int main(int argc, char *argv[])
/* main routine, calls optionInt and sets database */
{
char *outFile = NULL;
boolean memTest=FALSE;
char *db = NULL;
if(argc == 1)
usage();
optionInit(&argc, argv, optionSpecs);
if(optionExists("help"))
usage();
db = optionVal("db", NULL);
if(db == NULL)
errAbort("Must set -db flag. Try -help for usage.");
if(optionExists("killList"))
initKillList();
outFile = optionVal("agxOut", NULL);
singleExonOk = optionExists("singleExonOk");
if(outFile == NULL)
errAbort("Must specify output file with -agxOut flag. Try -help for usage.");
if(optionVal("chromNib", NULL) != NULL)
initializeChromNib(optionVal("chromNib", NULL));
minAli = optionFloat("minAli", 0.0);
minCover = optionFloat("minCover", 0.0);
memTest = optionExists("memTest");
weightMrna = optionExists("weightMrna");
if(memTest == TRUE)
warn("Testing for memory leaks, use top to monitor and CTRL-C to stop.");
uniqPos = newHash(10);
createAltSplices(db, outFile, memTest );
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
maxGap = optionInt("maxGap", maxGap);
maxChain = optionInt("maxChain", maxChain);
minIdRatio = optionFloat("minId", 0.0)/100.0;
minScore = optionFloat("minScore", minScore);
bedOut = optionExists("bed");
if (argc != 5)
usage();
doIt(argv[1], argv[2], argv[3], argv[4]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
markovTable = optionVal("markovTable", NULL);
originalCoordinates = optionExists("originalCoordinates");
minScoreCutoff = optionFloat("minScoreCutoff", 0);
prior = optionFloat("prior", prior);
priorBackoff = optionFloat("priorBackoff", priorBackoff);
topOnly = optionExists("topOnly");
uniformBackground = optionExists("uniformBackground");
if (argc < 4)
usage();
motifFinder(argv[1], argv[2], argc-3, argv+3);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
int minSizeT = 0;
int minSizeQ = 0;
int minChainT = 0;
int minChainQ = 0;
double minMatch = LIFTOVER_MINMATCH;
double minBlocks = LIFTOVER_MINBLOCKS;
optionInit(&argc, argv, optionSpecs);
minMatch = optionFloat("minMatch", minMatch);
minBlocks = optionFloat("minBlocks", minBlocks);
fudgeThick = optionExists("fudgeThick");
multiple = optionExists("multiple");
noSerial = optionExists("noSerial");
if ((!multiple) && (optionExists("minSizeT") || optionExists("minSizeQ") ||
optionExists("minChainT") || optionExists("minChainQ") ||
optionExists("chainTable") || optionExists("noSerial")))
errAbort("minSizeT/Q, minChainT/Q, noSerial and chainTable can only be used with -multiple.");
if (optionExists("minSizeT") && optionExists("minChainT"))
errAbort("minSizeT is currently a deprecated synonym for minChainT. Can't set both.");
minSizeT = optionInt("minSizeT", minChainT); /* note: we're setting minChainT */
minSizeQ = optionInt("minSizeQ", minSizeQ);
minChainT = optionInt("minChainT", minChainT);
minChainQ = optionInt("minChainQ", minChainQ);
if (optionExists("bedPlus"))
{
bedPlus = optionInt("bedPlus", bedPlus);
if (bedPlus < 3 || bedPlus > 15)
errAbort("-bedPlus=%d is out of range -- BED has between 3 and 15 fields.", bedPlus);
}
ends = optionInt("ends", ends);
hasBin = optionExists("hasBin");
