void hgGoldGapGl(char *database, char *gsDir, char *ooSubDir, boolean doGl, char *oneChrom)
/* hgGoldGapGl - Put chromosome .agp and .gl files into browser database.. */
{
struct fileInfo *chrFiList, *chrFi;
struct sqlConnection *conn = NULL;
char ooDir[512];
char pathName[512];
struct hash *cloneVerHash = newHash(0);
boolean gotAny = FALSE;
struct hash *chromDirHash = newHash(4);
char *chromLst = optionVal("chromLst", NULL);
if (! noLoad)
conn = sqlConnect(database);
verbose(2,"#\tcomplete gold, gap and .gl files produced\n");
if (chromLst != NULL)
{
struct lineFile *clf = lineFileOpen(chromLst, TRUE);
char *row[1];
while (lineFileRow(clf, row))
{
hashAdd(chromDirHash, row[0], NULL);
}
lineFileClose(&clf);
}
sprintf(ooDir, "%s/%s", gsDir, ooSubDir);
/* target prefix is used in zoo browser */
if (oneChrom != NULL && (startsWith("chr", oneChrom) || startsWith("target", oneChrom)))
oneChrom += 3;
if (doGl)
{
sprintf(pathName, "%s/ffa/sequence.inf", gsDir);
makeCloneVerHash(pathName, cloneVerHash);
}
chrFiList = listDirX(ooDir, "*", FALSE);
for (chrFi = chrFiList; chrFi != NULL; chrFi = chrFi->next)
{
if (chrFi->isDir &&
((strlen(chrFi->name) <= 2) || startsWith("NA_", chrFi->name) ||
(NULL != hashLookup(chromDirHash, chrFi->name))))
{
if (oneChrom == NULL || sameWord(chrFi->name, oneChrom))
{
sprintf(pathName, "%s/%s", ooDir, chrFi->name);
makeGoldAndGap(conn, pathName);
if (doGl)
makeGl(conn, pathName, cloneVerHash);
gotAny = TRUE;
uglyf("done %s\n", chrFi->name);
}
}
}
slFreeList(&chrFiList);
if (! noLoad)
sqlDisconnect(&conn);
hashFree(&chromDirHash);
if (!gotAny)
errAbort("No contig agp and gold files found");
}
void knownToVisiGene(char *database)
/* knownToVisiGene - Create knownToVisiGene table by riffling through various other knownTo tables. */
{
char *tempDir = ".";
FILE *f = hgCreateTabFile(tempDir, outTable);
struct sqlConnection *hConn = sqlConnect(database);
struct sqlConnection *iConn = sqlConnect(visiDb);
struct sqlResult *sr;
char **row;
struct hash *geneImageHash = newHash(18);
struct hash *locusLinkImageHash = newHash(18);
struct hash *refSeqImageHash = newHash(18);
struct hash *genbankImageHash = newHash(18);
struct hash *probeImageHash = newHash(18);
struct hash *knownToLocusLinkHash = newHash(18);
struct hash *knownToRefSeqHash = newHash(18);
struct hash *knownToGeneHash = newHash(18);
struct hash *favorHugoHash = newHash(18);
struct hash *knownToProbeHash = newHash(18);
struct hash *knownToAllProbeHash = newHash(18);
struct genePred *knownList = NULL, *known;
struct hash *dupeHash = newHash(17);
probesDb = optionVal("probesDb", database);
struct sqlConnection *probesConn = sqlConnect(probesDb);
vgProbes = sqlTableExists(probesConn,"vgProbes");
vgAllProbes = sqlTableExists(probesConn,"vgAllProbes");
/* Go through and make up hashes of images keyed by various fields. */
sr = sqlGetResult(iConn,
"NOSQLINJ select image.id,imageFile.priority,gene.name,gene.locusLink,gene.refSeq,gene.genbank"
",probe.id,submissionSet.privateUser,vgPrbMap.vgPrb,gene.id"
" from image,imageFile,imageProbe,probe,gene,submissionSet,vgPrbMap"
" where image.imageFile = imageFile.id"
" and image.id = imageProbe.image"
" and imageProbe.probe = probe.id"
" and probe.gene = gene.id"
" and image.submissionSet=submissionSet.id"
" and vgPrbMap.probe = probe.id");
while ((row = sqlNextRow(sr)) != NULL)
{
int id = sqlUnsigned(row[0]);
float priority = atof(row[1]);
int privateUser = sqlSigned(row[7]);
char vgPrb_Id[256];
safef(vgPrb_Id, sizeof(vgPrb_Id), "vgPrb_%s",row[8]);
int geneId = sqlUnsigned(row[9]);
if (privateUser == 0)
{
addPrioritizedImage(probeImageHash, id, priority, geneId, vgPrb_Id);
addPrioritizedImage(geneImageHash, id, priority, geneId, row[2]);
addPrioritizedImage(locusLinkImageHash, id, priority, geneId, row[3]);
addPrioritizedImage(refSeqImageHash, id, priority, geneId, row[4]);
addPrioritizedImage(genbankImageHash, id, priority, geneId, row[5]);
}
}
verbose(2, "Made hashes of image: geneImageHash %d, locusLinkImageHash %d, refSeqImageHash %d"
", genbankImageHash %d probeImageHash %d\n",
geneImageHash->elCount, locusLinkImageHash->elCount, refSeqImageHash->elCount,
genbankImageHash->elCount, probeImageHash->elCount);
sqlFreeResult(&sr);
/* Build up list of known genes. */
sr = sqlGetResult(hConn, "NOSQLINJ select * from knownGene");
while ((row = sqlNextRow(sr)) != NULL)
{
struct genePred *known = genePredLoad(row);
if (!hashLookup(dupeHash, known->name))
{
hashAdd(dupeHash, known->name, NULL);
slAddHead(&knownList, known);
}
}
slReverse(&knownList);
sqlFreeResult(&sr);
verbose(2, "Got %d known genes\n", slCount(knownList));
/* Build up hashes from knownGene to other things. */
if (vgProbes)
bestProbeOverlap(probesConn, "vgProbes", knownList, knownToProbeHash);
if (vgAllProbes)
bestProbeOverlap(probesConn, "vgAllProbes", knownList, knownToAllProbeHash);
foldIntoHash(hConn, "knownToLocusLink", "name", "value", knownToLocusLinkHash, NULL, FALSE);
foldIntoHash(hConn, "knownToRefSeq", "name", "value", knownToRefSeqHash, NULL, FALSE);
foldIntoHash(hConn, "kgXref", "kgID", "geneSymbol", knownToGeneHash, favorHugoHash, FALSE);
foldIntoHash(hConn, "kgAlias", "kgID", "alias", knownToGeneHash, favorHugoHash, TRUE);
foldIntoHash(hConn, "kgProtAlias", "kgID", "alias", knownToGeneHash, favorHugoHash, TRUE);
verbose(2, "knownToLocusLink %d, knownToRefSeq %d, knownToGene %d knownToProbe %d knownToAllProbe %d\n",
knownToLocusLinkHash->elCount, knownToRefSeqHash->elCount, knownToGeneHash->elCount,
knownToProbeHash->elCount, knownToAllProbeHash->elCount);
/* Try and find an image for each gene. */
for (known = knownList; known != NULL; known = known->next)
{
char *name = known->name;
struct prioritizedImage *best = NULL;
{
best = bestImage(name, knownToLocusLinkHash, locusLinkImageHash);
if (!best)
best = bestImage(name, knownToRefSeqHash, refSeqImageHash);
if (!best)
{
best = hashFindVal(genbankImageHash, name);
}
if (!best)
best = bestImage(name, knownToGeneHash, geneImageHash);
if (vgProbes && !best)
best = bestImage(name, knownToProbeHash, probeImageHash);
if (vgAllProbes && !best)
best = bestImage(name, knownToAllProbeHash, probeImageHash);
}
if (best)
{
fprintf(f, "%s\t%d\t%d\n", name, best->imageId, best->geneId);
}
}
createTable(hConn, outTable);
hgLoadTabFile(hConn, tempDir, outTable, &f);
hgRemoveTabFile(tempDir, outTable);
}
int main(int argc, char *argv[])
{
struct sqlConnection *conn, *conn3;
char query[256], query3[256];
struct sqlResult *sr, *sr3;
char **row, **row3;
FILE *o1, *o2;
char *locusID; /* LocusLink ID */
char *kgTempDbName, *roDbName;
char cond_str[200];
char *kgId;
char *mapID;
char *desc;
char *mRNA;
optionInit(&argc, argv, options);
if (argc != 3) usage();
kgTempDbName = argv[1];
roDbName = argv[2];
conn = hAllocConn(roDbName);
conn3= hAllocConn(roDbName);
o1 = fopen("j.dat", "w");
o2 = fopen("jj.dat", "w");
table = optionVal("table", "knownGene");
sqlSafef(query, sizeof(query), "select name from %s.%s", roDbName, table);
sr = sqlMustGetResult(conn, query);
row = sqlNextRow(sr);
while (row != NULL)
{
kgId = row[0];
sqlSafefFrag(cond_str, sizeof(cond_str), "kgId='%s'", kgId);
mRNA = sqlGetField(roDbName, "kgXref", "mRNA", cond_str);
sqlSafefFrag(cond_str, sizeof(cond_str), "mrna='%s'", mRNA);
locusID = sqlGetField("entrez", "entrezMrna", "geneId", cond_str);
/* look for RefSeq if not found in mRNAs */
if (locusID == NULL)
{
sqlSafefFrag(cond_str, sizeof(cond_str), "refseq='%s'", mRNA);
locusID = sqlGetField("entrez", "entrezRefseq", "geneId", cond_str);
}
if (locusID != NULL)
{
sqlSafef(query3, sizeof(query3), "select * from %s.keggList where locusID = '%s'", kgTempDbName, locusID);
sr3 = sqlGetResult(conn3, query3);
while ((row3 = sqlNextRow(sr3)) != NULL)
{
mapID = row3[1];
desc = row3[2];
fprintf(o1, "%s\t%s\t%s\n", kgId, locusID, mapID);
fprintf(o2, "%s\t%s\n", mapID, desc);
row3 = sqlNextRow(sr3);
}
sqlFreeResult(&sr3);
}
else
{
/* printf("%s not found in Entrez.\n", kgId);fflush(stdout);*/
if (differentString(table, "knownGene"))
{
sqlSafefFrag(cond_str, sizeof(cond_str), "name='%s'", kgId);
locusID = sqlGetField(roDbName, table, "name2", cond_str);
sqlSafef(query3, sizeof(query3), "select * from %s.keggList where locusID = '%s'", kgTempDbName, kgId);
sr3 = sqlGetResult(conn3, query3);
while ((row3 = sqlNextRow(sr3)) != NULL)
{
mapID = row3[1];
desc = row3[2];
fprintf(o1, "%s\t%s\t%s\n", kgId, locusID, mapID);
fprintf(o2, "%s\t%s\n", mapID, desc);
