int main(int argc, char *argv[])
/* Process command line. */
{
char *command;
bzpTime(NULL);
dnaUtilOpen();
setMaxAlloc(2LL*1024LL*1024LL*1024LL);
optionInit(&argc, argv, options);
port = optionInt("port", port);
host = optionVal("host", host);
netParseSubnet(optionVal("subnet", NULL), subnet);
cpuCount = optionInt("cpu", cpuCount);
if (argc < 2)
usage();
command = argv[1];
if (sameWord(command, "start"))
{
if (argc < 3)
usage();
serverStart(argv+2, argc-2);
}
else if (sameWord(command, "stop"))
{
serverStop();
}
else if (sameWord(command, "status"))
{
serverStatus();
}
else
usage();
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
char *scoreSchemeName = NULL;
optionHash(&argc, argv);
minScore = optionInt("minScore", minScore);
detailsName = optionVal("details", NULL);
gapFileName = optionVal("linearGap", NULL);
scoreSchemeName = optionVal("scoreScheme", NULL);
if (argc != 5)
usage();
if (scoreSchemeName != NULL)
{
verbose(1, "Reading scoring matrix from %s\n", scoreSchemeName);
scoreScheme = axtScoreSchemeRead(scoreSchemeName);
}
else
scoreScheme = axtScoreSchemeDefault();
dnaUtilOpen();
gapCalc = gapCalcReadOrDefault(gapFileName);
/* testGaps(); */
axtChain(argv[1], argv[2], argv[3], argv[4]);
return 0;
}
boolean gffOpen(struct gff *gff, char *fileName)
/* Initialize gff structure and open file for it. */
{
dnaUtilOpen();
/* Initialize structure and open file. */
zeroBytes(gff, sizeof(*gff));
gff->memPool = lmInit(16*1024);
gff->fileSize = fileSize(fileName);
if (gff->fileSize < 0 ||
(gff->file = fopen(fileName, "rb")) == NULL)
{
warn("Couldn't find the file named %s\n", fileName);
return FALSE;
}
strcpy(gff->fileName, fileName);
gff->bufSize = ArraySize(gff->buf);
/* Make sure it's a gff file. */
_gffSeekDoubleSharpLine(gff);
if (strncmp(gff->buf, _gffIdent, strlen(_gffIdent)) != 0)
{
warn("%s doesn't appear to be a .gff file\n", fileName);
return FALSE;
}
return TRUE;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
if (argc != 3)
usage();
clSeq = optionVal("seq", clSeq);
clStart = optionInt("start", clStart);
clEnd = optionInt("end", clEnd);
clSeqList = optionVal("seqList", clSeqList);
clBpt = optionVal("bpt", clBpt);
clBed = optionVal("bed", clBed);
clBedPos = optionExists("bedPos");
noMask = optionExists("noMask");
udcSetDefaultDir(optionVal("udcDir", udcDefaultDir()));
if (clBedPos && !clBed)
errAbort("the -bedPos option requires the -bed option");
if (clBed != NULL)
{
if (clSeqList != NULL)
errAbort("Can only have seqList or bed options, not both.");
if (clSeq != NULL)
errAbort("Can only have seq or bed options, not both.");
}
if ((clStart > clEnd) && (clSeq == NULL))
errAbort("must specify -seq with -start and -end");
if ((clSeq != NULL) && (clSeqList != NULL))
errAbort("can't specify both -seq and -seqList");
dnaUtilOpen();
twoBitToFa(argv[1], argv[2]);
return 0;
}
int main(int argc, char *argv[])
{
char *goodName, *badName = NULL;
double profile[16][4];
int alphabatize[4] = {A_BASE_VAL, C_BASE_VAL, G_BASE_VAL, T_BASE_VAL};
int i;
dnaUtilOpen();
if (argc < 2)
usage();
goodName = argv[1];
if (argc >= 3)
badName = argv[2];
fragFind(goodName, badName, 7, 2, profile);
printf("\n%s\n", unpacked);
for (i=0; i<4; ++i)
{
int baseVal = alphabatize[i];
printf("%c ", valToNt[baseVal]);
for (j=0; j<fragSize; ++j)
printf("%1.3f ", profile[j][baseVal]);
printf("\n");
}
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
if (argc != 2)
usage();
dnaUtilOpen();
foldGfx(argv[1]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
if (argc != 4)
usage();
dnaUtilOpen();
pslIntronsOnly(argv[1], argv[2], argv[3]);