tabSep = optionExists("tab") || optionExists("tabSep");
if ((hasBin || tabSep) && !bedPlus)
usage();
chainTable = optionVal("chainTable", chainTable);
if (optionExists("errorHelp"))
errAbort("%s", liftOverErrHelp());
if (argc != 5)
usage();
liftOver(argv[1], argv[2], minMatch, minBlocks, minSizeT, minSizeQ,
minChainT, minChainQ, multiple, noSerial, chainTable, argv[3], argv[4]);
return 0;
}
static float optionFrac(char *name, float def)
/* get an option that must be in the range 0.0 and 1.0, or -1.0 to disable. */
{
float val = optionFloat(name, def);
if (((val < 0.0) || (val > 1.0)) && (val != -1.0))
errAbort("-%s must be in the range 0.0..1.0 (or -1.0 to disable)", name);
return val;
}
int main(int argc, char *argv[])
/* Process command line. */
{
struct tm *tm;
if (argc < 2)
usage();
optionInit(&argc, argv, options);
if (!optionExists("age"))
{
verbose(1,"ERROR: must specify an age argument, e.g.: -age=8\n");
usage();
}
if (time(&timeNow) < 1)
errAbort("can not obtain current time via time() function\n");
tm = localtime(&timeNow);
ageHours = optionFloat("age", 0.0);
time_t ageSeconds = (time_t)(ageHours * 3600); /* age in seconds */
dropTime = timeNow - ageSeconds;
if (ageHours > 0.0)
{
verbose(2,"# specified age = %f hours = %ld seconds\n", ageHours,
(unsigned long)ageSeconds);
verbose(2,"# current time: %d-%02d-%02d %02d:%02d:%02d %ld\n",
1900+tm->tm_year, 1+tm->tm_mon, tm->tm_mday,
tm->tm_hour, tm->tm_min, tm->tm_sec, (unsigned long)timeNow);
tm = localtime(&dropTime);
verbose(2,"# drop time: %d-%02d-%02d %02d:%02d:%02d %ld\n",
1900+tm->tm_year, 1+tm->tm_mon, tm->tm_mday,
tm->tm_hour, tm->tm_min, tm->tm_sec, (unsigned long)dropTime);
}
else
{
verbose(1,"ERROR: specified age %.f must be greater than 0.0\n", ageHours);
usage();
}
drop = optionExists("drop");
historyToo = optionExists("historyToo");
db = optionVal("db",db);
extFileCheck = optionExists("extFile");
extDel = optionExists("extDel");
tableStatus = optionExists("tableStatus");
topDir = optionVal("topDir", topDir);
verbose(2,"# drop requested: %s\n", drop ? "TRUE" : "FALSE");
verbose(2,"# historyToo: %s\n", historyToo ? "TRUE" : "FALSE");
verbose(2,"# extFile: %s\n", extFileCheck ? "TRUE" : "FALSE");
verbose(2,"# extDel: %s\n", extDel ? "TRUE" : "FALSE");
verbose(2,"# tableStatus: %s\n", tableStatus ? "TRUE" : "FALSE");
verbose(2,"# topDir: %s\n", topDir);
verbose(2,"# database: %s\n", db);
dbTrash(db);
if (verboseLevel() > 1)
printVmPeak();
return 0;
}
void twinOrfStats(char *axtFile, char *raFile, char *outFile)
/* twinOrfStats - Collect stats on refSeq cDNAs aligned to another species via axtForEst. */
{
struct hash *rsiHash = readRefRa(raFile);
struct lineFile *lf = lineFileOpen(axtFile, TRUE);
FILE *f = mustOpen(outFile, "w");
struct axt *axt;
static struct countMatrix kozak[10], all, utr5, utr3, cds;
static struct c2Counts c2All, c2Utr5, c2Utr3, c2Cds;
char label[64];
char *predictFile = optionVal("predict", NULL);
int i;
struct codonCounts codons;
initCounts(&codons, 1);
threshold = optionFloat("threshold", threshold);
while ((axt = axtRead(lf)) != NULL)
{