row3 = sqlNextRow(sr3);
}
sqlFreeResult(&sr3);
}
}
row = sqlNextRow(sr);
}
fclose(o1);
fclose(o2);
hFreeConn(&conn);
mustSystem("cat j.dat|sort|uniq >keggPathway.tab");
mustSystem("cat jj.dat|sort|uniq >keggMapDesc.tab");
mustSystem("rm j.dat");
mustSystem("rm jj.dat");
return(0);
}
void altSummary(char *db, char *agxFileName, char *summaryOutName, char *htmlOutName, char *htmlFramesOutName)
/* Look through a bunch of splice sites and output some statistics and links. */
{
struct altGraphX *agList = NULL, *ag = NULL;
struct altSpliceSite *aSpliceList = NULL, *aSplice=NULL;
char *RDataName = optionVal("RData", NULL);
char *bedName = optionVal("bedName", NULL);
FILE *htmlOut = NULL;
FILE *htmlFramesOut = NULL;
FILE *summaryOut = NULL;
int altSpliceSites = 0, altSpliceLoci = 0, totalSpliceSites = 0;
warn("Loading splicing graphs.");
agList = altGraphXLoadAll(agxFileName);
htmlFramesOut = mustOpen(htmlFramesOutName, "w");
htmlOut = mustOpen(htmlOutName, "w");
summaryOut = mustOpen(summaryOutName, "w");
if(RDataName != NULL)
{
char buff[256];
safef(buff, sizeof(buff), "%s.control", RDataName);
RDataCont = mustOpen(buff, "w");
outputRHeader(RDataCont);
safef(buff, sizeof(buff), "%s.alt", RDataName);
RData = mustOpen(buff, "w");
outputRHeader(RData);
}
if(bedName != NULL)
{
openBedFiles(bedName);
}
writeOutFrames(htmlFramesOut, htmlOutName, db);
carefulClose(&htmlFramesOut);
warn("Examining splicing graphs.");
fprintf(htmlOut, "<html>\n<body bgcolor=\"#FFF9D2\"><b>Alt-Splice List</b>\n"
"<table border=1><tr><th>Name (count)</th><th>Type</th><th>Size</th></tr>\n");
for(ag=agList; ag != NULL; ag=ag->next)
{
lookForAltSplicing(db, ag, &aSpliceList, &altSpliceSites, &altSpliceLoci, &totalSpliceSites);
for(aSplice=aSpliceList; aSplice != NULL; aSplice= aSplice->next)
{
altSpliceSiteOutput(aSplice, summaryOut, '\t', '\n');
htmlLinkOut(db, aSplice, htmlOut);
if(bedViewOutFile != NULL)
bedViewOut(aSplice, bedViewOutFile);
}
altSpliceSiteFreeList(&aSpliceList);
}
warn("\nDone.");
fprintf(htmlOut,"</body></html>\n");
warn("%d altSpliced sites in %d alt-spliced loci out of %d total loci.",
altSpliceSites, altSpliceLoci, slCount(agList));
printSpliceTypeInfo(altSpliceLoci);
altGraphXFreeList(&agList);
if(RData != NULL)
{
carefulClose(&RData);
carefulClose(&RDataCont);
}
carefulClose(&htmlOut);
carefulClose(&summaryOut);
}
void paraNode()
/* paraNode - a net server. */
{
char *line;
char *command;
struct sockaddr_in sai;
/* We have to know who we are... */
hostName = getMachine();
initRandom();
getTicksToHundreths();
/* log init */
if (optionExists("log"))
logOpenFile("paraNode", optionVal("log", NULL));
else
logOpenSyslog("paraNode", optionVal("logFacility", NULL));
logSetMinPriority(optionVal("logMinPriority", "info"));
logInfo("starting paraNode on %s", hostName);
/* Make job lists. */
jobsRunning = newDlList();
jobsFinished = newDlList();
/* Set up socket and self to listen to it. */
ZeroVar(&sai);
sai.sin_family = AF_INET;
sai.sin_port = htons(paraNodePort);
sai.sin_addr.s_addr = INADDR_ANY;
mainRudp = rudpMustOpenBound(&sai);
mainRudp->maxRetries = 12;
/* Event loop. */
findNow();
for (;;)
{
/* Get next incoming message and optionally check to make
* sure that it's from a host we trust, and check signature
* on first bit of incoming data. */
if (pmReceive(&pmIn, mainRudp))
{
findNow();
if (hubName == NULL || ntohl(pmIn.ipAddress.sin_addr.s_addr) == hubIp
|| ntohl(pmIn.ipAddress.sin_addr.s_addr) == localIp)
{
/* Host and signature look ok, read a string and
* parse out first word as command. */
line = pmIn.data;
logDebug("message from %s: \"%s\"",
paraFormatIp(ntohl(pmIn.ipAddress.sin_addr.s_addr)),
line);
command = nextWord(&line);
if (command != NULL)
{
if (sameString("quit", command))
break;
else if (sameString("run", command))
doRun(line, &pmIn.ipAddress);
else if (sameString("jobDone", command))
jobDone(line);
else if (sameString("status", command))
doStatus();
else if (sameString("kill", command))
doKill(line);
else if (sameString("check", command))
doCheck(line, &pmIn.ipAddress);
else if (sameString("resurrect", command))
doResurrect(line, &pmIn.ipAddress);
else if (sameString("listJobs", command))
listJobs();
else if (sameString("fetch", command))
doFetch(line);
else
logWarn("invalid command: \"%s\"", command);
}
logDebug("done command");
}
else
{
logWarn("command from unauthorized host %s",
paraFormatIp(ntohl(pmIn.ipAddress.sin_addr.s_addr)));
}
}
}
rudpClose(&mainRudp);
}
void splitByCount(char *inName, int pieceSize, char *outRoot, off_t estSize, int extra)
/* Split up file into pieces pieceSize long. */
{
off_t pieces = (estSize + pieceSize-1)/pieceSize;
int digits = digitsBaseTen(pieces);
int maxN = optionInt("maxN", pieceSize-1);
boolean oneFile = optionExists("oneFile");
char fileName[PATH_LEN];
char dirOnly[PATH_LEN], noPath[128];
int pos, pieceIx = 0, writeCount = 0;
struct dnaSeq seq;
struct lineFile *lf = lineFileOpen(inName, TRUE);
FILE *f = NULL;
Bits *bits = NULL;
int seqCount = 0;
char *outFile = optionVal("out", NULL);
char *liftFile = optionVal("lift", NULL);
FILE *lift = NULL;
ZeroVar(&seq);
splitPath(outRoot, dirOnly, noPath, NULL);
if (oneFile)
{
sprintf(fileName, "%s.fa", outRoot);
f = mustOpen(fileName, "w");
}
if (liftFile)
lift = mustOpen(liftFile, "w");
/* Count number of N's from s[0] to s[size-1].
* Treat any parts past end of string as N's. */
while (faMixedSpeedReadNext(lf, &seq.dna, &seq.size, &seq.name))
{
bits = bitAlloc(seq.size);
setBitsN(seq.dna, seq.size, bits);
++seqCount;
if (outFile != NULL)
{
if (seqCount > 1)
errAbort("Can only handle in files with one sequence using out option");
bitsForOut(outFile, seq.size, bits);
}
for (pos = 0; pos < seq.size; pos += pieceSize)
{
char numOut[128];
int thisSize = seq.size - pos;
if (thisSize > (pieceSize + extra))
thisSize = pieceSize + extra;
if ((thisSize <= extra) && (pos > 0))
break; /* nobody wants duplicate smaller than extra overhang */
if (bitCountRange(bits, pos, thisSize) <= maxN)
{
if (!oneFile)
{
mkOutPath(fileName, outRoot, digits, pieceIx);
f = mustOpen(fileName, "w");
}
sprintf(numOut, "%s%0*d", noPath, digits, pieceIx);
faWriteNext(f, numOut, seq.dna + pos, thisSize);
if (lift)
fprintf(lift, "%d\t%s\t%d\t%s\t%d\n",
pos, numOut, thisSize, seq.name, seq.size);
++writeCount;
if (!oneFile)
carefulClose(&f);
}
pieceIx++;
}
bitFree(&bits);
}
carefulClose(&f);
carefulClose(&lift);
lineFileClose(&lf);
printf("%d pieces of %d written\n", writeCount, pieceIx);
}
int main(int argc, char *argv[])
{
struct lineFile *sif, *dsf, *daf, *gbf;
FILE *of, *opf, *oaf, *off, *asf, *dff;
char filename[256], *gbName;
int verb = 0;
verboseSetLevel(0);
optionInit(&argc, argv, optionSpecs);
if (argc < 3)
{
fprintf(stderr, "USAGE: updateStsInfo [-verbose=<level> -gb=<file>] <stsInfo file> <all.STS.fa> <dbSTS.sts> <dbSTS.aliases> <dbSTS.convert.fa> <outfile prefix>\n");
return 1;
}
verb = optionInt("verbose", 0);
verboseSetLevel(verb);
gbName = optionVal("gb", NULL);
if (gbName)
gbf = lineFileOpen(gbName, TRUE);
sif = lineFileOpen(argv[1], TRUE);
asf = mustOpen(argv[2], "r");
dsf = lineFileOpen(argv[3], TRUE);
daf = lineFileOpen(argv[4], TRUE);
dff = mustOpen(argv[5], "r");
safef(filename, ArraySize(filename), "%s.info", argv[6]);
of = mustOpen(filename, "w");
safef(filename, ArraySize(filename), "%s.primers", argv[6]);
opf = mustOpen(filename, "w");
safef(filename, ArraySize(filename), "%s.alias", argv[6]);
oaf = mustOpen(filename, "w");
safef(filename, ArraySize(filename), "%s.fa", argv[6]);
off = mustOpen(filename, "w");
/* Read in current stsInfo file */
verbose(1, "Reading current stsInfo file: %s\n", argv[1]);
readStsInfo(sif);
/* Read in genbank accessions that have sequences */
if (gbName)
{
verbose(1, "Reading genbank accession file: %s\n", gbName);
readGbAcc(gbf);
}
/* Read in primer and organism information from dbSTS.sts */
verbose(1, "Reading current dbSTS.sts file: %s\n", argv[3]);
readDbstsPrimers(dsf);
/* Read in names from dbSTS.alias and create new stsInfo records if needed */
verbose(1, "Reading current dbSTS.aliases file: %s\n", argv[4]);
readDbstsNames(daf);
/* Read in current sequences for sts markers */
verbose(1, "Reading current all.STS file: %s\n", argv[2]);
readAllSts(asf);
/* Read in new sequences from dbSTS.fa */
verbose(1, "Reading dbSTS.fa file: %s\n", argv[5]);
readDbstsFa(dff);
/* Print out the new files */
verbose(1, "Creating output files: %s .info .primers .alias .fa\n", argv[6]);
