4898794edd81be5285ea6e544acbedeaeb31bf78 max Tue Nov 23 08:10:57 2021 -0800 Fixing pointers to README file for license in all source code files. refs #27614 diff --git src/hg/orthoMap/orthoEvaluate.c src/hg/orthoMap/orthoEvaluate.c index 957ef87..1ab41c9 100644 --- src/hg/orthoMap/orthoEvaluate.c +++ src/hg/orthoMap/orthoEvaluate.c @@ -1,732 +1,732 @@ /** orthoEvaluate - Program to evaluate beds for: - Coding potenttial (Using Victor Solovyev's bestorf repeatedly.) - Overlap with native mRNAs/ESTs via altGraphX track. - Intron consensus sites. */ /* Copyright (C) 2013 The Regents of the University of California - * See README in this or parent directory for licensing information. */ + * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "hdb.h" #include "linefile.h" #include "hash.h" #include "options.h" #include "psl.h" #include "bed.h" #include "borf.h" #include "dnaseq.h" #include "fa.h" #include "portable.h" #include "dystring.h" #include "altGraphX.h" #include "bits.h" #include "dnautil.h" #include "orthoEval.h" #include "rbTree.h" #include "genePred.h" static struct rbTree *gpTree = NULL; static struct optionSpec optionSpecs[] = /* Our acceptable options to be called with. */ { {"help", OPTION_BOOLEAN}, {"db", OPTION_STRING}, {"bedFile", OPTION_STRING}, {"genePredFile", OPTION_STRING}, {"orthoEvalOut", OPTION_STRING}, {"bestOrfExe", OPTION_STRING}, {"tmpFa", OPTION_STRING}, {"tmpOrf", OPTION_STRING}, {"skipBorf", OPTION_BOOLEAN}, {"altGraphXTable", OPTION_STRING}, {NULL, 0} }; static char *optionDescripts[] = /* Description of our options for usage summary. */ { "Display this message.", "Database (i.e. hg15) that bedFile corresponds to.", "File with beds to be evaluated.", "[xor bedFile] File with gene predictions to be evaluated.", "File to output evaluation records.", "[optional default: borf] bestOrf executable name.", "[optional default: generated] temp fasta file for bestOrf.", "[optional default: generated] temp output file for bestOrf.", "[optional default: FALSE] skip doing orf prediction.", "[optional default: altGraphX] altGraphX tables." }; static boolean doHappyDots; /* output activity dots? */ void usage() /** Print usage and quit. */ { int i=0; warn("orthoEvaluate - Evaluate the coding potential of a bed.\n"); for(i=0; i<ArraySize(optionSpecs) -1; i++) fprintf(stderr, " -%s -- %s\n", optionSpecs[i].name, optionDescripts[i]); errAbort("\nusage:\n" " orthoEvaluate -db=hg15 -bedFile=mm3.hg15.orthoMap.bed -orthoEvalOut=orthoEval.tab\n"); } void occassionalDot() /* Write out a dot every 20 times this is called. */ { static int dotMod = 100; static int dot = 100; if (doHappyDots && (--dot <= 0)) { putc('.', stdout); fflush(stdout); dot = dotMod; } } struct bed *loadNativeAgxBedsForBed(char *db, struct bed *orthoBed, char *table) /* Load up all the beds that span the area in bed. */ { struct sqlConnection *conn = hAllocConn(db); int rowOffset; struct sqlResult *sr = hRangeQuery(conn, table, orthoBed->chrom, orthoBed->chromStart, orthoBed->chromEnd, NULL, &rowOffset); char **row; struct bed *bed = NULL, *bedList = NULL; if(!