struct refSeqInfo *rsi = hashFindVal(rsiHash, axt->tName);
if (rsi != NULL && rsi->cdsStart >= 5)
{
if (checkAtg(axt, rsi->cdsStart))
{
for (i=0; i<10; ++i)
addPos(&kozak[i], axt, rsi->cdsStart - 5 + i);
addRange(&all, &c2All, axt, 0, rsi->size);
addRange(&utr5, &c2Utr5, axt, 0, rsi->cdsStart);
addRange(&cds, &c2Cds, axt, rsi->cdsStart, rsi->cdsEnd);
addRange(&utr3, &c2Utr3, axt, rsi->cdsEnd, rsi->size);
addCodons(&codons, axt, rsi->cdsStart, rsi->cdsEnd-3);
}
}
axtFree(&axt);
}
lineFileClose(&lf);
dumpCounts(f, &all, "all");
dumpCounts(f, &utr5, "utr5");
dumpCounts(f, &cds, "cds");
dumpCounts(f, &utr3, "utr3");
dumpM1(f, &c2All, "c2_all");
dumpM1(f, &c2Utr5, "c2_utr5");
dumpM1(f, &c2Cds, "c2_cds");
dumpM1(f, &c2Utr3, "c2_utr3");
for (i=0; i<10; ++i)
{
sprintf(label, "kozak[%d]", i-5);
dumpCounts(f, &kozak[i], label);
}
dumpCodon(f, &codons, "codon");
if (predictFile)
{
predict(kozak, &all, axtFile, predictFile, rsiHash);
}
}
int main( int argc, char *argv[] )
{
optionInit(&argc, argv, optionSpecs);
obsolete = optionExists("obsolete");
if (! obsolete)
{
verbose(1,"ERROR: This loader is obsolete. Please use: 'wigEncode'\n");
verbose(1,"\t(use -obsolete flag to run this encoder despite it being obsolete)\n");
errAbort("ERROR: wigAsciiToBinary is obsolete, use 'wigEncode' instead");
}
if (argc < 2)
usage();
add_offset = optionLongLong("offset", 0);
binsize = optionLongLong("binsize", 1024);
dataSpan = optionLongLong("dataSpan", 1);
chrom = optionVal("chrom", NULL);
wibFile = optionVal("wibFile", NULL);
name = optionVal("name", NULL);
minVal = optionFloat("minVal", -1 * INFINITY);
maxVal = optionFloat("maxVal", INFINITY);
trimVals = optionExists("minVal") || optionExists("maxVal");
verbose(2, "options: -verbose, offset= %llu, binsize= %llu, dataSpan= %llu\n",
add_offset, binsize, dataSpan);
if (chrom)
{
verbose(2, "-chrom=%s\n", chrom);
}
if (wibFile)
{
verbose(2, "-wibFile=%s\n", wibFile);
}
if (name)
{
verbose(2, "-name=%s\n", name);
}
wigAsciiToBinary(argc, argv);
exit(0);
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, optionSpecs);
gExonOverlap = optionFloat("exonOverlap", 0.0);
gCdsOnly = optionExists("cds");
if (argc != 4)
usage();
geneOverlap(argv[1], argv[2], argv[3]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, optionSpecs);
if (argc != 4)
usage();
minAli = optionFloat("minAli", minAli);
nearTop = optionFloat("nearTop", nearTop);
minCover = optionFloat("minCover", minCover);
minNearTopSize = optionInt("minNearTopSize", minNearTopSize);
ignoreSize = optionExists("ignoreSize");
if (optionExists("sizeMatters"))
warn("warning: -sizeMatters is deprecated and is now the default");
noIntrons = optionExists("noIntrons");
singleHit = optionExists("singleHit");
noHead = optionExists("nohead");
ignoreNs = optionExists("ignoreNs");
coverQSizeFile = optionVal("coverQSizes", NULL);
pslReps(argv[1], argv[2], argv[3]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionHash(&argc, argv);
scale = optionFloat("scale", scale);
maxGap = optionInt("maxGap", maxGap);
near = optionInt("near", near);
sampleList = optionVal("samples", cloneString(sampleList));