writeOut(of, opf, oaf, off);
fclose(asf);
lineFileClose(&dsf);
lineFileClose(&daf);
fclose(dff);
if (gbName)
lineFileClose(&gbf);
fclose(of);
fclose(opf);
fclose(oaf);
fclose(off);
return(0);
}
void hgExpDistance(char *database, char *posTable, char *expTable, char *outTable)
/* hgExpDistance - Create table that measures expression distance between pairs. */
{
struct sqlConnection *conn = sqlConnect(database);
struct sqlResult *sr;
char query[256];
char **row;
struct hash *expHash = hashNew(16);
int realExpCount = -1;
struct microData *gene;
int rc, t;
pthread_t *threads = NULL;
pthread_attr_t attr;
int *threadID = NULL;
void *status;
char *tempDir = ".";
int arrayNum;
struct microDataDistance *geneDistPtr = NULL;
struct microDataDistance *geneDistArray = NULL;
int geneIx;
FILE *f = NULL;
/* Get list/hash of all items with expression values. */
safef(query, sizeof(query), "select name,expCount,expScores from %s", posTable);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
char *name = row[0];
if (!hashLookup(expHash, name))
{
int expCount = sqlUnsigned(row[1]);
int commaCount;
float *expScores = NULL;
sqlFloatDynamicArray(row[2], &expScores, &commaCount);
if (expCount != commaCount)
errAbort("expCount and expScores don't match on %s in %s", name, posTable);
if (realExpCount == -1)
realExpCount = expCount;
if (expCount != realExpCount)
errAbort("In %s some rows have %d experiments others %d",
name, expCount, realExpCount);
AllocVar(gene);
gene->expCount = expCount;
gene->expScores = expScores;
hashAddSaveName(expHash, name, gene, &gene->name);
slAddHead(&geneList, gene);
}
}
sqlFreeResult(&sr);
conn = sqlConnect(database);
slReverse(&geneList);
geneCount = slCount(geneList);
printf("Have %d elements in %s\n", geneCount, posTable);
weights = getWeights(realExpCount);
if (optionExists("lookup"))
geneList = lookupGenes(conn, optionVal("lookup", NULL), geneList);
geneCount = slCount(geneList);
printf("Got %d unique elements in %s\n", geneCount, posTable);
sqlDisconnect(&conn); /* Disconnect because next step is slow. */
if (geneCount < 1)
errAbort("ERROR: unique gene count less than one ?");
f = hgCreateTabFile(tempDir, outTable);
synQ = synQueueNew();
/* instantiate threads */
AllocArray( threadID, numThreads );
AllocArray( threads, numThreads );
pthread_attr_init( &attr );
pthread_mutex_init( &mutexDotOut, NULL );
pthread_attr_setdetachstate( &attr, PTHREAD_CREATE_JOINABLE );
for (t = 0; t < numThreads; t++) {
threadID[t] = t;
rc = pthread_create( &threads[t], &attr, computeDistance,
(void *) &threadID[t]);
if (rc)
errAbort("ERROR: in pthread_create() %d\n", rc );
}
/* this thread will write to the file from the queue */
for (arrayNum = 0; arrayNum < geneCount; arrayNum++) {
geneDistArray = (struct microDataDistance *)synQueueGet( synQ );
geneDistPtr = geneDistArray;
/* Print out closest GENEDISTS distances in tab file. */
for (geneIx=0; geneIx < GENEDISTS && geneIx < geneCount;
++geneIx, geneDistPtr++)
if (geneDistPtr != NULL)
fprintf(f, "%s\t%s\t%f\n", geneDistPtr->name1,
geneDistPtr->name2, geneDistPtr->distance);
else
errAbort("ERROR: writing distance %d to file\n",
geneIx);
freeMem( geneDistArray );
}
/* synchronize all threads */
for (t = 0; t < numThreads; t++) {
rc = pthread_join( threads[t], &status);
if (rc)
errAbort("ERROR: in pthread_join() %d\n", rc );
}
printf("Made %s.tab\n", outTable);
slFreeList( &geneList );
pthread_mutex_destroy( &mutexDotOut );
pthread_attr_destroy( &attr );
/* Create and load table. */
conn = sqlConnect(database);
distanceTableCreate(conn, outTable);
hgLoadTabFile(conn, tempDir, outTable, &f);
printf("Loaded %s\n", outTable);
/* Add indices. */
safef(query, sizeof(query), "alter table %s add index(query(12))", outTable);
sqlUpdate(conn, query);
printf("Made query index\n");
if (optionExists("targetIndex"))
{
safef(query, sizeof(query), "alter table %s add index(target(12))", outTable);
sqlUpdate(conn, query);
printf("Made target index\n");
}
hgRemoveTabFile(tempDir, outTable);
}
void pickIntrons()
/** Top level routine, actually picks the introns. */
{
char *htmlFileName=NULL, *htmlFrameFileName=NULL;
char *bedFileName=NULL, *orthoBedFileName=NULL;
FILE *htmlOut=NULL, *htmlFrameOut=NULL;
FILE *bedOut=NULL, *orthoBedOut=NULL;
char *orthoEvalFile = NULL;
char *db = NULL;
struct orthoEval *ev=NULL, *evList = NULL;
struct intronEv *iv=NULL, *ivList = NULL;
int maxPicks = optionInt("numPicks", 100);
int i=0;
boolean isRefSeq=FALSE, isMgcBad=FALSE;
struct hash *posHash = newHash(12), *agxHash = newHash(12);
struct bed *bed = NULL;
char buff[256];
htmlFileName = optionVal("htmlFile", NULL);
htmlFrameFileName = optionVal("htmlFrameFile", "frame.html");
orthoEvalFile = optionVal("orthoEvalFile", NULL);
db = optionVal("db", NULL);
bedFileName = optionVal("bedOutFile", NULL);
orthoBedFileName = optionVal("orthoBedOut", NULL);
if(htmlFileName == NULL || orthoEvalFile == NULL || db == NULL ||
bedFileName == NULL || orthoBedFileName == NULL )
errAbort("Missing parameters. Use -help for usage.");
warn("Loading orthoEvals.");
evList = orthoEvalLoadAll(orthoEvalFile);
warn("Creating intron records");
for(ev = evList; ev != NULL; ev = ev->next)
{
for(i=0; i<ev->numIntrons; i++)
{
occassionalDot();
iv = intronIvForEv(ev, i);
slAddHead(&ivList, iv);
}
}
warn("\nDone");
warn("Sorting");
slSort(&ivList, intronEvalCmp);
warn("Done.");
htmlOut = mustOpen(htmlFileName, "w");
bedOut = mustOpen(bedFileName, "w");
htmlFrameOut = mustOpen(htmlFrameFileName, "w");
orthoBedOut = mustOpen(orthoBedFileName, "w");
i=0;
fprintf(htmlOut, "<html><body><table border=1><tr><th>Num</th><th>Mouse Acc.</th><th>Score</th><th>TS Pick</th></tr>\n");
warn("Filtering");
safef(buff, sizeof(buff), "tmp");
for(iv = ivList; iv != NULL && maxPicks > 0; iv = iv->next)
{
if(isUniqueCoordAndAgx(db, iv, posHash, agxHash) && iv->support == 0 && !isOverlappedByRefSeq(db, iv) &&
! isOverlappedByEst(db, iv) && ! isOverlappedByMRna(db, iv))
{
boolean twinScan = (coordOverlappedByTable(db, iv->chrom, iv->e1S, iv->e1E, "mgcTSExpPcr") &&
coordOverlappedByTable(db, iv->chrom, iv->e2S, iv->e2E, "mgcTSExpPcr"));
bed = bedForIv(iv);
if(sameString(buff, "tmp"))
safef(buff, sizeof(buff), "%s:%d-%d", bed->chrom, bed->chromStart-50, bed->chromEnd+50);
// isMgcBad = isOverlappedByMgcBad(iv);
fprintf(htmlOut, "<tr><td>%d</td><td><a target=\"browser\" "
"href=\"http://mgc.cse.ucsc.edu/cgi-bin/hgTracks?db=hg15&position=%s:%d-%d\"> "
"%s </a></td><td>%d</td><td>%s</td></tr>\n",
++i,bed->chrom, bed->chromStart-50, bed->chromEnd+50, bed->name, bed->score,
twinScan ? "yes" : "no");
bedTabOutN(bed, 12, bedOut);
bedTabOutN(iv->ev->orthoBed, 12, orthoBedOut);
bedFree(&bed);
maxPicks--;
}
}
writeOutFrames(htmlFrameOut, htmlFileName, db, bedFileName, buff);
fprintf(htmlOut, "</table></body></html>\n");
carefulClose(&bedOut);
carefulClose(&htmlOut);
carefulClose(&htmlFrameOut);
carefulClose(&orthoBedOut);
warn("Done.");
hashFree(&posHash);
hashFree(&agxHash);
}
void outputBedsFromPsls(struct hash *pslHash,char *bedOutName, char *expRecordOutName,
char *affyFileName, char *expFileName)
/** For each set of entries in affyFile find matching psl and create a bed. */
{
struct bed *bed = NULL, *b=NULL;
struct psl *pslList = NULL, *psl = NULL;
struct hash *expHash = NULL;
int numExps = 0;
int expCount = 0;
int i =0;
char *probeSet = NULL;
char *row[4];
char key[128];
struct slName *expNames = NULL, *name = NULL;
FILE *bedOut = NULL;
FILE *expRecordOut = NULL;
char *toDiffFileName = optionVal("toDiffFile", NULL);
FILE *toDiffOut = NULL;
struct lineFile *lf = NULL;
fillInExpHash(expFileName, &expHash, &expNames, &expCount);
lf = lineFileOpen(affyFileName, TRUE);
bedOut = mustOpen(bedOutName, "w");
if(toDiffFileName != NULL)
toDiffOut = mustOpen(toDiffFileName, "w");
/* Loop through either adding experiments to beds or if new
probeset create bed from psl and start over. */
while(lineFileChopNextTab(lf, row, sizeof(row)))
{
/* Do we have to make a new bed? */
if(probeSet == NULL || differentWord(probeSet, row[0]))
{
occassionalDot();
numExps = 0;
/* If we have probeset print out the current beds. */
if(probeSet != NULL)
{
for(b = bed; b != NULL; b = b->next)
{
int avgCount = 0;
for(i = 0; i < b->expCount; i++)
if(b->expScores[i] != -10000)
avgCount++;
if(avgCount != 0 && b->score > 0)
b->score = log(b->score / avgCount) * 100;
else
b->score = 0;
bedTabOutN(b, 15, bedOut);
if(toDiffOut != NULL)