(hTableExists(db, table))) errAbort("orthoEvaluate::loadNativeAgxBedsForBed() - Please create table '%s' before accessing", table); while ((row = sqlNextRow(sr)) != NULL) { bed = bedLoadN(row + rowOffset, 12); slAddHead(&bedList, bed); } slSort(&bedList, bedCmp); sqlFreeResult(&sr); hFreeConn(&conn); return bedList; } void calcBasesOverlap(char *db, struct orthoEval *ev) /* Load the agxBed for the orthoEval and get the number of bases that overlap. Fill in the primary agxBed name with agxBed record that overlaps most. */ { Bits *nativeBits = NULL; Bits *orthoBits = NULL; unsigned int bitSize = 0; unsigned int minCoord = BIGNUM, maxCoord = 0; unsigned int offSet = 0; int i=0; int start = 0; int end = 0; int maxOverlap = 0; int currentOverlap =0; char *agxTable = optionVal("agxTable", "agxBed"); struct bed *bed = NULL, *orthoBed = NULL; //ev->orthoBed; assert(ev); assert(ev->orthoBed); orthoBed = ev->orthoBed; /* Load beds in this range. */ ev->agxBed = loadNativeAgxBedsForBed(db, ev->orthoBed, agxTable); if(ev->agxBed != NULL) ev->basesOverlap++; /* Find the minimum and maximum coordinates spans. */ for(bed = ev->agxBed; bed != NULL; bed = bed->next) { minCoord = min(bed->chromStart, minCoord); maxCoord = max(bed->chromEnd, maxCoord); } /* If we don't have any beds return. */ if(minCoord == BIGNUM || maxCoord == 0 || ev->agxBed == NULL) return; /* Finish off getting the min and max and allocate bitmaps. */ maxCoord = max(ev->orthoBed->chromEnd, maxCoord); minCoord = min(ev->orthoBed->chromStart, minCoord); bitSize = maxCoord - minCoord; nativeBits = bitAlloc(bitSize); orthoBits = bitAlloc(bitSize); /* Set the bits for each exon in the orthoBed. */ for(i=0; i<orthoBed->blockCount; i++) { start = orthoBed->chromStart + orthoBed->chromStarts[i] - minCoord; end = orthoBed->chromStart + orthoBed->chromStarts[i] + orthoBed->blockSizes[i] - minCoord; bitSetRange(orthoBits, start, end-start); } /* Set the bits for each exon in each bed. */ for(bed=ev->agxBed; bed != NULL; bed = bed->next) { for(i=0; i<bed->blockCount; i++) { start = bed->chromStart + bed->chromStarts[i] - minCoord; end = bed->chromStart + bed->chromStarts[i] + bed->blockSizes[i] - minCoord; bitSetRange(nativeBits, start, end-start); bitAnd(nativeBits, orthoBits, bitSize); currentOverlap = bitCountRange(orthoBits, 0, bitSize); ev->basesOverlap += currentOverlap; if(currentOverlap >= maxOverlap) { freez(&ev->agxBedName); ev->agxBedName = cloneString(bed->name); } bitClear(nativeBits, bitSize); } } bitFree(&orthoBits); bitFree(&nativeBits); } struct altGraphX *loadNativeAgxForBed(char *db, struct bed *orthoBed, char *table) /* Load up all the altGraphX's that span the area in bed. */ { struct sqlConnection *conn = hAllocConn(db); int rowOffset; struct sqlResult *sr = hRangeQuery(conn, table, orthoBed->chrom, orthoBed->chromStart, orthoBed->chromEnd, NULL, &rowOffset); char **row; struct altGraphX *agx = NULL, *agxList = NULL; if(!(hTableExists(db, table))) errAbort("orthoEvaluate::loadNativeAgxForBed() - Please create table '%s' before accessing", table); while ((row = sqlNextRow(sr)) != NULL) { agx = altGraphXLoad(row + rowOffset); if(sameString(orthoBed->strand, agx->strand)) slAddHead(&agxList, agx); else altGraphXFree(&agx); } sqlFreeResult(&sr); hFreeConn(&conn); return agxList; } void printIntArray(int *array, int count) /* Useful in gdb to see what is in an array. */ { int i; for(i=0;i<count; i++) printf("%d,", array[i]); printf("\n"); } int numInArray(int *array, int count, int val) /* Return the index in the array that val is found at or -1 if not found. */ { int i=0; for(i=0; i<count; i++) { if(array[i] == val) return i; } return -1; } int agxSupportForSplice(struct altGraphX *agx, struct bed *bed, int intron) /* Check to see if there is an set of edges in agx that support the exon, intron, exon juction centered on the intron in bed. */ { bool **em = NULL; /* Edge matrix for splicing graph. */ int support = 0; /* Number of mRNAs/ESTs supporting intron. */ int e1Start=0, e1End=0, /* Coordinates of exons. */ e2Start=0, e2End=0; int e1VS=-1, e1VE=-1, /* Vertex numbers in agx graph. */ e2VS=-1, e2VE=-1; /* --- Convenient shorthand for bits of agx --- */ int vC = 0; /* Number of vertices. */ int *vPos = NULL; /* Positions of vertices. */ unsigned char *vTypes = NULL; /* Types of vertices. */ struct evidence *ev = NULL; /* Evidence for edges. */ /* Sanity checks. */ assert(agx); assert(bed); assert(intron < bed->blockCount && intron >= 0); /* Initialization. */ vC = agx->vertexCount; vPos = agx->vPositions; vTypes = agx->vTypes; /* Get chromsomal starts/ends for exons. */ e1Start = bed->chromStart + bed->chromStarts[intron]; e1End = e1Start + bed->blockSizes[intron]; e2Start = bed->chromStart + bed->chromStarts[intron+1]; e2End = e2Start + bed->blockSizes[intron+1]; /* Find them in the graph if possible. */ e1VS = numInArray(vPos, vC, e1Start); e1VE = numInArray(vPos, vC, e1End); e2VS = numInArray(vPos, vC, e2Start); e2VE = numInArray(vPos, vC, e2End); /* If we found them get the support for each edge and sum them. */ if(e1VS == -1 || e1VE == -1 || e2VS == -1 || e2VE == -1) return 0; em = altGraphXCreateEdgeMatrix(agx); if(em[e1VS][e1VE] && em[e1VE][e2VS] && em[e2VS][e2VE]) { int edgeNum = -1; edgeNum = altGraphXGetEdgeNum(agx, e1VS, e1VE); ev = slElementFromIx(agx->evidence, edgeNum); support += ev->evCount; edgeNum = altGraphXGetEdgeNum(agx, e1VE, e2VS); ev = slElementFromIx(agx->evidence, edgeNum); support += ev->evCount; edgeNum = altGraphXGetEdgeNum(agx, e2VS, e2VE); ev = slElementFromIx(agx->evidence, edgeNum); support += ev->evCount; } altGraphXFreeEdgeMatrix(&em, vC); return support; } void agxSupportForEdge(struct altGraphX *agxList, struct bed *bed, int intron, int *support, char **agxNames) /* Scroll through native splicing graphs looking for native support of intron in bed if support is found fill in the support array and name array. */ { struct altGraphX *agx = NULL; int ev = 0; for(agx = agxList; agx != NULL; agx = agx->next) { ev = agxSupportForSplice(agx, bed, intron); if(ev > 0) { support[intron] = ev; agxNames[intron] = agx->name; return; } } } /* int agxSupportForEdge(struct altGraphX *agxList, int chromStart, int chromEnd) */ /* /\* Return the number of mRNA evidence for a given chromStart, chromEnd edge */ /* in altGraphX. *\/ */ /* { */ /* int vC = 0; //agx->vertexCount; */ /* int *vPos = NULL; //agx->vPositions; */ /* struct altGraphX *agx = NULL; */ /* int i,j,k; */ /* for(agx = agxList; agx != NULL; agx = agx->next) */ /* { */ /* vC = agx->vertexCount; */ /* vPos = agx->vPositions; */ /* for(i=0; i< vC; i++) */ /* { */ /* if(vPos[i] == chromStart) */ /* { */ /* for(j=0; j<vC; j++) */ /* { */ /* if(vPos[j] == chromEnd) */ /* { */ /* for(k=0; k<agx->edgeCount; k++) */ /* { */ /* if(agx->edgeStarts[k] == i && agx->edgeEnds[k] == j) */ /* { */ /* struct evidence *ev = slElementFromIx(agx->evidence, k); */ /* return ev->evCount; */ /* } */ /* } */ /* } */ /* } */ /* } */ /* } */ /* } */ /* return 0; */ /* } */ void evaluateAnIntron(char *db, struct orthoEval *ev, struct bed *orthoBed, int intron, struct altGraphX *agxList, struct dnaSeq *genoSeq, int *orientation, int *support, int *inCodInt, char **agxNames) /* Fill in the orientation, support, inCodInt values for a particular intron. */ { struct altGraphX *agx = NULL; unsigned int chromStart = orthoBed->chromStart + orthoBed->chromStarts[intron] + orthoBed->blockSizes[intron]; unsigned int chromEnd = orthoBed->chromStart + orthoBed->chromStarts[intron+1]; agxNames[intron] = ev->orthoBedName; agxSupportForEdge(agxList, orthoBed, intron, support, agxNames); orientation[intron] = intronOrientation(genoSeq->dna - orthoBed->chromStart + chromStart, genoSeq->dna - orthoBed->chromStart + chromEnd); inCodInt[intron] = (chromStart >= orthoBed->thickStart && chromEnd <= orthoBed->thickEnd); } void calcIntronStats(char *db, struct orthoEval *ev) /* Calculate the overlap for each intron. */ { struct altGraphX *agx = NULL, *agxList = NULL; char *agxTable = optionVal("altGraphXTable", "altGraphX"); int i=0, start=0, end=0; int numIntrons = 0; int *support = NULL; int *orientation = NULL; int *inCodInt = NULL; char **agxNames = NULL; struct bed *orthoBed = NULL; struct dnaSeq *genoSeq = NULL; assert(ev); assert(ev->orthoBed); orthoBed = ev->orthoBed; /* Allocate the directories. */ if(orthoBed->blockCount == 1) return; AllocArray(orientation, orthoBed->blockCount -1); AllocArray(support, orthoBed->blockCount -1); AllocArray(inCodInt, orthoBed->blockCount -1); AllocArray(agxNames, orthoBed->blockCount -1); genoSeq = hChromSeq(db, orthoBed->chrom, orthoBed->chromStart, orthoBed->chromEnd); agxList = loadNativeAgxForBed(db, orthoBed, agxTable); for(i=0; i<orthoBed->blockCount -1; i++) evaluateAnIntron(db, ev, orthoBed, i, agxList, genoSeq, orientation, support, inCodInt, agxNames); ev->agx = agxList; ev->numIntrons = orthoBed->blockCount -1; ev->inCodInt = inCodInt; ev->orientation = orientation; ev->support = support; ev->agxNames = agxNames; dnaSeqFree(&genoSeq); } char *mustFindLine(struct lineFile *lf, char *pat) /* Find line that starts (after skipping white space) * with pattern or die trying. Skip over pat in return*/ { char *line; while (lineFileNext(lf, &line, NULL)) { line = skipLeadingSpaces(line); if (startsWith(pat, line)) { line += strlen(pat); return skipLeadingSpaces(line); } } errAbort("Couldn't find %s in %s\n", pat, lf->fileName); return NULL; } struct borf *convertBorfOutput(char *fileName) /* Convert bestorf output to our database format. */ { struct lineFile *lf = lineFileOpen(fileName, TRUE); char *line = mustFindLine(lf, "BESTORF"); char *word=NULL; char *row[13]; struct borf *borf = NULL; int i=0; struct dnaSeq seq; int seqSize = 0; AllocVar(borf); ZeroVar(&seq); line = mustFindLine(lf, "Seq name:"); word = nextWord(&line); borf->name = cloneString(word); /* Name */ line = mustFindLine(lf, "Length of sequence:"); borf->size = atoi(line); /* Size */ lineFileNeedNext(lf, &line, NULL); line = skipLeadingSpaces(line); if (startsWith("no reliable", line)) { return borf; } else { line = mustFindLine(lf, "G Str F"); lineFileSkip(lf, 1); lineFileRow(lf, row); safef(borf->strand, sizeof(borf->strand),"%s", row[1]); /* Strand. */ borf->feature = cloneString(row[3]); /* Feature. */ borf->cdsStart = lineFileNeedNum(lf, row, 4) - 1; /* cdsStart */ borf->cdsEnd = lineFileNeedNum(lf, row, 6); /* cdsEnd */ borf->score = atof(row[7]); /* score */ borf->orfStart = lineFileNeedNum(lf, row, 8) - 1; /* orfStart */ borf->orfEnd = lineFileNeedNum(lf, row, 10); /* orfEnd */ borf->cdsSize = atoi(row[11]); /* cdsSize. */ safef(borf->frame, sizeof(borf->frame), "%s", row[12]); /* Frame */ line = mustFindLine(lf, "Predicted protein"); if (!faPepSpeedReadNext(lf, &seq.dna, &seq.size, &seq.name)) errAbort("Can't find peptide in %s", lf->fileName); borf->protein = cloneString(seq.dna); /* Protein. */ } lineFileClose(&lf); return borf; } struct borf *borfForBed(char *db, struct bed *bed) /* borfBig - Run Victor Solovyev's bestOrf on a bed. */ { char *exe = optionVal("bestOrfExe", "/cluster/home/sugnet/bin/bestorf /cluster/home/sugnet/bin/hume.dat"); static char *tmpFa = NULL; static char *tmpOrf = NULL; struct borf *borf = NULL; struct dnaSeq *seq = NULL; struct dyString *cmd = newDyString(256); int retVal = 0; if(tmpFa == NULL) tmpFa = optionVal("tmpFa", cloneString(rTempName("/tmp", "borf", ".fa"))); if(tmpOrf == NULL) tmpOrf = optionVal("tmpOrf", cloneString(rTempName("/tmp", "borf", ".out"))); seq = hSeqForBed(db, bed); faWrite(tmpFa, seq->name, seq->dna, seq->size); dyStringClear(cmd); dyStringPrintf(cmd, "%s %s > %s", exe, tmpFa, tmpOrf); retVal = system(cmd->string); borf = convertBorfOutput(tmpOrf); remove(tmpFa); remove(tmpOrf); dyStringFree(&cmd); dnaSeqFree(&seq); return borf; } void setThickStartStop(struct orthoEval *ev) /* Use the borf strucutre to insert coding start/stop. */ { int thickStart = -1, thickEnd =-1; int baseCount = -0; int i=0; struct borf *borf = ev->borf; struct bed *bed = ev->orthoBed; assert(bed); assert(borf); for(i=0; i<bed->blockCount; i++) { baseCount += bed->blockSizes[i]; if(baseCount >= borf->cdsStart && thickStart == -1) thickStart = bed->chromStart + bed->chromStarts[i] + bed->blockSizes[i] - (baseCount - borf->cdsStart); if(baseCount >= borf->cdsEnd && thickEnd == -1) thickEnd = bed->chromStart + bed->chromStarts[i] + bed->blockSizes[i] - (baseCount - borf->cdsEnd) ; } bed->thickStart = thickStart; bed->thickEnd = thickEnd; } struct borf *makeUpBorf() { struct borf *borf = NULL; AllocVar(borf); borf->name = cloneString("dummy"); safef(borf->strand, sizeof(borf->strand),"+"); borf->feature = cloneString("CDSo"); safef(borf->frame, sizeof(borf->frame), "+1"); borf->protein = cloneString("dummy"); return borf; } int bedRangeCmp(void *va, void *vb) { struct bed *a = va; struct bed *b = vb; int diff = strcmp(a->chrom, b->chrom); if(diff == 0) { if(a->chromEnd <= b->chromStart) diff = -1; else if(b->chromEnd <= a->chromStart) diff = 1; } return diff; } void initGpTree(char *db) /* Create a rbTree and populate it with blocks from gene predictions. */ { struct bed *bed = NULL; struct genePred *gp = NULL, *gpList = NULL; int i = 0, j=0; char query[256]; struct sqlResult *sr = NULL; char **row=NULL; struct sqlConnection *conn = hAllocConn(db); char *tableNames[] = {"sgpGene","softberryGene", "twinscan", "genscan"}; gpTree = rbTreeNew(bedRangeCmp); warn("Loading tree."); for(i=0; i<ArraySize(tableNames); i++) { warn("Loading table: %s", tableNames[i]); sqlSafef(query,sizeof(query),"select * from %s", tableNames[i]); sr = sqlGetResult(conn, query); while((row = sqlNextRow(sr)) != NULL) { gp = genePredLoad(row); slAddHead(&gpList, gp); } sqlFreeResult(&sr); for(gp = gpList; gp != NULL; gp = gp->next) { for(j=0; j<gp->exonCount; j++) { AllocVar(bed); bed->chrom = cloneString(gp->chrom); bed->name = cloneString(gp->name); safef(bed->strand, sizeof(bed->strand), "%s", gp->strand); bed->chromStart = gp->exonStarts[j]; bed->chromEnd = gp->exonEnds[j]; rbTreeAdd(gpTree, bed); } } genePredFreeList(&gpList); } warn("Tree loaded"); hFreeConn(&conn); } float codingBasesForBed(char *db, struct bed *bed) /* Calculate how many bases of the bed are overlapped by gene predictions. */ { struct slRef *refList = NULL, *ref = NULL; static struct bed searchLo, searchHi; struct