if (argc != 2)
usage();
calcGap(argv[1]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, optionSpecs);
aHitAny = optionExists("aHitAny");
bScore = optionExists("bScore");
minCoverage = optionFloat("minCoverage", minCoverage);
strictTab = optionExists("tab");
allowStartEqualEnd = optionExists("allowStartEqualEnd");
if (argc != 4)
usage();
bedIntersect(argv[1], argv[2], argv[3]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
userName = cloneString(getUser());
optionHashSome(&argc, argv, TRUE);
if (argc < 2)
usage();
paraHubHost = optionVal("host", paraHubHost);
cpuUsage = optionFloat("cpu", cpuUsage);
if (cpuUsage < 0)
usage();
ramUsage = paraParseRam(optionVal("ram","0"));
if (ramUsage == -1)
usage();
parasol(argv[1], argc-2, argv+2);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionHash(&argc, argv);
clRegion = optionVal("region", clRegion);
bigWinSize = optionInt("bigWinSize", bigWinSize);
bigStepSize = optionInt("bigStepSize", bigStepSize);
smallWinSize = optionInt("smallWinSize", smallWinSize);
threshold = optionFloat("threshold", threshold);
picksPer = optionInt("picksPer", picksPer);
htmlOutput = optionVal("html", htmlOutput);
avoidFile = optionVal("avoid", avoidFile);
randSeed = optionInt("randSeed", randSeed);
printWin = optionExists("printWin");
dnaUtilOpen();
if (argc != 4)
usage();
regionPicker(argv[1], argv[2], argv[3]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, optionSpecs);
if (argc != 6)
usage();
if (optionExists("prot"))
qType = tType = "prot";
qType = optionVal("q", qType);
tType = optionVal("t", tType);
if (sameWord(tType, "prot") || sameWord(tType, "dnax") || sameWord(tType, "rnax"))
minIdentity = 25;
minIdentity = optionFloat("minIdentity", minIdentity);
minScore = optionInt("minScore", minScore);
dots = optionInt("dots", 0);
outputFormat = optionVal("out", outputFormat);
/* set global for fuzzy find functions */
setFfIntronMax(optionInt("maxIntron", ffIntronMaxDefault));
gfClient(argv[1], argv[2], argv[3], argv[4], argv[5], tType, qType);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
if (argc < 2)
usage();
minCover = optionFloat("minCover", 80.0);
maxGap = optionInt("maxGap", 1000);
agp = optionExists("agp");
allowDuplicates = optionExists("allowDuplicates");
verbose(2,"#\tminCover: %% %g\n", minCover);
verbose(2,"#\tmaxGap: %u\n", maxGap);
verbose(2,"#\toutput type: %s\n", agp ? "AGP" : "BED");
clusterClone(argc, argv);
return(0);
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionHash(&argc, argv);
if (argc != 2)
usage();
xBins = optionInt("xBins", xBins);
yBins = optionInt("yBins", yBins);
xBinSize = optionInt("xBinSize", xBinSize);
yBinSize = optionInt("yBinSize", yBinSize);
xMin = optionInt("xMin", xMin);
yMin = optionInt("yMin", yMin);
psFile = optionVal("ps", NULL);
psSize = optionInt("psSize", psSize);
margin = optionInt("margin", margin);
doLog = optionExists("log");
labelStep = optionInt("labelStep", labelStep);
postScale = optionFloat("postScale", postScale);
textHist2(argv[1]);
return 0;
}
void borfMatcher(char *bedIn, char *borfIn, char *bedOutFile, char *genePredOutFile)