outputToDiffRecord(b, expNames, toDiffOut);
}
}
bedFreeList(&bed);
/* Lookup key in pslHash to find list of psl. */
safef(key, sizeof(key), "%s", row[0]);
pslList = hashFindVal(pslHash, key);
/* Can have multiple psls. */
for(psl = pslList; psl != NULL; psl = psl->next)
{
b = bedFromPsl(psl);
AllocArray(b->expIds, expCount );
AllocArray(b->expScores, expCount);
b->expCount = expCount;
initBedScores(b, expCount);
slAddHead(&bed, b);
}
}
if(bed != NULL)
{
/* Allocate larger arrays if necessary. */
if(numExps > expCount)
{
errAbort("Supposed to be %d experiments but probeset %s has at least %d",
expCount, bed->name, numExps);
}
for(b = bed; b != NULL; b = b->next)
{
int exp = hashIntVal(expHash, row[1]);
if(differentWord(row[3], "NaN"))
b->expScores[exp] = atof(row[3]);
if(differentWord(row[2], "NaN"))
b->score += atof(row[2]);
}
numExps++;
}
freez(&probeSet);
probeSet = cloneString(row[0]);
}
expRecordOut = mustOpen(expRecordOutName, "w");
i = 0;
for(name = expNames; name != NULL; name = name->next)
{
subChar(name->name, ',', '_');
subChar(name->name, ' ', '_');
fprintf(expRecordOut, "%d\t%s\tuclaExp\tuclaExp\tuclaExp\tuclaExp\t1\t%s,\n", i++, name->name, name->name);
}
hashFree(&expHash);
slFreeList(&expNames);
carefulClose(&expRecordOut);
carefulClose(&bedOut);
lineFileClose(&lf);
}
void featureBits(char *database, int tableCount, char *tables[])
/* featureBits - Correlate tables via bitmap projections and booleans. */
{
struct sqlConnection *conn = NULL;
char *bedName = optionVal("bed", NULL), *faName = optionVal("fa", NULL);
char *binName = optionVal("bin", NULL);
char *bedRegionInName = optionVal("bedRegionIn", NULL);
char *bedRegionOutName = optionVal("bedRegionOut", NULL);
FILE *bedFile = NULL, *faFile = NULL, *binFile = NULL;
FILE *bedRegionOutFile = NULL;
struct bed *bedRegionList = NULL;
boolean faIndependent = FALSE;
struct chromInfo *cInfo;
if (bedName)
bedFile = mustOpen(bedName, "w");
if (binName)
binFile = mustOpen(binName, "w");
if ((bedRegionInName && !bedRegionOutName) || (!bedRegionInName && bedRegionOutName))
errAbort("bedRegionIn and bedRegionOut must both be specified");
if (faName)
{
boolean faMerge = optionExists("faMerge");
faFile = mustOpen(faName, "w");
if (tableCount > 1)
{
if (!faMerge)
errAbort("For fa output of multiple tables you must use the "
"faMerge option");
}
faIndependent = (!faMerge);
}
if (chromSizes != NULL)
chromInfoList = chromInfoLoadAll(chromSizes);
else
chromInfoList = fbCreateChromInfoList(clChrom, database);
if (!countGaps)
conn = hAllocConn(database);
checkInputExists(conn, database, chromInfoList, tableCount, tables);
if (!faIndependent)
{
double totalBases = 0, totalBits = 0;
int firstTableBits = 0, secondTableBits = 0;
int *pFirstTableBits = NULL, *pSecondTableBits = NULL;
double totalFirstBits = 0, totalSecondBits = 0;
static int dotClock = 1;
if (calcEnrichment)
{
pFirstTableBits = &firstTableBits;
pSecondTableBits = &secondTableBits;
}
if (bedRegionInName)
{
struct lineFile *lf = lineFileOpen(bedRegionInName, TRUE);
struct bed *bed;
char *row[3];
bedRegionOutFile = mustOpen(bedRegionOutName, "w");
while (lineFileRow(lf, row))
{
if (startsWith(row[0],"#")||startsWith(row[0],"chrom"))
continue;
bed = bedLoad3(row);
slAddHead(&bedRegionList, bed);
}
lineFileClose(&lf);
slReverse(&bedRegionList);
}
for (cInfo = chromInfoList; cInfo != NULL; cInfo = cInfo->next)
{
if (inclChrom(cInfo->chrom))
{
int chromBitSize;
int chromSize = cInfo->size;
verbose(3,"chromFeatureBits(%s)\n", cInfo->chrom);
chromFeatureBits(conn, database, cInfo->chrom, tableCount, tables,
bedFile, faFile, binFile, bedRegionList, bedRegionOutFile,
chromSize, &chromBitSize, pFirstTableBits, pSecondTableBits
);
totalBases += countBases(conn, cInfo->chrom, chromSize, database);
totalBits += chromBitSize;
totalFirstBits += firstTableBits;
totalSecondBits += secondTableBits;
if (dots > 0)
{
if (--dotClock <= 0)
{
fputc('.', stdout);
fflush(stdout);
dotClock = dots;
}
}
}
}
if (dots > 0)
{
fputc('\n', stdout);
fflush(stdout);
}
if (calcEnrichment)
fprintf(stderr,"%s %5.3f%%, %s %5.3f%%, both %5.3f%%, cover %4.2f%%, enrich %4.2fx\n",
tables[0],
100.0 * totalFirstBits/totalBases,
tables[1],
100.0 * totalSecondBits/totalBases,
100.0 * totalBits/totalBases,
100.0 * totalBits / totalFirstBits,
(totalBits/totalSecondBits) / (totalFirstBits/totalBases) );
else
fprintf(stderr,"%1.0f bases of %1.0f (%4.3f%%) in intersection\n",
totalBits, totalBases, 100.0*totalBits/totalBases);
}
else
{
int totalItems = 0;
double totalBases = 0;
int itemCount, baseCount;
for (cInfo = chromInfoList; cInfo != NULL; cInfo = cInfo->next)
{
if (inclChrom(cInfo->chrom))
{
chromFeatureSeq(conn, database, cInfo->chrom, tables[0],
bedFile, faFile, &itemCount, &baseCount);
totalBases += countBases(conn, cInfo->chrom, baseCount, database);
totalItems += itemCount;
}
}
}
hFreeConn(&conn);
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, optionSpecs);
if (optionExists("algoHelp"))
prAlgo();
if (argc != 3)
usage("wrong # of args");
gLocalNearBest = optionFrac("localNearBest", gLocalNearBest);
gGlobalNearBest = optionFrac("globalNearBest", gGlobalNearBest);
if ((gLocalNearBest >= 0.0) && (gGlobalNearBest >= 0.0))
errAbort("can only specify one of -localNearBest and -globalNearBest");
if (optionExists("usePolyTHead"))
gCDnaOpts |= cDnaUsePolyTHead;
if (optionExists("ignoreNs"))
gCDnaOpts |= cDnaIgnoreNs;
if (optionExists("ignoreIntrons"))
gCDnaOpts |= cDnaIgnoreIntrons;
if (optionExists("repsAsMatch"))
gCDnaOpts |= cDnaRepsAsMatch;
gMinId = optionFrac("minId", gMinId);
gMinCover = optionFrac("minCover", gMinCover);
gMinSpan = optionFrac("minSpan", gMinSpan);
gMinQSize = optionInt("minQSize", gMinQSize);
gMaxAligns = optionInt("maxAligns", gMaxAligns);
gMaxAlignsDrop = optionInt("maxAlignsDrop", gMaxAlignsDrop);
if ((gMaxAligns >= 0) && (gMaxAlignsDrop >= 0))
errAbort("cannot specify both -maxAligns and -maxAlignsDrop");
gMinAlnSize = optionInt("minAlnSize", gMinAlnSize);
gMinNonRepSize = optionInt("minNonRepSize", gMinNonRepSize);
gMaxRepMatch = optionFrac("maxRepMatch", gMaxRepMatch);
gPolyASizes = optionVal("polyASizes", NULL);
if (optionExists("usePolyTHead") && (gPolyASizes == NULL))
errAbort("must specify -polyASizes with -usePolyTHead");
gHapRegions = optionVal("hapRegions", NULL);
gBestOverlap = optionExists("bestOverlap");
gDropped = optionVal("dropped", NULL);
gWeirdOverlappped = optionVal("weirdOverlapped", NULL);
gFilterWeirdOverlapped = optionExists("filterWeirdOverlapped");
gHapRefMapped = optionVal("hapRefMapped", NULL);
gHapRefCDnaAlns = optionVal("hapRefCDnaAlns", NULL);
gHapLociAlns = optionVal("hapLociAlns", NULL);
if (optionExists("noValidate"))
gValidate = FALSE;
cDnaAlignsAlnIdQNameMode = optionExists("alnIdQNameMode");
if (optionExists("ignoreNs"))
gCDnaOpts |= cDnaIgnoreNs;
gUniqueMapped = optionExists("uniqueMapped");
gDecayMinCover = optionExists("decayMinCover");
char *blackList = optionVal("blackList", NULL);
if (blackList != NULL)
gBlackListRanges = genbankBlackListParse(blackList);
if ( gDecayMinCover && (gMinCover > 0.0))
errAbort("can only specify one of -minCoverage and -decayMinCoverage");
pslCDnaFilter(argv[1], argv[2]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
boolean drop, move, copy;
struct sigaction sigSpec;
setlinebuf(stdout);
setlinebuf(stderr);
ZeroVar(&sigSpec);
sigSpec.sa_handler = sigStopSignaled;
sigSpec.sa_flags = SA_RESTART;
if (sigaction(SIGUSR1, &sigSpec, NULL) < 0)
errnoAbort("can't set SIGUSR1 handler");
optionInit(&argc, argv, optionSpecs);
drop = optionExists("drop");
move = optionExists("move");
copy = optionExists("copy");
gReload = optionExists("reload");
if (move || copy)
{
if (argc != 3)
usage();
}
else if (argc != 2)
usage();
if ((drop+move+copy) > 1)
errAbort("can only specify one of -drop, -move, or -copy");
gbVerbInit(optionInt("verbose", 0));
if (gbVerbose >= 6)
sqlMonitorEnable(JKSQL_TRACE);
if (drop)
dropAll(argv[1]);
else if (move)
moveAll(argv[1], argv[2]);
else if (copy)
copyAll(argv[1], argv[2]);
else
{
char *reloadList = optionVal("reloadList", NULL);
gDatabase = argv[1];
gOptions = dbLoadOptionsParse(gDatabase);
gForceIgnoreDelete = optionExists("forceIgnoreDelete");
if (optionExists("rebuildDerived"))
gOptions.flags |= DBLOAD_BYPASS_GBLOADED|DBLOAD_REBUILD_DERIVED;
gMaxShrinkage = optionFloat("maxShrinkage", 0.1);
gGbdbGenBank = optionVal("gbdbGenBank", NULL);
if (gGbdbGenBank == NULL)
