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/companion/regCompanionGraphVsFixedPoints/regCompanionGraphVsFixedPoints.c src/hg/regulate/companion/regCompanionGraphVsFixedPoints/regCompanionGraphVsFixedPoints.c index 033a90f..f6c7719 100644 --- src/hg/regulate/companion/regCompanionGraphVsFixedPoints/regCompanionGraphVsFixedPoints.c +++ src/hg/regulate/companion/regCompanionGraphVsFixedPoints/regCompanionGraphVsFixedPoints.c @@ -1,252 +1,252 @@ /* regCompanionGraphVsFixedPoints - Given a bunch of fixed point in genome as input * (promoters perhaps) help make graphs of many features in bins relative to that point. */ /* 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 "basicBed.h" #include "bigWig.h" #include "obscure.h" #include "localmem.h" #include "verbose.h" #include "bits.h" int fetchBefore = 50000, fetchAfter = 50000; boolean fromCenter = FALSE; void usage() /* Explain usage and exit. */ { errAbort( "regCompanionGraphVsFixedPoints - Given a bunch of fixed point in genome as input\n" " (promoters perhaps) help make graphs of many features in bins relative to that point.\n" "usage:\n" " regCompanionGraphVsFixedPoints in.bed input.tab out.tab\n" "where:\n" " in.bed is the regions to collect data around. By default the bed is treated as\n" " a gene, and the region is before and after the txStart, strand considered\n" " but with the -fromCenter it is taken from the center instead\n" " input.tab is a tab-separated file with the following fields\n" " name - Short human and machine readable name.\n" " normFactor - Multiply every val in wig by this. Use . for no normalizatin\n" " maxVal - Clamp values above this to this. Use . for no max.\n" " missingZero - true or false. If true treat missing values as 0.\n" " fileName - Name of bigWigFile.\n" " out.tab is the output with one line per bigWig. The first word in line is\n" " the name from the input.tab, the rest of the words are floating point numbers\n" " one for each base between fetchBefore and fetchAfter below (so they are long\n" " lines!)\n" "options:\n" " -fetchBefore=N (default %d)\n" " -fetchAfter=N (default %d)\n" " -fromCenter - fetch out from center point of in beds rather than stranded start\n" " Happy to ignore strand (treats . as +)\n" , fetchBefore, fetchAfter ); } static struct optionSpec options[] = { {"fetchBefore", OPTION_INT}, {"fetchAfter", OPTION_INT}, {"fromCenter", OPTION_BOOLEAN}, {NULL, 0}, }; struct rcgInputInfo /* Input list to regCompanionGraphVsFixedPoints */ { struct rcgInputInfo *next; char *name; /* Short human and machine readable name. */ double normFactor; /* Multiply every val in wig by this. */ double maxVal; /* Clamp values above this to this. */ boolean missingZero; /* If true treat missing values as 0 */ char *fileName; /* Name of bigWigFile. */ }; struct rcgInputInfo *readInputInfo(char *fileName) /* Read input info. */ { struct rcgInputInfo *list = NULL, *el; char *row[5]; struct lineFile *lf = lineFileOpen(fileName, TRUE); while (lineFileRow(lf, row)) { AllocVar(el); el->name = cloneString(row[0]); if (!sameString(row[1], ".")) el->normFactor = lineFileNeedDouble(lf, row, 1); if (sameString(row[2], ".")) el->maxVal = BIGDOUBLE; else el->maxVal = lineFileNeedDouble(lf, row, 2); char *missingZero = row[3]; if (sameWord(missingZero, "TRUE")) el->missingZero = 1; else if (sameWord(missingZero, "FALSE")) el->missingZero = 0; else errAbort("Expecting 'true' or 'false' in missingZero field line %d of %s", lf->lineIx, lf->fileName); el->fileName = cloneString(row[4]); if (!isBigWig(el->fileName)) errAbort("%s is not