bed *b = NULL; int i,intersect=0; int baseCount = 0; float *overlap = NULL; float ave = 0; AllocArray(overlap, bed->blockCount); if(gpTree == NULL) initGpTree(db); searchLo.chrom = bed->chrom; searchLo.chromStart = bed->chromStart; searchLo.chromEnd = bed->chromEnd; /* searchHi.chrom = bed->chrom; */ /* searchHi.chromStart = bed->chromEnd; */ /* searchHi.chromEnd = bed->chromEnd; */ refList = rbTreeItemsInRange(gpTree, &searchLo, &searchLo); for(ref = refList; ref != NULL; ref = ref->next) { b = ref->val; for(i=0; i<bed->blockCount; i++) { intersect = rangeIntersection(bed->chromStarts[i] + bed->chromStart, bed->chromStarts[i] + bed->chromStart + bed->blockSizes[i], b->chromStart, b->chromEnd); if(intersect > 0) overlap[i] += ((float)intersect) /bed->blockSizes[i]; } } slFreeList(&refList); for(i=0;i<bed->blockCount; i++) ave+=overlap[i]; freez(&overlap); if(ave == 0) return 0; ave = ave/bed->blockCount; return ave; } struct orthoEval *scoreOrthoBeds(char *bedFile, char *genePredFile, char *db, FILE *out) /* Score each bed in the orhtoBed file. */ { struct bed *bedList = NULL, *bed = NULL; struct genePred *genePredList = NULL, *genePred = NULL; struct borf *borf = NULL; boolean skipBorf = optionExists("skipBorf"); struct orthoEval *evList = NULL, *ev = NULL; if(genePredFile != NULL) //input from genePred file { genePredList = genePredLoadAll(genePredFile); for(genePred = genePredList; genePred != NULL; genePred = genePred->next ) { bed = bedFromGenePred(genePred); slAddHead(&bedList,bed); } slReverse(&bedList); } else //input from bed file bedList = bedLoadNAll(bedFile, 12); warn("Scoring beds"); for(bed = bedList; bed != NULL; bed = bed->next) { occassionalDot(); AllocVar(ev); ev->orthoBedName = cloneString(bed->name); ev->agxBedName = cloneString(bed->name); ev->orthoBed = bed; if(skipBorf != TRUE) { ev->borf = borf = borfForBed(db, bed); setThickStartStop(ev); } else { ev->borf = makeUpBorf(); ev->borf->score = codingBasesForBed(db, bed); } // calcBasesOverlap(ev); calcIntronStats(db, ev); borfTabOut(borf, stdout); if(ev->numIntrons > 0) orthoEvalTabOut(ev, out); orthoEvalFree(&ev); // slAddHead(&evList, ev); } warn("\nDone."); //bedFreeList(&bedList); return evList; } void orthoEvaluate(char *bedFile, char *genePredFile, char *db) /* Create orthoEval records and find best introns where best is: 1) Supported by native transcripts. 2) Has conserved intron gt-ag. 3) Is in coding region. */ { struct orthoEval *evList = NULL, *ev = NULL; char *orthoEvalOutName=NULL; FILE *orthoEvalOut = NULL; orthoEvalOutName = optionVal("orthoEvalOut", NULL); if(orthoEvalOutName == NULL) errAbort("Please specify an orthoEvalOut file. Use -help for usage."); orthoEvalOut = mustOpen(orthoEvalOutName, "w"); evList = scoreOrthoBeds(bedFile, genePredFile, db, orthoEvalOut); carefulClose(&orthoEvalOut); } int main(int argc, char *argv[]) /* Where it all starts. */ { char *db = NULL; char *bedFile = NULL; char *genePredFile = NULL; doHappyDots = isatty(1); /* stdout */ if(argc == 1) usage(); optionInit(&argc, argv, optionSpecs); if(optionExists("help")) usage(); db = optionVal("db", NULL); if(db == NULL) errAbort("Must specify db. Use -help for usage."); bedFile = optionVal("bedFile", NULL); genePredFile = optionVal("genePredFile", NULL); if((bedFile == NULL && genePredFile == NULL)||(bedFile != NULL && genePredFile != NULL)) errAbort("Must specify bedFile xor genePredFile. Use -help for usage."); orthoEvaluate(bedFile, genePredFile, db); return 0; }