gGbdbGenBank = gbConfGet(gOptions.conf, "gbdb.genbank");
if (gGbdbGenBank == NULL)
gGbdbGenBank = "/gbdb/genbank";
gWorkDir = optionVal("workdir", "work/load");
if (gOptions.flags & DBLOAD_DRY_RUN)
printf("*** using dry run mode ***\n");
gbLoadRna(reloadList);
}
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
char *db, *cdsDb, *cdsFile, *pslSpec, *genePredFile;
int optCnt;
optionInit(&argc, argv, optionSpecs);
if (argc != 3)
usage();
pslSpec = argv[1];
genePredFile = argv[2];
db = optionVal("db", NULL);
cdsDb = optionVal("cdsDb", NULL);
cdsFile = optionVal("cdsFile", NULL);
gRequireUtr = optionExists("requireUtr");
if (optionExists("cdsMergeMod3") && !optionExists("cdsMergeSize"))
errAbort("must specify -cdsMergeSize with -cdsMergeMod3");
if (optionExists("cdsMergeSize") || optionExists("utrMergeSize"))
{
gCdsMergeSize = optionInt("cdsMergeSize", -1);
gUtrMergeSize = optionInt("utrMergeSize", -1);
if (optionExists("cdsMergeMod3"))
gPslOptions |= genePredPslCdsMod3;
if (optionExists("smallInsertSize") || optionExists("insertMergeSize"))
errAbort("can't specify -smallInsertSize or -insertMergeSize with -cdsMergeSize or -utrMergeSize");
}
else
{
int insertMergeSize = genePredStdInsertMergeSize;
if (optionExists("smallInsertSize"))
insertMergeSize = optionInt("smallInsertSize", genePredStdInsertMergeSize);
insertMergeSize = optionInt("insertMergeSize", genePredStdInsertMergeSize);
gCdsMergeSize = gUtrMergeSize = insertMergeSize;
}
gGenePredExt = optionExists("genePredExt");
gKeepInvalid = optionExists("keepInvalid");
gAllCds = optionExists("allCds");
gNoCds = optionExists("noCds");
gQuiet = optionExists("quiet");
gIgnoreUniqSuffix = optionExists("ignoreUniqSuffix");
if ((gAllCds || gNoCds) && ((cdsDb != NULL) || (cdsFile != NULL)))
errAbort("can't specify -allCds or -noCds with -cdsDb or -cdsFile");
if (gAllCds && gRequireUtr)
errAbort("can't specify -allCds with -requireUtr");
/* this is a bit of work to implement */
if ((gAllCds || gNoCds) && (db != NULL))
errAbort("can't specify -allCds or -noCds with -db");
optCnt = 0;
if (db != NULL)
optCnt++;
if (cdsDb == NULL)
optCnt++;
if (cdsFile != NULL)
optCnt++;
if (gAllCds)
optCnt++;
if (gNoCds)
optCnt++;
if (optCnt == 1)
errAbort("must specify one and only one of -db, -cdsDb, -cdsFile, -allCds, or -noCds");
mrnaToGene(db, cdsDb, cdsFile, pslSpec, genePredFile);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
char *chromInfo;
optionInit(&argc, argv, optionSpecs);
if (argc < 4)
usage();
noBin = optionExists("noBin") || optionExists("nobin");
noSort = optionExists("noSort");
strictTab = optionExists("tab");
oldTable = optionExists("oldTable");
sqlTable = optionVal("sqlTable", sqlTable);
renameSqlTable = optionExists("renameSqlTable");
trimSqlTable = optionExists("trimSqlTable");
as = optionVal("as", as);
type = optionVal("type", type);
hasBin = optionExists("hasBin");
noLoad = optionExists("noLoad");
noHistory = optionExists("noHistory");
bedGraph = optionInt("bedGraph",0);
bedDetail = optionExists("bedDetail");
minScore = optionInt("minScore",100);
if (minScore<0 || minScore>1000)
errAbort("minScore must be between 0-1000\n");
notItemRgb = optionExists("notItemRgb");
if (notItemRgb) itemRgb = FALSE;
maxChromNameLength = optionInt("maxChromNameLength",0);
dotIsNull = optionInt("dotIsNull",dotIsNull);
noStrict = optionExists("noStrict") || optionExists("nostrict");
allowStartEqualEnd = optionExists("allowStartEqualEnd");
tmpDir = optionVal("tmpDir", tmpDir);
nameIx = ! optionExists("noNameIx");
ignoreEmpty = optionExists("ignoreEmpty");
allowNegativeScores = optionExists("allowNegativeScores");
customTrackLoader = optionExists("customTrackLoader");
parseType();
/* turns on: noNameIx, ignoreEmpty, allowStartEqualEnd, allowNegativeScores
* -verbose=0 */
if (customTrackLoader)
{
type = NULL; /* because customTrack/Factory has already validated the input */
ignoreEmpty = TRUE;
noHistory = TRUE;
nameIx = FALSE;
allowStartEqualEnd = TRUE;
allowNegativeScores = TRUE;
verboseSetLevel(0);
expireSeconds = 1200; /* 20 minutes */
(void) signal(SIGALRM, selfApoptosis);
(void) alarm(expireSeconds); /* CGI timeout */
}
fillInScoreColumn = optionVal("fillInScore", NULL);
chromInfo=optionVal("chromInfo", NULL);
if (chromInfo)
{
if (!type)
errAbort("Only use chromInfo with type for validate");
// Get chromInfo from file
chrHash = chromHashFromFile(chromInfo);
}
else if (type)
{
// Get chromInfo from DB
chrHash = chromHashFromDatabase(argv[1]);
}
hgLoadBed(argv[1], argv[2], argc-3, argv+3);
return 0;
}
int main(int argc, char *argv[])
{
struct lineFile *pf, *ef, *apf;
FILE *of, *nf, *enf=NULL;
char *efName=NULL, filename[256];
int verb = 0;
verboseSetLevel(0);
optionInit(&argc, argv, optionSpecs);
if (argc < 3)
{
fprintf(stderr, "USAGE: pslAnal [-epcr=<file> -verbose=<level>] <isPCR psl file> <all.primers> <outfile>\n");
return 1;
}
verb = optionInt("verbose", 0);
verboseSetLevel(verb);
efName = optionVal("epcr", NULL);
pf = pslFileOpen(argv[1]);
apf = lineFileOpen(argv[2], TRUE);
of = mustOpen(argv[3], "w");
sprintf(filename, "%s.notfound.primers", argv[3]);
nf = mustOpen(filename, "w");
verbose(1, "Reading all.primers file\n");
readPrimerInfo(apf);
if (efName)
{
ef = lineFileOpen(efName, TRUE);
verbose(1, "Reading epcr file\n");
readEpcr(ef);
}
verbose(1, "Reading and processing isPCR file\n");
processPrimers(pf, of);
if (efName)
{
verbose(1, "Writing epcr.not.found file\n");
sprintf(filename, "epcr.not.found");
enf = mustOpen(filename, "w");
writeEpcrNotFound(enf);
}
verbose(1, "Writing out primers not found\n");
writePrimersNotFound(nf);
if (efName)
{
lineFileClose(&ef);
fclose(enf);
}
lineFileClose(&pf);
lineFileClose(&apf);
fclose(of);
fclose(nf);
return(0);
}
int main(int argc, char *argv[])
/* Process command line. */
{
struct sqlConnection *conn = NULL;
char *command = NULL;
optionInit(&argc, argv, options);
database = optionVal("database", database);
sqlPath = optionVal("sqlPath", sqlPath);
if (argc < 2)
usage();
command = argv[1];
if (argc >= 3)
setCurrentDir(argv[2]);
conn = sqlConnect(database);
if (sameWord(command,"INIT"))
{
if (argc != 2)
usage();
errAbort("INIT is probably too dangerous. DO NOT USE.");
/*
init(conn);
*/
}
else if (sameWord(command,"POP"))
{
if (argc != 2)
usage();
/* populate vgPrb where missing */
populateMissingVgPrb(conn);
}
else if (sameWord(command,"SEQ"))
{
if (argc != 4)
usage();
/* make fake probe sequences */
makeFakeProbeSeq(conn,argv[3]);
}
else if (sameWord(command,"ALI"))
{
if (argc != 4)
usage();
/* blat anything left that is not aligned,
nor even attempted */
doAlignments(conn,argv[3]);
}
else if (sameWord(command,"EXT"))
{
if (argc != 4)
usage();
/* update seq and extfile as necessary */
doSeqAndExtFile(conn,argv[3],"vgProbes");
}
else if (sameWord(command,"PSLMAP"))
{
if (argc != 5)
usage();
/* pslMap anything left that is not aligned,
nor even attempted */
doAlignmentsPslMap(conn,argv[3],argv[4]);
}
else if (sameWord(command,"REMAP"))
{
if (argc != 7)
usage();
/* re-map anything in track specified that is not aligned,
nor even attempted yet, using specified fasta file. */
doAlignmentsReMap(conn,argv[3],argv[4],argv[5],argv[6]);
}
else if (sameWord(command,"SELFMAP"))
{
if (argc != 4)
usage();
/* re-map anything in track specified that is not aligned,
nor even attempted yet, using specified fasta file. */
doAlignmentsSelfMap(conn,argv[3]);
}
else if (sameWord(command,"EXTALL"))
{
if (argc != 4)
usage();
/* update seq and extfile as necessary */
doSeqAndExtFile(conn,argv[3],"vgAllProbes");
}
else
usage();
sqlDisconnect(&conn);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
int i;
char *cp;
unsigned long long reversed;
size_t maxAlloc;
char asciiAlloc[32];
optionInit(&argc, argv, options);
if (argc < 2)
usage();
maxAlloc = 2100000000 *
(((sizeof(size_t)/4)*(sizeof(size_t)/4)*(sizeof(size_t)/4)));
sprintLongWithCommas(asciiAlloc, (long long) maxAlloc);
verbose(4, "#\tmaxAlloc: %s\n", asciiAlloc);
setMaxAlloc(maxAlloc);
/* produces: size_t is 4 == 2100000000 ~= 2^31 = 2Gb
* size_t is 8 = 16800000000 ~= 2^34 = 16 Gb
*/
dnaUtilOpen();
motif = optionVal("motif", NULL);
chr = optionVal("chr", NULL);
strand = optionVal("strand", NULL);
bedOutput = optionExists("bedOutput");
wigOutput = optionExists("wigOutput");
if (wigOutput)
bedOutput = FALSE;
else
bedOutput = TRUE;
if (chr)
verbose(2, "#\tprocessing chr: %s\n", chr);
if (strand)
verbose(2, "#\tprocessing strand: '%s'\n", strand);
if (motif)