return 0;
}
void doMiddle(struct cart *theCart)
/* Write header and body of html page. */
{
cart = theCart;
dnaUtilOpen();
cartWebStart(cart, NULL, "UCSC In-Silico PCR");
dispatch();
cartWebEnd();
}
int main(int argc, char *argv[])
/* Process command line. */
{
if (argc != 5)
usage();
dnaUtilOpen();
bedDown(argv[1], argv[2], argv[3], argv[4]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
if (argc != 3)
usage();
dnaUtilOpen();
sangPairs(argv[1], argv[2]);
return 0;
}
int main(int argc, char *argv[])
{
char *outDir;
struct cdaAli *cdaList;
struct clonePair *pairList;
struct dlList **goodEntities, **badEntities; /* Array of lists, one for each chromosome. */
int i;
if (argc != 2)
{
errAbort("genieCon - generates constraint GFF files for Genie from cDNA alignments\n"
"usage\n"
" genieCon outputDir\n"
"genieCon will create one file of form conXX.gff for each chromosome, where\n"
"the XX is replaced by the chromosome name.");
}
outDir = argv[1];
dnaUtilOpen();
anyChromNames(&chromNames, &chromCount);
goodEntities = needMem(chromCount * sizeof(goodEntities[0]));
badEntities = needMem(chromCount * sizeof(badEntities[0]));
for (i=0; i<chromCount; ++i)
{
goodEntities[i] = newDlList();
badEntities[i] = newDlList();
}
cdaList = readAllCda();
printf("Read in %d alignments\n", slCount(cdaList));
cdaCoalesceBlocks(cdaList);
printf("Coalesced blocks\n");
pairList = pairClones(cdaList);
printf("Before weeding genomic had %d clones\n", slCount(pairList));
pairList = weedGenomic(pairList);
printf("after weeding genomic had %d clones\n", slCount(pairList));
makeEntities(pairList, goodEntities);
for (i=0; i<chromCount; ++i)
{
printf("Made %d gene-like entities on chromosome %s\n",
dlCount(goodEntities[i]), chromNames[i]);
}
for (i=0; i<chromCount; ++i)
{
if (dlCount(goodEntities[i]) > 0)
{
separateEntities(goodEntities[i], badEntities[i]);
printf("%d good %d bad entities on chromosome %s\n",
dlCount(goodEntities[i]), dlCount(badEntities[i]), chromNames[i]);
saveEntities(goodEntities[i], outDir, "ez", chromNames[i]);
saveEntities(badEntities[i], outDir, "odd", chromNames[i]);
}
}
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionHash(&argc, argv);
if (argc != 5)
usage();
dnaUtilOpen();
pickCassettePcrPrimers(argv[1], argv[2], argv[3], argv[4]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
if (argc < 3)
usage();
dnaUtilOpen();
itsaMake(argc-2, argv+1, argv[argc-1]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
if (argc != 4)
usage();
dnaUtilOpen();
txCdsOrfInfo(argv[1], argv[2], argv[3]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionHash(&argc, argv);
dnaUtilOpen();
if (argc < 2)
usage();
axtCalcMatrix(argc-1, argv+1);
return 0;
}
int main(int argc, char** argv)
/* entry */
{
optionInit(&argc, argv, optionSpecs);
if (argc != 3)
usage("wrong # args");
gNoRc = optionExists("noRc");
dnaUtilOpen();
pslRcFile(argv[1], argv[2]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
dnaUtilOpen();
optionInit(&argc, argv, options);
maxSize = optionInt("maxSize", maxSize);
if (argc != 3)
usage();
itsaDump(argv[1], argv[2]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
dnaUtilOpen();
optionInit(&argc, argv, options);
if (argc != 4)
usage();
hardMask = optionExists("hardMask");
seqFromPsl(argv[1], argv[2], argv[3]);
return 0;
}
void dnaOrAaFilter(char *in, char *out, char filter[256])
/* Run chars through filter. */
{
char c;
dnaUtilOpen();
while ((c = *in++) != 0)
{
if ((c = filter[(int)c]) != 0) *out++ = c;
}
*out++ = 0;
}
long dnaOrAaFilteredSize(char *raw, char filter[256])