/* Top level function to open files and call other functions. */
{
struct borf *borf = NULL, *borfList = NULL;
struct bed *bed = NULL, *bedList = NULL;
struct genePred *gp = NULL;
float threshold = optionFloat("minScore", 50);
FILE *bedOut = mustOpen(bedOutFile, "w");
FILE *genePredOut = mustOpen(genePredOutFile, "w");
boolean keepSmall = optionExists("keepSmall");
boolean keepNmd = optionExists("keepNmd");
borfList = borfLoadAll(borfIn);
bedList = bedLoadAll(bedIn);
dotForUserInit(slCount(bedList)/10);
for(bed = bedList, borf = borfList; bed != NULL && borf != NULL; bed = bed->next, borf = borf->next)
{
dotForUser();
if(!stringIn(bed->name, borf->name))
errAbort("Trying to match up %s bed with %s borf - bad idea!", bed->name, borf->name);
/* Have to adjust cds end. Borf puts stop codon outside of cds,
we put it inside. */
borf->cdsEnd = min(borf->cdsEnd+3, borf->size);
if((borf->score > threshold || (keepSmall && borf->cdsSize > 0)) && sameString(borf->strand, "+"))
{
setThickStartStop(bed, borf);
if(keepNmd || !nmdTarget(bed))
{
gp = bedToGenePred(bed);
bedTabOutN(bed, 12, bedOut);
genePredTabOut(gp, genePredOut);
genePredFree(&gp);
}
}
}
warn("Done.");
carefulClose(&bedOut);
carefulClose(&genePredOut);
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
if (argc != 3)
usage();
database = optionVal("database", database);
doAverage = optionExists("average");
transpose = optionExists("transpose");
minAbsVal = optionFloat("minAbsVal", minAbsVal);
minMaxVal = optionInt("minMaxVal", minMaxVal);
c = optionDouble("addConst", c);
clump = optionVal("clump", clump);
doLoad = !optionExists("noLoad");
if (optionExists("tab"))
{
tabDir = optionVal("tab", tabDir);
makeDir(tabDir);
}
limit = optionInt("limit", limit);
hgRatioMicroarray(argv[1], argv[2]);
return 0;
}
int main(int argc, char *argv[])
{
struct lineFile *pf, *prf;
char filename[64], *pslTable;
optionInit(&argc, argv, optionSpecs);
if (argc < 4)
usage();
VERBOSE = optionExists("verbose");
SLOP = optionExists("slop");
SHORT = optionExists("short");
LONG = optionExists("long");
MISMATCH = optionExists("mismatch");
ORPHAN = optionExists("orphan");
NORANDOM = optionExists("noRandom");
NOBIN = optionExists("noBin");
MIN = optionInt("min",MIN);
MAX = optionInt("max",MAX);
TINSERT = optionInt("tInsert",TINSERT);
HARDMAX = optionInt("hardMax",HARDMAX);
if (SLOP)
SLOPVAL = optionInt("slopval",SLOPVAL);
else
SLOPVAL = 0;
NEARTOP = optionFloat("nearTop",NEARTOP);
NEARTOP = 1 - NEARTOP;
MIN_ID = optionFloat("minId",MIN_ID);
MIN_ORPHAN_ID = optionFloat("minOrphanId",MIN_ORPHAN_ID);
pf = pslFileOpen(argv[1]);
prf = lineFileOpen(argv[2],TRUE);
pslTable = cloneString(argv[3]);
sprintf(filename, "%s.pairs", argv[4]);
of = mustOpen(filename, "w");
if (SLOP)
{
sprintf(filename, "%s.slop", argv[4]);
sf = mustOpen(filename, "w");
}
if (ORPHAN)
{
sprintf(filename, "%s.orphan", argv[4]);
orf = mustOpen(filename, "w");
}
if (MISMATCH)
{
sprintf(filename, "%s.mismatch", argv[4]);
mf = mustOpen(filename, "w");
}
if (SHORT)
{
sprintf(filename, "%s.short", argv[4]);
esf = mustOpen(filename, "w");
}
if (LONG)
{
sprintf(filename, "%s.long", argv[4]);