verbose(2, "#\tsearching for motif: %s\n", motif);
else {
warn("ERROR: -motif string empty, please specify a motif\n");
usage();
}
verbose(2, "#\ttype output: %s\n", wigOutput ? "wiggle data" : "bed format");
verbose(2, "#\tspecified sequence: %s\n", argv[1]);
verbose(2, "#\tsizeof(motifVal): %d\n", (int)sizeof(motifVal));
if (strand)
{
if (! (sameString(strand,"+") | sameString(strand,"-")))
{
warn("ERROR: -strand specified ('%s') is not + or - ?\n", strand);
usage();
}
/* They are both on by default, turn off the one not specified */
if (sameString(strand,"-"))
doPlusStrand = FALSE;
if (sameString(strand,"+"))
doMinusStrand = FALSE;
}
motifLen = strlen(motif);
/* at two bits per character, size limit of motif is
* number of bits in motifVal / 2
*/
if (motifLen > (4*sizeof(motifVal))/2 )
{
warn("ERROR: motif string too long, limit %d\n", (4*(int)sizeof(motifVal))/2 );
usage();
}
cp = motif;
motifVal = 0;
complementVal = 0;
for (i = 0; i < motifLen; ++i)
{
switch (*cp)
{
case 'a':
case 'A':
motifVal = (motifVal << 2) | A_BASE_VAL;
complementVal = (complementVal << 2) | T_BASE_VAL;
break;
case 'c':
case 'C':
motifVal = (motifVal << 2) | C_BASE_VAL;
complementVal = (complementVal << 2) | G_BASE_VAL;
break;
case 'g':
case 'G':
motifVal = (motifVal << 2) | G_BASE_VAL;
complementVal = (complementVal << 2) | C_BASE_VAL;
break;
case 't':
case 'T':
motifVal = (motifVal << 2) | T_BASE_VAL;
complementVal = (complementVal << 2) | A_BASE_VAL;
break;
default:
warn(
"ERROR: character in motif: '%c' is not one of ACGT\n", *cp);
usage();
}
++cp;
}
reversed = 0;
for (i = 0; i < motifLen; ++i)
{
int base;
base = complementVal & 3;
reversed = (reversed << 2) | base;
complementVal >>= 2;
}
complementVal = reversed;
verbose(2, "#\tmotif numerical value: %llu (%#llx)\n", motifVal, motifVal);
verbose(2, "#\tcomplement numerical value: %llu (%#llx)\n", complementVal, complementVal);
if (motifLen < 5)
{
warn("ERROR: motif string must be more than 4 characters\n");
usage();
}
findMotif(argv[1]);
return 0;
}
/* entry */
int main(int argc, char** argv)
{
char *selectFile, *inFile, *outFile, *dropFile;
optionInit(&argc, argv, optionSpecs);
if (argc != 4)
usage("wrong # args");
selectFile = argv[1];
inFile = argv[2];
outFile = argv[3];
/* select file options */
if (optionExists("selectFmt") && optionExists("selectCoordCols"))
errAbort("can't specify both -selectFmt and -selectCoordCols");
if (optionExists("selectFmt"))
selectFmt = parseFormatSpec(optionVal("selectFmt", NULL));
else if (optionExists("selectCoordCols"))
{
selectCoordCols = coordColsParseSpec("selectCoordCols",
optionVal("selectCoordCols", NULL));
selectFmt = COORD_COLS_FMT;
}
else
selectFmt = getFileFormat(selectFile);
if (optionExists("selectCds"))
selectCaOpts |= chromAnnCds;
if (optionExists("selectRange"))
selectCaOpts |= chromAnnRange;
if ((selectFmt == PSLQ_FMT) || (selectFmt == CHAINQ_FMT))
selectCaOpts |= chromAnnUseQSide;
/* in file options */
if (optionExists("inFmt") && optionExists("inCoordCols"))
errAbort("can't specify both -inFmt and -inCoordCols");
if (optionExists("inFmt"))
inFmt = parseFormatSpec(optionVal("inFmt", NULL));
else if (optionExists("inCoordCols"))
{
inCoordCols = coordColsParseSpec("inCoordCols",
optionVal("inCoordCols", NULL));
inFmt = COORD_COLS_FMT;
}
else
inFmt = getFileFormat(inFile);
inCaOpts = chromAnnSaveLines; // need lines for output
if (optionExists("inCds"))
inCaOpts |= chromAnnCds;
if (optionExists("inRange"))
inCaOpts |= chromAnnRange;
if ((inFmt == PSLQ_FMT) || (inFmt == CHAINQ_FMT))
inCaOpts |= chromAnnUseQSide;
/* select options */
useAggregate = optionExists("aggregate");
nonOverlapping = optionExists("nonOverlapping");
if (optionExists("strand") && optionExists("oppositeStrand"))
errAbort("can only specify one of -strand and -oppositeStrand");
if (optionExists("strand"))
selectOpts |= selStrand;
if (optionExists("oppositeStrand"))
selectOpts |= selOppositeStrand;
if (optionExists("excludeSelf") && (optionExists("idMatch")))
errAbort("can't specify both -excludeSelf and -idMatch");
if (optionExists("excludeSelf"))
selectOpts |= selExcludeSelf;
if (optionExists("idMatch"))
selectOpts |= selIdMatch;
criteria.threshold = optionFloat("overlapThreshold", 0.0);
criteria.thresholdCeil = optionFloat("overlapThresholdCeil", 1.1);
criteria.similarity = optionFloat("overlapSimilarity", 0.0);
criteria.similarityCeil = optionFloat("overlapSimilarityCeil", 1.1);
criteria.bases = optionInt("overlapBases", -1);
/* output options */
mergeOutput = optionExists("mergeOutput");
idOutput = optionExists("idOutput");
statsOutput = optionExists("statsOutput") || optionExists("statsOutputAll") || optionExists("statsOutputBoth");
if ((mergeOutput + idOutput + statsOutput) > 1)
errAbort("can only specify one of -mergeOutput, -idOutput, -statsOutput, -statsOutputAll, or -statsOutputBoth");
outputAll = optionExists("statsOutputAll");
outputBoth = optionExists("statsOutputBoth");
if (outputBoth)
outputAll = TRUE;
if (mergeOutput)
{
if (nonOverlapping)
errAbort("can't use -mergeOutput with -nonOverlapping");
if (useAggregate)
errAbort("can't use -mergeOutput with -aggregate");
if ((selectFmt == CHAIN_FMT) || (selectFmt == CHAINQ_FMT)
|| (inFmt == CHAIN_FMT) || (inFmt == CHAINQ_FMT))
if (useAggregate)
errAbort("can't use -mergeOutput with chains");
selectCaOpts |= chromAnnSaveLines;
}
dropFile = optionVal("dropped", NULL);
/* check for options incompatible with aggregate mode */
if (useAggregate)
{
int i;
for (i = 0; aggIncompatible[i] != NULL; i++)
{
if (optionExists(aggIncompatible[i]))
errAbort("-%s is not allowed -aggregate", aggIncompatible[i]);
}
}
overlapSelect(selectFile, inFile, outFile, dropFile);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
if (optionExists("help"))
{
printHelp();
}
if (argc != 3)
{
usage();
}
outMdb = optionVal("outMdb", outMdb);
onlyCompTdb = optionExists("onlyCompTdb");
release = optionVal("release", release);
releaseNum = optionInt("releaseNum", releaseNum);
char *database = argv[1];
char *composite = argv[2];
char defaultMetaDb[1024];
char defaultDownloadDir[1024];
char tempDownloadDir[1024];
char *src = getSrcDir();
char *org = cloneString(hOrganism(database));
org[0] = tolower(org[0]);
/* If user doesn't provide a metaDB, assume the path using the database and composite */
safef(defaultMetaDb, sizeof(defaultMetaDb), "%s/hg/makeDb/trackDb/%s/%s/metaDb/%s/%s.ra", src, org, database, release, composite);
/* If user doesn't provide a downloadDir, assume the path using the database and composite */
safef(defaultDownloadDir, sizeof(defaultDownloadDir), "/usr/local/apache/htdocs-hgdownload/goldenPath/%s/encodeDCC/%s", database, composite);
safef(tempDownloadDir, sizeof(tempDownloadDir), "/usr/local/apache/htdocs-hgdownload/goldenPath/%s/encodeDCC/%s", database, composite);
if (releaseNum)
safef(defaultDownloadDir, sizeof(defaultDownloadDir), "%s/release%d", tempDownloadDir, releaseNum);
/* If user doesn't provide a trackDB, assume the path using the database and composite */
char defaultTrackDb[1024];
/* Load encode composite-includer trackDb.wgEncode.ra */
char trackDbIncluder[1024];
safef(trackDbIncluder, sizeof(trackDbIncluder), "%s/hg/makeDb/trackDb/%s/%s/%s", src, org, database, "trackDb.wgEncode.ra");
struct raFile *includerFile = raFileRead(trackDbIncluder);
/* Find the correct trackDb.ra for the composite */
int numTagsFound = -1;
char *compositeName = findCompositeRa(includerFile, composite, release, &numTagsFound);
if (!compositeName)
errAbort("unable to find composite .ra for the track in trackDb.wgEncode.ra\n");
// if numTagsFound == 1 then a composite .ra with a single alpha tag exists already,
// so no further work required on trackDb.wgEncode.ra
safef(defaultTrackDb, sizeof(defaultTrackDb), "%s/hg/makeDb/trackDb/%s/%s/%s", src, org, database, compositeName);
verbose(1,"database: %s\ncomposite: %s\nrelease %s\ndefault trackDb: %s\ndefault metaDb: %s\ndefault downloadDir: %s\n",
database, composite, release, defaultTrackDb, defaultMetaDb, defaultDownloadDir);
char *metaDb = optionVal("metaDb",defaultMetaDb);
replaceTildeWithHome(&metaDb);
if (!fileExists(metaDb))
errAbort("metaDb %s does not exist.", metaDb);
char *trackDb = optionVal("trackDb",defaultTrackDb);
replaceTildeWithHome(&trackDb);
if (!fileExists(trackDb))
errAbort("trackDb %s does not exist.", trackDb);
char *downloadDir = optionVal("downloadDir",defaultDownloadDir);
replaceTildeWithHome(&downloadDir);