/* Return how long DNA will be after non-DNA is filtered out. */
{
char c;
long count = 0;
dnaUtilOpen();
while ((c = *raw++) != 0)
{
if (filter[(int)c]) ++count;
}
return count;
}
int main(int argc, char *argv[])
/* Process command line. */
{
dnaUtilOpen();
optionInit(&argc, argv, options);
if (argc != 6)
usage();
if (optionExists("conflictLog"))
conflictLog = mustOpen(optionVal("conflictLog", NULL), "w");
vgLoadMahoney(argv[1], argv[2], argv[3], argv[4], argv[5]);
return 0;
}
int main(int argc, char *argv[])
{
char *inName = "../lumpRep/repeats.out";
char *outName = "repeats.fa";
struct lump *lumpList;
dnaUtilOpen();
lumpList = readLumps(inName);
slSort(&lumpList, cmpCount);
saveBigLumps(lumpList, 6, outName);
return 0;
}
boolean isAllNt(char *seq, int size)
/* Return TRUE if all letters in seq are ACGTNU-. */
{
int i;
dnaUtilOpen();
for (i=0; i<size-1; ++i)
{
if (ntChars[(int)seq[i]] == 0)
return FALSE;
}
return TRUE;
}
int main(int argc, char *argv[])
{
char *geneName;
char title[256];
if (argc == 2 && sameWord(argv[1], "test"))
putenv("QUERY_STRING=geneName=I:4000-5500&hiliteNear=0.917112&intronsLowerCase=On");
geneName = cgiString("geneName");
sprintf(title, "%s DNA Sequence", geneName);
dnaUtilOpen();
htmShell(title, doMiddle, "QUERY");
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
dnaUtilOpen();
optionInit(&argc, argv, optionSpecs);
qChain = optionExists("qChain");
maxGap = optionInt("maxGap", maxGap);
splitOnInsert = !optionExists("noSplit");
if (argc != 6)
usage();
netToAxt(argv[1], argv[2], argv[3], argv[4], argv[5]);
return 0;
}
int main(int argc, char *argv[])
{
char *outputFormat = NULL;
if(argc < 4)
usage();
cgiSpoof(&argc, argv);
dnaUtilOpen();
outputFormat = cgiOptionalString("output");
if(outputFormat == NULL)
outputFormat = "sample";
mergeAffyFiles(argv[1], argv[2], argc-3, argv+3, outputFormat);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
if (argc < 3)
usage();
noMask = optionExists("noMask");
stripVersion = optionExists("stripVersion");
ignoreDups = optionExists("ignoreDups");
dnaUtilOpen();
faToTwoBit(argv+1, argc-2, argv[argc-1]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
bzpTime(NULL);
dnaUtilOpen();
optionInit(&argc, argv, options);
port = optionInt("port", port);
host = optionVal("host", host);
if (argc != 3)
usage();
blatzClient(argv[1], argv[2]);
return 0;
}
boolean isDna(char *poly, int size)
/* Return TRUE if letters in poly are at least 90% ACGTU */
{
int i;
int dnaCount = 0;
dnaUtilOpen();
for (i=0; i<size; ++i)
{
if (ntChars[(int)poly[i]])
dnaCount += 1;
}
return (dnaCount >= round(0.9 * size));
}
int test(int argc, char *argv[])
{
int start, stop;
if (argc != 9 && argc != 10)
usageErr();
inName = argv[0];
cdnaName = argv[1];
chromDir = argv[2];
goodLogName = argv[3];
badLogName = argv[4];
unusualName = argv[5];
errName = argv[6];
start = atoi(argv[7]);
stop = atoi(argv[8]);
if (start >= stop)
usageErr();
if (argc == 10)
c2gName = argv[9];
inFile = mustOpen(inName, "r");
goodLogFile = mustOpen(goodLogName, "w");
badLogFile = mustOpen(badLogName, "w");
unusualFile = mustOpen(unusualName, "w");
errFile = mustOpen(errName, "w");
pushWarnHandler(reportWarning);
dnaUtilOpen();
printf("Loading chromosomes\n");
loadGenome(chromDir, &chroms, &chromNames, &chromCount);
startRedoHash();
printf("Analysing %s\n", inName);
if (weAreWeb())
htmlHorizontalLine();
analyse(start, stop);
//endRedoHash();
freeGenome(&chroms, &chromNames, chromCount);
popWarnHandler();
fclose(inFile);
fclose(goodLogFile);
fclose(badLogFile);
fclose(unusualFile);
fclose(errFile);
return 0;
}
