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/regulate/regCluster/regCluster.c src/hg/regulate/regCluster/regCluster.c index c592cb8..3641742 100644 --- src/hg/regulate/regCluster/regCluster.c +++ src/hg/regulate/regCluster/regCluster.c @@ -1,169 +1,169 @@ /* regCluster - Cluster regulator regions. */ /* Copyright (C) 2011 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 "linefile.h" #include "hash.h" #include "options.h" #include "localmem.h" #include "rangeTree.h" #include "peakCluster.h" int clDims = 1; double clScoreScale = 1.0; double clForceJoinScore = 2; double clWeakLevel = 0.1; boolean clAveScore = FALSE; boolean clBedSources = FALSE; void usage() /* Explain usage and exit. */ { errAbort( "regCluster - Cluster regulator regions\n" "usage:\n" " regCluster tableOfTables output.cluster output.bed\n" "Where the table-of-tables is space or tab separated in the format:\n" " <fileName> <chrom> <start> <end> <score> <normScore> <dim1 label> ... <dimN label>\n" "where chrom, start, end, score are the indexes (starting with 0) of the chromosome, start, \n" "and end fields in the file, normScore is a factor to multiply score by to get it into the\n" "0-1000 range, and the dim# labels are the labels in each dimension.\n" "for example\n" " simpleReg.bed 0 1 2 4 10.7234 aCell aFactor\n" "options:\n" " -dims=N - number of dimensions in data. Would be 2 for cell-line + antibody. Default %d\n" " -scoreScale=0.N - scale score by this factor. Default %g\n" " -weakLevel=0.N - within a cluster ratio of highest depth of coverage of cluster to lowest\n" " Default %g\n" " -forceJoinScore=0.N - if combined score of elements joining 2 clusters above this, the\n" " clusters will be joined. Default %g\n" " -aveScore - if set cluster score is average of components, not max\n" " -bedSources - output bed8 (source count, comma-sep source id and source score fields)\n" , clDims , clScoreScale , clWeakLevel , clForceJoinScore ); } static struct optionSpec options[] = { {"dims", OPTION_INT}, {"scoreScale", OPTION_DOUBLE}, {"forceJoinScore", OPTION_DOUBLE}, {"weakLevel", OPTION_DOUBLE}, {"aveScore", OPTION_BOOLEAN}, {"bedSources", OPTION_BOOLEAN}, {NULL, 0}, }; static int clusterIx = 0; void outputClustersForChrom(char *chrom, struct rbTree *tree, FILE *fCluster, FILE *fBed) /* Write out clusters on one chromosome */ { struct range *range, *rangeList = rangeTreeList(tree); verbose(2, "Got %d ranges on %s\n", slCount(rangeList), chrom); struct lm *lm = lmInit(0); for (range = rangeList; range != NULL; range = range->next) { struct peakCluster *cluster, *clusterList = peakClusterItems(lm, range->val, clForceJoinScore, clWeakLevel); for (cluster = clusterList; cluster != NULL; cluster = cluster->next) { struct slRef *ref, *refList=cluster->itemRefList; ++clusterIx; struct hash *uniqHash = hashNew(0); for (ref = refList; ref != NULL; ref = ref->next) { struct peakItem *item = ref->val; hashStore(uniqHash, item->source->dataSource); fprintf(fCluster, "%d\t%s\t", clusterIx, item->chrom); fprintf(fCluster, "%d\t%d\t", item->chromStart, item->chromEnd); fprintf(fCluster, "%g", item->score); int i; for (i=0; i<clDims; ++i) fprintf(fCluster, "\t%s", item->source->labels[i]); fprintf(fCluster, "\n"); } double score; if (clAveScore) score = clScoreScale * (cluster->score / uniqHash->elCount); else score = clScoreScale * cluster->maxSubScore; if (score > 1000) score = 1000; fprintf(fBed, "%s\t%d\t%d\t%d\t%d", chrom, cluster->chromStart, cluster->chromEnd, uniqHash->elCount, round(score)); if (clBedSources) { /* print expCount, expNums, exScores */ fprintf(fBed, "\t%d\t", slCount(cluster->itemRefList)); for (ref = cluster->itemRefList; ref != NULL; ref = ref->next) { struct peakItem *item = ref->val; int i; for (i=0; i<clDims; ++i) { fprintf(fBed, "%s", item->source->labels[i]); if (i<clDims-1) fprintf(fBed, "+"); } fprintf(fBed, ","); } fprintf(fBed, "\t"); for (ref = cluster->itemRefList; ref != NULL; ref = ref->next) { struct peakItem *item = ref->val; fprintf(fBed, "%d,", round(item->score)); } } fprintf(fBed, "\n"); hashFree(&uniqHash); } } lmCleanup(&lm); } void regCluster(char *tableOfTables, char *outCluster, char *outBed) /* regCluster - Cluster regulator regions. */ { struct peakSource *source, *sourceList = peakSourceLoadAll(tableOfTables, clDims); verbose(1, "Read %d sources from %s\n", slCount(sourceList), tableOfTables); struct peakClusterMaker *maker = peakClusterMakerNew(); for (source = sourceList; source != NULL; source = source->next) peakClusterMakerAddFromSource(maker, source); /* Get out list of chromosomes and process one at a time. */ FILE *fCluster = mustOpen(outCluster, "w"); FILE *fBed = mustOpen(outBed, "w"); struct hashEl *chrom; struct hashEl *chromList = peakClusterMakerChromList(maker); int totalClusters = 0; for (chrom = chromList; chrom != NULL; chrom = chrom->next) { struct rbTree *tree = chrom->val; totalClusters += tree->n; outputClustersForChrom(chrom->name, tree, fCluster, fBed); } verbose(1, "%d singly-linked clusters, %d clusters in %d chromosomes\n", totalClusters, clusterIx, maker->chromHash->elCount); carefulClose(&fCluster); carefulClose(&fBed); peakClusterMakerFree(&maker); } int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, options); if (argc != 4) usage(); clDims = optionInt("dims", clDims); clScoreScale = optionDouble("scoreScale", clScoreScale); clWeakLevel = optionDouble("weakLevel", clWeakLevel); clAveScore = optionExists("aveScore"); clBedSources = optionExists("bedSources"); regCluster(argv[1], argv[2], argv[3]); return 0; }