, TRUE);
FILE *f = mustOpen(outName, "w");
char ctgFaName[512];
char *words[2];
int liftChromSize = 0;
int actualChromSize = 0;
boolean isFirst = TRUE;
chromInsertsRead(insertFile, insertHash);
chromInserts = hashFindVal(insertHash, chromName);
fprintf(f, ">%s\n", chromName);
while (lineFileNextRow(lf, words, 1))
{
char *contig = words[0];
int nSize;
if (liftHash != NULL)
{
struct lift *lift = hashMustFindVal(liftHash, contig);
nSize = lift->nBefore;
liftChromSize = lift->chromSize;
}
else
nSize = chromInsertsGapSize(chromInserts, rmChromPrefix(contig), isFirst);
hashAddUnique(uniq, contig, NULL);
addN(f, nSize);
actualChromSize += nSize;
isFirst = FALSE;
sprintf(ctgFaName, "%s/%s/%s.fa", chromDir, contig, contig);
if (fileExists(ctgFaName))
{
actualChromSize += addFa(f, ctgFaName);
}
else
{
warn("%s does not exist\n", ctgFaName);
if (!cgiVarExists("missOk"))
noWarnAbort();
}
}
lineFileClose(&lf);
if (chromInserts != NULL)
if ((bi = chromInserts->terminal) != NULL)
{
addN(f, bi->size);
actualChromSize += bi->size;
}
if (liftHash != NULL)
{
if (actualChromSize > liftChromSize)
errAbort("Error: chromosome size from lift file is %d, but actual fa size is %d. Possible inconsistency between lift and inserts?",
liftChromSize, actualChromSize);
else if (actualChromSize < liftChromSize)
addN(f, (liftChromSize - actualChromSize));
}
if (linePos != 0)
fputc('\n', f);
fclose(f);
}
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 ticksToWig(int startTick, char *inTable, char *outDensity, char *outAverage)
/* ticksToWig - Convert tab-delimited file of Unix time ticks, and possibly also
* numerical values to wig file(s).. */
{
struct lineFile *lf = lineFileOpen(inTable, TRUE);
FILE *densityFile = mustOpen(outDensity, "w");
printVarStepHead(densityFile);
FILE *averageFile = NULL;
if (outAverage != NULL)
{
averageFile = mustOpen(outAverage, "w");
printVarStepHead(averageFile);
}
int colsToParse = 1 + max(tickCol, valCol);
char *row[colsToParse];
time_t curTick = 0;
int sameTickCount = 0;
double tickTotal = 0;
double val = 0;
time_t tick;
while (lineFileNextRow(lf, row, colsToParse))
{
tick = lineFileNeedNum(lf, row, tickCol);
if (averageFile != NULL)
val = lineFileNeedDouble(lf, row, valCol);
if (curTick != tick)
{
if (curTick > tick)
errAbort("Input isn't sorted - %ld > %ld line %d of %s\n",
(long)curTick, (long)tick, lf->lineIx, lf->fileName);
if (startTick == 0)
startTick = tick;
if (sameTickCount > 0)
{
fprintf(densityFile, "%ld\t%d\n", curTick - startTick + 1, sameTickCount);
time_t i;
for (i=curTick+1; i<tick; ++i)
{
fprintf(densityFile, "%ld\t%d\n", i - startTick + 1, 0);
}
if (averageFile != NULL)
{
fprintf(averageFile, "%ld\t%f\n",
(long)curTick - startTick + 1, tickTotal/sameTickCount);
tickTotal = 0;
}
sameTickCount = 0;
}
curTick = tick;
}
tickTotal += val;
sameTickCount += 1;
}
if (sameTickCount > 0)
{
fprintf(densityFile, "%ld\t%d\n", curTick - startTick + 1, sameTickCount);
if (averageFile != NULL)
fprintf(averageFile, "%ld\t%f\n",
(long)curTick - startTick + 1, tickTotal/sameTickCount);
}
carefulClose(&densityFile);
carefulClose(&averageFile);
}
void rcvs(char *codingTable, char *clusterTable)
/* rcvs - Compare riken noncoding vs. nonspliced. */
{
struct hash *idHash = newHash(16); // Key id1, val id2
struct hash *nonCodingHash = newHash(16); // Key clusterId, value
struct hash *splicedHash = newHash(16); // Key id2, present if spliced
struct sqlConnection *conn = sqlConnect("mgsc");
struct sqlResult *sr;
char **row;
char *words[16];
int wordCount;
struct lineFile *lf;
int codingSpliced = 0;
int noncodingSpliced = 0;
int codingNonspliced = 0;
int noncodingNonspliced = 0;
/* Read id's into hash */
sr = sqlGetResult(conn, NOSQLINJ "select id1,id2 from rikenIds");
while ((row = sqlNextRow(sr)) != NULL)
hashAdd(idHash, row[0], cloneString(row[1]));
sqlFreeResult(&sr);
/* Read spliced into hash */
sr = sqlGetResult(conn,
NOSQLINJ "select name from rikenOrientInfo where intronOrientation != 0");
while ((row = sqlNextRow(sr)) != NULL)
hashAdd(splicedHash, row[0], NULL);
sqlFreeResult(&sr);
/* Read noncoding clusters into hash */