a bigWig file\n", el->fileName); slAddHead(&list, el); } lineFileClose(&lf); slReverse(&list); return list; } void regCompanionGraphVsFixedPoints(char *inBed, char *inBigWigFileList, char *outTab) /* regCompanionGraphVsFixedPoints - Given a bunch of fixed point in genome as input * (promoters perhaps) help make graphs of many features in bins relative to that point. */ { struct bed *bedList = bedLoadAll(inBed); slSort(&bedList, bedCmp); struct rcgInputInfo *inTabList = readInputInfo(inBigWigFileList); FILE *f = mustOpen(outTab, "w"); /* Set up some buffers and variables to hold unpacked double-per-base representation. */ struct bigWigValsOnChrom *chromVals = bigWigValsOnChromNew(); int sumBufSize = fetchBefore + fetchAfter; double *sumBuf; AllocArray(sumBuf, sumBufSize); long *nBuf; AllocArray(nBuf, sumBufSize); struct rcgInputInfo *inTab; int inCount = slCount(inTabList); int inIx = 1; for (inTab = inTabList; inTab != NULL; inTab = inTab->next, ++inIx) { verbose(1, "%d of %d processing %s", inIx, inCount, inTab->fileName); boolean missingZero = inTab->missingZero; double maxVal = (inTab->maxVal == 0 ? BIGDOUBLE : inTab->maxVal); /* Zero out sum buffers. */ int i; for (i=0; i<sumBufSize; ++i) { sumBuf[i] = 0.0; nBuf[i] = 0; } struct bbiFile *bbi = bigWigFileOpen(inTab->fileName); struct bed *startChrom, *endChrom; for (startChrom = bedList; startChrom != NULL; startChrom = endChrom) { /* Figure out end condition. */ endChrom = bedListNextDifferentChrom(startChrom); char *chrom = startChrom->chrom; if (bigWigValsOnChromFetchData(chromVals, chrom, bbi)) { verboseDot(); /* Fetch intervals and use them to paint array of doubles. */ int chromSize = chromVals->chromSize; /* Now loop through beds for this chromosome, adding to sums. */ struct bed *bed; for (bed = startChrom; bed != endChrom; bed = bed->next) { char strand = bed->strand[0]; int bufIx, bufIxInc; int start, end, pos; if (fromCenter) { pos = (bed->chromStart + bed->chromEnd)/2; if (strand == '-') { start = pos - fetchAfter; end = pos + fetchBefore; bufIx = sumBufSize - 1; bufIxInc = -1; } else { start = pos - fetchBefore; end = pos + fetchAfter; bufIx = 0; bufIxInc = 1; } } else { if (strand == '+') { pos = bed->chromStart; start = pos - fetchBefore; end = pos + fetchAfter; bufIx = 0; bufIxInc = 1; } else if (strand == '-') { pos = bed->chromEnd; start = pos - fetchAfter; end = pos + fetchBefore; bufIx = sumBufSize - 1; bufIxInc = -1; } else { // Keep compiler happy about uninitialized vars then abort. bufIx = bufIxInc = start = end = pos = 0; errAbort("Expecting input bed to be stranded\n"); } } if (rangeIntersection(start, end, 0, chromSize) == sumBufSize) { Bits *covBuf = chromVals->covBuf; double *valBuf = chromVals->valBuf; for (i=start; i<end; ++i) { if (bitReadOne(covBuf, i)) { double val = valBuf[i]; if (val > maxVal) val = maxVal; sumBuf[bufIx] += val; nBuf[bufIx] += 1; } else if (missingZero) nBuf[bufIx] += 1; bufIx += bufIxInc; } } } } } bigWigFileClose(&bbi); /* Now go and print results: file name first and then a bunch of numbers then newline */ fprintf(f, "%s", inTab->name); for (i=0; i<sumBufSize; ++i) { int n = nBuf[i]; double ave = (n>0 ? sumBuf[i]/n : 0); fprintf(f, "\t%g", ave); } fprintf(f, "\n"); verbose(1, "\n"); } carefulClose(&f); } int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, options); fetchBefore = optionInt("fetchBefore", fetchBefore); fetchAfter = optionInt("fetchAfter", fetchAfter); fromCenter = optionExists("fromCenter"); if (argc != 4) usage(); regCompanionGraphVsFixedPoints(argv[1], argv[2], argv[3]); return 0; }