if (!fileExists(downloadDir))
errAbort("downloadDir %s does not exist.", downloadDir);
printf("metaDb = %s\n trackDb = %s\n downloadDir = %s\n",metaDb,trackDb,downloadDir);
metaCheck(database, composite, metaDb, trackDb, downloadDir);
return 0;
}
int main(int argc, char *argv[])
{
struct lineFile *pf, *ef, *apf;
FILE *of, *nf, *enf=NULL;
char *efName=NULL, filename[256], notFound[256];
int verb = 0;
verboseSetLevel(0);
optionInit(&argc, argv, optionSpecs);
if (argc < 3)
{
verbose(0, "usage: pslFilterPrimers [-epcr=<file> -verbose=<level>] <isPCR psl file> <all.primers> <outfile>\n");
return 1;
}
verb = optionInt("verbose", 0);
verboseSetLevel(verb);
efName = optionVal("epcr", NULL);
pf = pslFileOpen(argv[1]);
apf = lineFileOpen(argv[2], TRUE);
of = mustOpen(argv[3], "w");
safef(notFound, sizeof(filename), "%s.notfound.primers", argv[3]);
nf = mustOpen(notFound, "w");
verbose(1, "Reading all primers file: '%s'\n", argv[2]);
readPrimerInfo(apf);
if (efName)
{
ef = lineFileOpen(efName, TRUE);
verbose(1, "Reading epcr file: '%s'\n", efName);
readEpcr(ef);
}
verbose(1, "Reading isPCR file: '%s' processing output to: '%s'\n", argv[1], argv[3]);
processPrimers(pf, of);
if (efName)
{
safef(filename, sizeof(filename), "epcr.not.found");
verbose(1, "Writing %s file\n", filename);
enf = mustOpen(filename, "w");
writeEpcrNotFound(enf);
}
verbose(1, "Writing primers not found to file: '%s'\n", notFound);
writePrimersNotFound(nf);
if (efName)
{
lineFileClose(&ef);
fclose(enf);
}
lineFileClose(&pf);
lineFileClose(&apf);
fclose(of);
fclose(nf);
return(0);
}
void splitByGap(char *inName, int pieceSize, char *outRoot, long long estSize)
/* Split up file into pieces at most pieceSize bases long, at gap boundaries
* if possible. */
{
off_t pieces = (estSize + pieceSize-1)/pieceSize;
int digits = digitsBaseTen(pieces);
int minGapSize = optionInt("minGapSize", 1000);
boolean noGapDrops = optionExists("noGapDrops");
int maxN = optionInt("maxN", pieceSize-1);
boolean oneFile = optionExists("oneFile");
char fileName[512];
char dirOnly[256], noPath[128];
int pos, pieceIx = 0, writeCount = 0;
struct dnaSeq seq;
struct lineFile *lf = lineFileOpen(inName, TRUE);
FILE *f = NULL;
Bits *bits = NULL;
int seqCount = 0;
char *outFile = optionVal("out", NULL);
char *liftFile = optionVal("lift", NULL);
FILE *lift = NULL;
ZeroVar(&seq);
if (minGapSize < 1)
errAbort("ERROR: minGapSize must be > 0");
splitPath(outRoot, dirOnly, noPath, NULL);
if (oneFile)
{
sprintf(fileName, "%s.fa", outRoot);
f = mustOpen(fileName, "w");
}
else
fileName[0] = '\0';
if (liftFile)
lift = mustOpen(liftFile, "w");
while (faMixedSpeedReadNext(lf, &seq.dna, &seq.size, &seq.name))
{
bits = bitAlloc(seq.size);
setBitsN(seq.dna, seq.size, bits);
++seqCount;
if (outFile != NULL)
{
if (seqCount > 1)
errAbort("Can only handle in files with one sequence using out option");
bitsForOut(outFile, seq.size, bits);
}
pos = 0;
while (pos < seq.size)
{
boolean gotGap = FALSE;
int gapStart = 0;
int gapSize = 0;
int endSize = seq.size - pos;
int thisSize = min(endSize, pieceSize);
int startGapLen = 0;
if (seq.dna[pos] == 'n' || seq.dna[pos] == 'N')
{
startGapLen = bitFindClear(bits, pos, endSize) - pos;
verbose(3,"#\tstarting gap at %d for length: %d\n", pos,
startGapLen );
}
/* if a block is all gap for longer than minGapSize, then
* keep it all together in one large piece
*/
if (startGapLen > minGapSize)
{
if (noGapDrops)
{
writeOneByGap(oneFile, outRoot, digits, &pieceIx,
f, noPath, pos, startGapLen, &seq, lift,
&writeCount, fileName);
}
else
verbose(3,"#\tbeginning gap of %d size skipped\n", startGapLen);
thisSize = startGapLen;
}
else if (thisSize > 0 && bitCountRange(bits, pos, thisSize) <= maxN)
{
if (endSize>pieceSize) /* otherwise chops tiny piece at very end */
{
gotGap = findLastGap(&(seq.dna[pos]), thisSize, endSize,
minGapSize, &gapStart, &gapSize);
if (gotGap)
thisSize = gapStart;
}
writeOneByGap(oneFile, outRoot, digits, &pieceIx,
f, noPath, pos, thisSize, &seq, lift, &writeCount, fileName);
}
pos += thisSize;
if (gotGap)
{
/* last block is all gap, write it all out */
/*if ((pos + gapSize) >= seq.size)*/
if (noGapDrops)
{
writeOneByGap(oneFile, outRoot, digits, &pieceIx,
f, noPath, pos, gapSize, &seq ,lift, &writeCount, fileName);
verbose(3,
"#\tadding gapSize %d to pos %d -> %d and writing gap\n",
gapSize, pos, pos+gapSize);
}
else
verbose(3,"#\tadding gapSize %d to pos %d -> %d\n",
gapSize, pos, pos+gapSize);
pos += gapSize;
}
}
bitFree(&bits);
}
carefulClose(&f);
carefulClose(&lift);
lineFileClose(&lf);
printf("%d pieces of %d written\n", writeCount, pieceIx);
}
void hgLoadChromGraph(boolean doLoad, char *db, char *track, char *fileName)
/* hgLoadChromGraph - Load up chromosome graph. */
{
double minVal,maxVal;
struct chromGraph *el, *list;
FILE *f;
char *tempDir = ".";
char path[PATH_LEN], gbdbPath[PATH_LEN];
char *idTable = optionVal("idTable", NULL);
char *pathPrefix = NULL;
if (idTable == NULL)
list = chromGraphLoadAll(fileName);
else
list = chromGraphListWithTable(fileName, db, idTable);
if (list == NULL)
errAbort("%s is empty", fileName);
/* Figure out min/max values */
minVal = maxVal = list->val;
for (el = list->next; el != NULL; el = el->next)
{
if (optionExists("minusLog10"))
{
if (el->val == 1)
el->val = 0;
else if (el->val > 0)
el->val = -1 * log(el->val)/log(10);
}
if (el->val < minVal)
minVal = el->val;
if (el->val > maxVal)
maxVal = el->val;
}
/* Sort and write out temp file. */
slSort(&list, chromGraphCmp);
f = hgCreateTabFile(tempDir, track);
for (el = list; el != NULL; el = el->next)
chromGraphTabOut(el, f);
if (doLoad)
{
struct dyString *dy = dyStringNew(0);
struct sqlConnection *conn;
/* Set up connection to database and create main table. */
conn = hAllocConn(db);
sqlDyStringPrintf(dy, createString, track, hGetMinIndexLength(db));
sqlRemakeTable(conn, track, dy->string);
/* Load main table and clean up file handle. */
hgLoadTabFile(conn, tempDir, track, &f);
hgRemoveTabFile(tempDir, track);
/* If need be create meta table. If need be delete old row. */
if (!sqlTableExists(conn, "metaChromGraph"))
sqlUpdate(conn, metaCreateString);
else
{
dyStringClear(dy);
sqlDyStringPrintf(dy, "delete from metaChromGraph where name = '%s'",
track);
sqlUpdate(conn, dy->string);
}
/* Make chrom graph file */
safef(path, sizeof(path), "%s.cgb", track);
chromGraphToBin(list, path);
safef(path, sizeof(path), "/gbdb/%s/chromGraph", db);
pathPrefix = optionVal("pathPrefix", path);
safef(gbdbPath, sizeof(gbdbPath), "%s/%s.cgb", pathPrefix, track);
/* Create new line in meta table */
dyStringClear(dy);
sqlDyStringPrintf(dy, "insert into metaChromGraph values('%s',%f,%f,'%s');",
track, minVal, maxVal, gbdbPath);
sqlUpdate(conn, dy->string);
}
}
void hgExpDistance(char *database, char *posTable, char *expTable, char *outTable)
/* hgExpDistance - Create table that measures expression distance between pairs. */
{
struct sqlConnection *conn = sqlConnect(database);
struct sqlResult *sr;
char query[256];
char **row;
struct hash *expHash = hashNew(16);
int realExpCount = -1;
struct microData *geneList = NULL, *curGene, *gene;
int geneIx, geneCount = 0;
struct microData **geneArray = NULL;
float *weights = NULL;
char *tempDir = ".";
FILE *f = hgCreateTabFile(tempDir, outTable);
long time1, time2;
time1 = clock1000();
/* Get list/hash of all items with expression values. */
/* uglyf("warning: temporarily limited to 1000 records\n"); */
sqlSafef(query, sizeof(query), "select name,expCount,expScores from %s", posTable);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
char *name = row[0];
if (!hashLookup(expHash, name))
{
int expCount = sqlUnsigned(row[1]);
int commaCount;
float *expScores = NULL;
sqlFloatDynamicArray(row[2], &expScores, &commaCount);
if (expCount != commaCount)
errAbort("expCount and expScores don't match on %s in %s", name, posTable);
if (realExpCount == -1)
realExpCount = expCount;
if (expCount != realExpCount)
errAbort("In %s some rows have %d experiments others %d",
name, expCount, realExpCount);
AllocVar(gene);
gene->expCount = expCount;
gene->expScores = expScores;
hashAddSaveName(expHash, name, gene, &gene->name);
slAddHead(&geneList, gene);
}
}
sqlFreeResult(&sr);
conn = sqlConnect(database);
slReverse(&geneList);
geneCount = slCount(geneList);
printf("Have %d elements in %s\n", geneCount, posTable);
weights = getWeights(realExpCount);
if (optionExists("lookup"))