lf = lineFileOpen(codingTable, TRUE);
while (lineFileNextRow(lf, words, 2))
{
if (sameString(words[1], "NoPProt"))
hashAdd(nonCodingHash, words[0], NULL);
}
lineFileClose(&lf);
/* Stream through cluster table counting and correlating. */
lf = lineFileOpen(clusterTable, TRUE);
while (lineFileNextRow(lf, words, 2))
{
char *cluster = words[0];
char *id1 = words[1];
char *id2 = hashMustFindVal(idHash, id1);
if (hashLookup(nonCodingHash, cluster))
{
if (hashLookup(splicedHash, id2))
++noncodingSpliced;
else
++noncodingNonspliced;
}
else
{
if (hashLookup(splicedHash, id2))
++codingSpliced;
else
++codingNonspliced;
}
}
printf("noncodingNonspliced %d\n", noncodingNonspliced);
printf("noncodingSpliced %d\n", noncodingSpliced);
printf("codingNonspliced %d\n", codingNonspliced);
printf("codingSpliced %d\n", codingSpliced);
printf("total %d\n", noncodingNonspliced + noncodingSpliced + codingNonspliced + codingSpliced);
}
void bedItemOverlapCount(struct hash *chromHash, char *infile, char *outfile){
unsigned maxChromSize = 0;
unitSize *counts = (unitSize *)NULL;
FILE *f = mustOpen(outfile, "w");
struct hashCookie hc = hashFirst(chromHash);
struct hashEl *hel;
while( (hel = hashNext(&hc)) != NULL) {
unsigned num = (unsigned) ptToInt(hel->val);
maxChromSize = max(num, maxChromSize);
}
verbose(2,"#\tmaxChromSize: %u\n", maxChromSize);
if (maxChromSize < 1)
errAbort("maxChromSize is zero ?");
/* Allocate just once for the largest chrom and reuse this array */
counts = needHugeMem(sizeof(unitSize) * maxChromSize);
/* Reset the array to be zero to be reused */
memset((void *)counts, 0, sizeof(unitSize)*(size_t)maxChromSize);
unsigned chromSize = 0;
char *prevChrom = (char *)NULL;
boolean outputToDo = FALSE;
struct hash *seenHash = newHash(5);
struct lineFile *bf = lineFileOpen(infile , TRUE);
struct bed *bed = (struct bed *)NULL;
char *row[12];
int numFields = doBed12 ? 12 : 3;
while (lineFileNextRow(bf,row, numFields))
{
int i;
bed = bedLoadN(row, numFields);
verbose(3,"#\t%s\t%d\t%d\n",bed->chrom,bed->chromStart, bed->chromEnd);
if (prevChrom && differentWord(bed->chrom,prevChrom)) // End a chr
{
verbose(2,"#\tchrom %s done, size %d\n", prevChrom, chromSize);
if (outputToDo)
outputCounts(counts, prevChrom, chromSize, f);
outputToDo = FALSE;
memset((void *)counts, 0,
sizeof(unitSize)*(size_t)maxChromSize); /* zero counts */
freez(&prevChrom);
// prevChrom is now NULL so it will be caught by next if!
}
if ((char *)NULL == prevChrom) // begin a chr
{
if (hashLookup(seenHash, bed->chrom))
errAbort("ERROR:input file not sorted. %s seen before on line %d\n",
bed->chrom, bf->lineIx);
hashAdd(seenHash, bed->chrom, NULL);
prevChrom = cloneString(bed->chrom);
chromSize = hashIntVal(chromHash, prevChrom);
verbose(2,"#\tchrom %s starting, size %d\n", prevChrom,chromSize);
}
if (bed->chromEnd > chromSize)
{
// check for circular chrM
if (doBed12 || bed->chromStart>=chromSize
|| differentWord(bed->chrom,"chrM"))
{
warn("ERROR: %s\t%d\t%d", bed->chrom, bed->chromStart,
bed->chromEnd);
errAbort("chromEnd > chromSize ? %d > %d",
bed->chromEnd,chromSize);
}
for (i = bed->chromStart; i < chromSize; ++i)
INCWOVERFLOW(counts,i);
for (i = 0; i < (bed->chromEnd - chromSize); ++i)
INCWOVERFLOW(counts,i);
}
else if (doBed12)
{
int *starts = bed->chromStarts;
int *sizes = bed->blockSizes;
int *endStarts = &bed->chromStarts[bed->blockCount];
for(; starts < endStarts; starts++, sizes++)
{
unsigned int end = *starts + *sizes + bed->chromStart;
for (i = *starts + bed->chromStart; i < end; ++i)
INCWOVERFLOW(counts,i);
}
}
else
{
for (i = bed->chromStart; i < bed->chromEnd; ++i)
INCWOVERFLOW(counts, i);
}
outputToDo = TRUE;
bedFree(&bed); // plug the memory leak
}
lineFileClose(&bf);
// Note, next file could be on same chr!
if (outputToDo)
outputCounts(counts, prevChrom, chromSize, f);
if (doOutBounds)
fprintf(stderr, "min %lu max %lu\n", (unsigned long)overMin, (unsigned long)overMax);
verbose(2,"#\tchrom %s done, size %d\n", prevChrom, chromSize);
carefulClose(&f);
freeMem(counts);
freez(&prevChrom);
// hashFreeWithVals(&chromHash, freez);
freeHash(&seenHash);
}
