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; }