elf = mustOpen(filename, "w");
}
if (VERBOSE)
printf("Reading pair file\n");
clones = newHash(23);
leftNames = newHash(23);
rightNames = newHash(23);
readPairFile(prf);
if (VERBOSE)
printf("Reading psl file\n");
readPslFile(pf);
if (VERBOSE)
printf("Creating Pairs\n");
pslPairs();
if (VERBOSE)
printf("Writing to files\n");
printOut(pslTable);
lineFileClose(&pf);
lineFileClose(&prf);
fclose(of);
if (ORPHAN)
fclose(orf);
if (SLOP)
fclose(sf);
if (MISMATCH)
fclose(mf);
if (SHORT)
fclose(esf);
if (LONG)
fclose(elf);
return 0;
}
void twinOrfStats(char *axtFile, char *raFile, char *outFile)
/* twinOrfStats - Collect stats on refSeq cDNAs aligned to another species via axtForEst. */
{
struct hash *rsiHash = readRefRa(raFile);
struct lineFile *lf = lineFileOpen(axtFile, TRUE);
FILE *f = mustOpen(outFile, "w");
struct axt *axt;
static struct c1Counts c1Kozak[10], c1all, c1utr5, c1utr3, c1cds;
static struct c2Counts c2Kozak[10], c2All, c2Utr5, c2Utr3, c2Cds;
static struct c3Counts c3All, c3Utr5, c3Utr3, c3Cds;
char label[64];
char *predictFile = optionVal("predict", NULL);
int i;
static struct c3Counts cod1, cod2, cod3, stop, earlyCod1, earlyCod2, earlyCod3;
int earlySize;
initC3Counts(&cod1, 0);
initC3Counts(&cod2, 0);
initC3Counts(&cod3, 0);
initC3Counts(&earlyCod1, 0);
initC3Counts(&earlyCod2, 0);
initC3Counts(&earlyCod3, 0);
initC3Counts(&c3Utr3, 0);
initC3Counts(&c3Utr5, 0);
initC3Counts(&stop, 0);
threshold = optionFloat("threshold", threshold);
earlyAaSize = optionInt("earlyAaSize", earlyAaSize);
earlySize = 3*earlyAaSize;
while ((axt = axtRead(lf)) != NULL)
{
struct refSeqInfo *rsi = hashFindVal(rsiHash, axt->tName);
if (rsi != NULL && rsi->cdsStart >= 6)
{
if (checkAtg(axt, rsi->cdsStart))
{
for (i=0; i<10; ++i)
addPos(&c1Kozak[i], &c2Kozak[i], axt, rsi->cdsStart - 5 + i);
addRange(&c1all, &c2All, &c3All, axt, 0, rsi->size);
addRange(&c1utr5, &c2Utr5, &c3Utr5, axt, 0, rsi->cdsStart);
addRange(&c1cds, &c2Cds, &c3Cds, axt, rsi->cdsStart, rsi->cdsEnd);
addRange(&c1utr3, &c2Utr3, &c3Utr3, axt, rsi->cdsEnd, rsi->size);
/* The +3+1 in the expression below breaks down as so: the
* +3 is to move past the first 'ATG' codon, which is part of
* the Kozak consensus model, not the coding model. The +1
* is so that we look at the 2nd and 3rd bases of the previous
* codon, and the first base of the current codon. */
addCodons(&earlyCod1, axt, rsi->cdsStart+3+1, rsi->cdsStart+1+earlySize);
addCodons(&earlyCod2, axt, rsi->cdsStart+3+2, rsi->cdsStart+2+earlySize);
addCodons(&earlyCod3, axt, rsi->cdsStart+3+3, rsi->cdsStart+3+earlySize);
addCodons(&cod1, axt, rsi->cdsStart+3+1+earlySize, rsi->cdsEnd-5);
addCodons(&cod2, axt, rsi->cdsStart+3+2+earlySize, rsi->cdsEnd-4);
addCodons(&cod3, axt, rsi->cdsStart+3+3+earlySize, rsi->cdsEnd-3);
addCodons(&stop, axt, rsi->cdsEnd-3, rsi->cdsEnd);
}
}
axtFree(&axt);
}
lineFileClose(&lf);
dumpC1(f, &c1all, "c1_all");
dumpC2(f, &c2All, "c2_all");
dumpC3(f, &c3All, "c3_all");
dumpC1(f, &c1utr5, "c1_utr5");
dumpC2(f, &c2Utr5, "c2_utr5");
dumpC3(f, &c3Utr5, "c3_utr5");
dumpC1(f, &c1cds, "c1_cds");
dumpC2(f, &c2Cds, "c2_cds");