geneList = lookupGenes(conn, optionVal("lookup", NULL), geneList);
geneCount = slCount(geneList);
printf("Got %d unique elements in %s\n", geneCount, posTable);
sqlDisconnect(&conn); /* Disconnect because next step is slow. */
if (geneCount < 1)
errAbort("ERROR: unique gene count less than one ?");
time2 = clock1000();
verbose(2, "records read time: %.2f seconds\n", (time2 - time1) / 1000.0);
/* Get an array for sorting. */
AllocArray(geneArray, geneCount);
for (gene = geneList,geneIx=0; gene != NULL; gene = gene->next, ++geneIx)
geneArray[geneIx] = gene;
/* Print out closest 1000 in tab file. */
for (curGene = geneList; curGene != NULL; curGene = curGene->next)
{
calcDistances(curGene, geneList, weights);
qsort(geneArray, geneCount, sizeof(geneArray[0]), cmpMicroDataDistance);
for (geneIx=0; geneIx < 1000 && geneIx < geneCount; ++geneIx)
{
gene = geneArray[geneIx];
fprintf(f, "%s\t%s\t%f\n", curGene->name, gene->name, gene->distance);
}
dotOut();
}
printf("Made %s.tab\n", outTable);
time1 = time2;
time2 = clock1000();
verbose(2, "distance computation time: %.2f seconds\n", (time2 - time1) / 1000.0);
/* Create and load table. */
conn = sqlConnect(database);
distanceTableCreate(conn, outTable);
hgLoadTabFile(conn, tempDir, outTable, &f);
printf("Loaded %s\n", outTable);
/* Add indices. */
sqlSafef(query, sizeof(query), "alter table %s add index(query(12))", outTable);
sqlUpdate(conn, query);
printf("Made query index\n");
if (optionExists("targetIndex"))
{
sqlSafef(query, sizeof(query), "alter table %s add index(target(12))", outTable);
sqlUpdate(conn, query);
printf("Made target index\n");
}
hgRemoveTabFile(tempDir, outTable);
time1 = time2;
time2 = clock1000();
verbose(2, "table create/load/index time: %.2f seconds\n", (time2 - time1) / 1000.0);
}
void hgExpDistance(char *database, char *posTable, char *expTable, char *outTable)
/* hgExpDistance - Create table that measures expression distance between pairs. */
{
struct sqlConnection *conn = sqlConnect(database);
struct sqlResult *sr;
char query[256];
char **row;
struct hash *expHash = hashNew(16);
int realExpCount = -1;
struct microData *gene;
int rc, t;
pthread_t *threads = NULL;
pthread_attr_t attr;
int *threadID = NULL;
void *status;
char *tempDir = ".";
long time1, time2;
time1 = clock1000();
/* Get list/hash of all items with expression values. */
sqlSafef(query, sizeof(query), "select name,expCount,expScores from %s", posTable);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
char *name = row[0];
if (!hashLookup(expHash, name))
{
int expCount = sqlUnsigned(row[1]);
int commaCount;
float *expScores = NULL;
sqlFloatDynamicArray(row[2], &expScores, &commaCount);
if (expCount != commaCount)
errAbort("expCount and expScores don't match on %s in %s", name, posTable);
if (realExpCount == -1)
realExpCount = expCount;
if (expCount != realExpCount)
errAbort("In %s some rows have %d experiments others %d",
name, expCount, realExpCount);
AllocVar(gene);
gene->expCount = expCount;
gene->expScores = expScores;
hashAddSaveName(expHash, name, gene, &gene->name);
slAddHead(&geneList, gene);
}
}
sqlFreeResult(&sr);
conn = sqlConnect(database);
slReverse(&geneList);
geneCount = slCount(geneList);
printf("Have %d elements in %s\n", geneCount, posTable);
weights = getWeights(realExpCount);
if (optionExists("lookup"))
geneList = lookupGenes(conn, optionVal("lookup", NULL), geneList);
geneCount = slCount(geneList);
printf("Got %d unique elements in %s\n", geneCount, posTable);
sqlDisconnect(&conn); /* Disconnect because next step is slow. */
if (geneCount < 1)
errAbort("ERROR: unique gene count less than one ?");
time2 = clock1000();
verbose(2, "records read time: %.2f seconds\n", (time2 - time1) / 1000.0);
f = hgCreateTabFile(tempDir, outTable);
/* instantiate threads */
AllocArray( threadID, numThreads );
AllocArray( threads, numThreads );
pthread_attr_init( &attr );
pthread_mutex_init( &mutexfilehandle, NULL );
pthread_attr_setdetachstate( &attr, PTHREAD_CREATE_JOINABLE );
for (t = 0; t < numThreads; t++) {
threadID[t] = t;
rc = pthread_create( &threads[t], &attr, computeDistance,
(void *) &threadID[t]);
if (rc)
errAbort("ERROR: in pthread_create() %d\n", rc );
}
/* synchronize all threads */
for (t = 0; t < numThreads; t++) {
rc = pthread_join( threads[t], &status);
if (rc)
errAbort("ERROR: in pthread_join() %d\n", rc );
}
printf("Made %s.tab\n", outTable);
slFreeList( &geneList );
pthread_mutex_destroy( &mutexfilehandle );
pthread_attr_destroy( &attr );
time1 = time2;
time2 = clock1000();
verbose(2, "distance computation time: %.2f seconds\n", (time2 - time1) / 1000.0);
/* Create and load table. */
conn = sqlConnect(database);
distanceTableCreate(conn, outTable);
hgLoadTabFile(conn, tempDir, outTable, &f);
printf("Loaded %s\n", outTable);
/* Add indices. */
sqlSafef(query, sizeof(query), "alter table %s add index(query(12))", outTable);
sqlUpdate(conn, query);
printf("Made query index\n");
if (optionExists("targetIndex"))
{
sqlSafef(query, sizeof(query), "alter table %s add index(target(12))", outTable);
sqlUpdate(conn, query);
printf("Made target index\n");
}
hgRemoveTabFile(tempDir, outTable);
time1 = time2;
time2 = clock1000();
verbose(2, "table create/load/index time: %.2f seconds\n", (time2 - time1) / 1000.0);
}
void consForBed()
/* Open and read the bed file. Load consFile into an double
array for easy access and process. */
{
char *bedFileName = NULL;
char *chrom = NULL;
struct bed *bedList = NULL, *bed = NULL;
char *consFileName = NULL;
int *consProb = NULL;
char *consBedName = NULL;
FILE *consBedOut = NULL;
char *summaryBedName = NULL;
FILE *summaryBedOut = NULL;
/* Get the output file names. */
consBedName = optionVal("bedConsOut", NULL);
if(consBedName == NULL)
errAbort("Must specify an output file for bed conservation.");
summaryBedName = optionVal("summary", NULL);
/* What chromosome are we on? */
chrom = optionVal("chrom", NULL);
if(chrom == NULL)
errAbort("Must specify a chromosome.");
/* read in the beds. */
warn("Reading in beds.");
bedFileName = optionVal("bedFile", NULL);
if(bedFileName != NULL)
bedList = bedLoadAll(bedFileName);
else
errAbort("Must specify a bedFile.\n");
/* Read in the conservation scores. */
consFileName = optionVal("consFile", NULL);
if(consFileName != NULL)
consProb = readInConservationVals(consFileName);
else
errAbort("Must specify a conservation file.");
/* Open output files */
consBedOut = mustOpen(consBedName,"w");
if(summaryBedName != NULL)
summaryBedOut = mustOpen(summaryBedName, "w");
/* Process each individual bed. */
warn("Writing out conservation for beds.");
for(bed = bedList; bed != NULL; bed = bed->next)
{
if(differentString(chrom, bed->chrom))
continue;
outputBedConservation(bed, consProb, consBedOut, summaryBedOut);
}
warn("Cleaning up");
carefulClose(&consBedOut);
carefulClose(&summaryBedOut);
freez(&consProb);
warn("Done.");
}
void xmfaToMaf(char *in, char *out)
/* xmfaToMaf - Convert from xmfa to maf format. */
{
int c;
FILE *input = mustOpen(in, "r");
FILE *output = mustOpen(out, "w");
char* commentLine;
struct dnaSeq* sequence;
struct mafAli *ali;
struct sqlConnection* conn = hAllocConn();
mafWriteStart(output, "mlagan");
AllocVar(ali);
while(myFaReadMixedNext(input, TRUE, "default name", TRUE, &commentLine, &sequence)) {
char srcName[128];
c = fgetc(input);
if(c == '=' || c == '>') { /* add the current sequence and process the block if we've see an '='*/
char org[32];
char chrom[32];
int start;
int stop;
char strand;
struct mafComp *comp;
double score;
char buffer[1024];
ungetc(c, input);
AllocVar(comp);
/* parse the comment line */
sscanf(commentLine, ">%s %[^:]:%d-%d %c", org, chrom, &start, &stop, &strand);
/* build the name */
safef(srcName, sizeof(srcName), "%s.%s", optionVal(org, org), chrom);
comp->src = cloneString(srcName);
sqlSafef(buffer, 1024, "SELECT size FROM %s.chromInfo WHERE chrom = \"%s\"", optionVal(org, org), chrom);
assert(sqlQuickQuery(conn, buffer, buffer, 1024) != 0);
comp->srcSize = atoi(buffer);
comp->strand = strand;
start = start - 1;
comp->start = start;
comp->size = ungappedSize(sequence);
if(strand == '-')
comp->start = comp->srcSize - (comp->start + comp->size);
comp->text = sequence->dna;
sequence->dna = 0;
slAddHead(&ali->components, comp);
freeDnaSeq(&sequence);
if(c == '=') {
fscanf(input, "= score=%lf\n", &score);
ali->score = score;
slReverse(&ali->components);
mafWrite(output, ali);
mafAliFree(&ali);
AllocVar(ali);
}
}
}
mafWriteEnd(output);
}