dumpC3(f, &c3Cds, "c3_cds");
dumpC1(f, &c1utr3, "c1_utr3");
dumpC2(f, &c2Utr3, "c2_utr3");
dumpC3(f, &c3Utr3, "c3_utr3");
for (i=0; i<10; ++i)
{
sprintf(label, "c1_kozak[%d]", i-5);
dumpC1(f, &c1Kozak[i], label);
sprintf(label, "c2_kozak[%d]", i-5);
dumpC2(f, &c2Kozak[i], label);
}
dumpC3(f, &earlyCod1, "earlyCod1");
dumpC3(f, &earlyCod2, "earlyCod2");
dumpC3(f, &earlyCod3, "earlyCod3");
dumpC3(f, &cod1, "cod1");
dumpC3(f, &cod2, "cod2");
dumpC3(f, &cod3, "cod3");
dumpC3(f, &stop, "stop");
if (predictFile)
{
predict(c1Kozak, &c1all, axtFile, predictFile, rsiHash);
}
}
/* 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. */
{
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;
}
void netFilter(int inCount, char *inFiles[])
/* netFilter - Filter out parts of net.. */
{
FILE *f = stdout;
int i;
boolean doLine = optionExists("line");
tHash = hashCommaOption("t");
notTHash = hashCommaOption("notT");
qHash = hashCommaOption("q");
notQHash = hashCommaOption("notQ");
minScore = optionInt("minScore", -BIGNUM);
maxScore = optionFloat("maxScore", 9e99);
qStartMin = optionInt("qStartMin", -BIGNUM);
qStartMax = optionInt("qStartMax", BIGNUM);
qEndMin = optionInt("qEndMin", -BIGNUM);
qEndMax = optionInt("qEndMax", BIGNUM);
tStartMin = optionInt("tStartMin", -BIGNUM);
tStartMax = optionInt("tStartMax", BIGNUM);
tEndMin = optionInt("tEndMin", -BIGNUM);
tEndMax = optionInt("tEndMax", BIGNUM);
qOverlapStart = optionInt("qOverlapStart", -BIGNUM);
qOverlapEnd = optionInt("qOverlapEnd", BIGNUM);
tOverlapStart = optionInt("tOverlapStart", -BIGNUM);
tOverlapEnd = optionInt("tOverlapEnd", BIGNUM);
doSyn = optionExists("syn");
minTopScore = optionFloat("minTopScore", minTopScore);
minSynScore = optionFloat("minSynScore", minSynScore);
minSynSize = optionFloat("minSynSize", minSynSize);
minSynAli = optionFloat("minSynAli", minSynAli);
maxFar = optionFloat("maxFar", maxFar);
doChimpSyn = optionExists("chimpSyn");
doNonSyn = optionExists("nonsyn");
minGap = optionInt("minGap", minGap);
minAli = optionInt("minAli", minAli);
minSizeT = optionInt("minSizeT", minSizeT);
minSizeQ = optionInt("minSizeQ", minSizeQ);
fillOnly = optionExists("fill");
gapOnly = optionExists("gap");
types = optionMultiVal("type", types);
noRandom = optionExists("noRandom");
noHap = optionExists("noHap");
for (i=0; i<inCount; ++i)
{
struct lineFile *lf = lineFileOpen(inFiles[i], TRUE);
if (doLine)
{
netLineFilter(lf, f);
}
else
{
struct chainNet *net;
while ((net = chainNetRead(lf)) != NULL)
{
boolean writeIt = TRUE;
if (tHash != NULL && !hashLookup(tHash, net->name))
writeIt = FALSE;
if (notTHash != NULL && hashLookup(notTHash, net->name))
writeIt = FALSE;
if (noRandom && (endsWith(net->name, "_random")
|| startsWith("chrUn", net->name)
|| sameWord("chrNA", net->name) /* danRer */
|| sameWord("chrU", net->name))) /* dm */
writeIt = FALSE;
if (noHap && stringIn("_hap",net->name))
writeIt = FALSE;
if (writeIt)
{
writeFiltered(net, f);
}
chainNetFree(&net);
}
}
lineFileClose(&lf);
}
}
int main(int argc, char *argv[])
/* Process command line into global variables and call blat. */
{
boolean tIsProtLike, qIsProtLike;
#ifdef DEBUG
{
char *cmd = "blat hCrea.geno hCrea.mrna foo.psl -t=dnax -q=rnax";
char *words[16];
printf("Debugging parameters\n");
cmd = cloneString(cmd);
argc = chopLine(cmd, words);
argv = words;
}
#endif /* DEBUG */
optionInit(&argc, argv, options);
if (argc != 4)
usage();
/* Get database and query sequence types and make sure they are
* legal and compatable. */
if (optionExists("prot"))
qType = tType = gftProt;
if (optionExists("t"))
tType = gfTypeFromName(optionVal("t", NULL));
trimA = optionExists("trimA") || optionExists("trima");
trimT = optionExists("trimT") || optionExists("trimt");
trimHardA = optionExists("trimHardA");
switch (tType)
{
case gftProt:
case gftDnaX:
tIsProtLike = TRUE;
break;
case gftDna:
tIsProtLike = FALSE;
break;
default:
tIsProtLike = FALSE;
errAbort("Illegal value for 't' parameter");
break;
}
if (optionExists("q"))
qType = gfTypeFromName(optionVal("q", NULL));
if (qType == gftRnaX || qType == gftRna)
trimA = TRUE;
if (optionExists("noTrimA"))
trimA = FALSE;
switch (qType)
{
case gftProt:
case gftDnaX:
case gftRnaX:
minIdentity = 25;
qIsProtLike = TRUE;
break;
default:
qIsProtLike = FALSE;
break;
}
if ((tIsProtLike ^ qIsProtLike) != 0)
errAbort("t and q must both be either protein or dna");
/* Set default tile size for protein-based comparisons. */
if (tIsProtLike)
{
tileSize = 5;
minMatch = 1;
oneOff = FALSE;
maxGap = 0;
}
/* Get tile size and related parameters from user and make sure
* they are within range. */
tileSize = optionInt("tileSize", tileSize);
stepSize = optionInt("stepSize", tileSize);
minMatch = optionInt("minMatch", minMatch);
oneOff = optionExists("oneOff");
fastMap = optionExists("fastMap");
minScore = optionInt("minScore", minScore);
maxGap = optionInt("maxGap", maxGap);
minRepDivergence = optionFloat("minRepDivergence", minRepDivergence);
minIdentity = optionFloat("minIdentity", minIdentity);
gfCheckTileSize(tileSize, tIsProtLike);
if (minMatch < 0)
errAbort("minMatch must be at least 1");
if (maxGap > 100)
errAbort("maxGap must be less than 100");
/* Set repMatch parameter from command line, or
* to reasonable value that depends on tile size. */
if (optionExists("repMatch"))
repMatch = optionInt("repMatch", repMatch);
else
repMatch = gfDefaultRepMatch(tileSize, stepSize, tIsProtLike);
/* Gather last few command line options. */
noHead = optionExists("noHead");
ooc = optionVal("ooc", NULL);
makeOoc = optionVal("makeOoc", NULL);
mask = optionVal("mask", NULL);
qMask = optionVal("qMask", NULL);
repeats = optionVal("repeats", NULL);
if (repeats != NULL && mask != NULL && differentString(repeats, mask))
errAbort("The -mask and -repeat settings disagree. "
"You can just omit -repeat if -mask is on");
if (mask != NULL) /* Mask setting will also set repeats. */
repeats = mask;
outputFormat = optionVal("out", outputFormat);
dotEvery = optionInt("dots", 0);
/* set global for fuzzy find functions */
setFfIntronMax(optionInt("maxIntron", ffIntronMaxDefault));
setFfExtendThroughN(optionExists("extendThroughN"));
/* Call routine that does the work. */
blat(argv[1], argv[2], argv[3]);
return 0;
}
