b95ff3835509b242bd9007ba55c4f60c1022da47 markd Thu Dec 30 14:58:16 2010 -0800 moved to programs to hg/utils, fixed build of distributed utilities diff --git src/hg/overlapSelect/overlapSelect.c src/hg/overlapSelect/overlapSelect.c deleted file mode 100644 index 976e8b8..0000000 --- src/hg/overlapSelect/overlapSelect.c +++ /dev/null @@ -1,482 +0,0 @@ -/* overlapSelect - select records based on overlap of chromosome ranges */ - -#include "common.h" -#include "selectTable.h" -#include "coordCols.h" -#include "chromAnn.h" -#include "dystring.h" -#include "options.h" - -static char const rcsid[] = "$Id: overlapSelect.c,v 1.42 2009/07/31 18:09:23 markd Exp $"; - -/* FIXME: - * - would be nice to be able to specify ranges in the same manner - * as featureBits - * - should keep header lines in files - * - don't need to save if infile records if stats output - */ - -static struct optionSpec optionSpecs[] = { - {"selectFmt", OPTION_STRING}, - {"selectCoordCols", OPTION_STRING}, - {"selectCds", OPTION_BOOLEAN}, - {"selectRange", OPTION_BOOLEAN}, - {"inFmt", OPTION_STRING}, - {"inCoordCols", OPTION_STRING}, - {"inCds", OPTION_BOOLEAN}, - {"inRange", OPTION_BOOLEAN}, - {"nonOverlapping", OPTION_BOOLEAN}, - {"strand", OPTION_BOOLEAN}, - {"oppositeStrand", OPTION_BOOLEAN}, - {"excludeSelf", OPTION_BOOLEAN}, - {"idMatch", OPTION_BOOLEAN}, - {"dropped", OPTION_STRING}, - {"overlapThreshold", OPTION_FLOAT}, - {"overlapThresholdCeil", OPTION_FLOAT}, - {"overlapSimilarity", OPTION_FLOAT}, - {"overlapSimilarityCeil", OPTION_FLOAT}, - {"overlapBases", OPTION_INT}, - {"merge", OPTION_BOOLEAN}, - {"mergeOutput", OPTION_BOOLEAN}, - {"statsOutput", OPTION_BOOLEAN}, - {"statsOutputAll", OPTION_BOOLEAN}, - {"statsOutputBoth", OPTION_BOOLEAN}, - {"idOutput", OPTION_BOOLEAN}, - {"aggregate", OPTION_BOOLEAN}, - {NULL, 0} -}; - -/* incompatible with aggregate */ -static char *aggIncompatible[] = -{ - "overlapSimilarity", "overlapSimilarityCeil", "overlapThresholdCeil", "overlapBases", "merge", "mergeOutput", "idMatch", NULL -}; - -/* file format constants */ -enum recordFmt { - UNKNOWN_FMT, - PSL_FMT, - PSLQ_FMT, - CHAIN_FMT, - CHAINQ_FMT, - GENEPRED_FMT, - BED_FMT, - COORD_COLS_FMT -}; - -/* Options parsed from the command line */ -enum recordFmt selectFmt = UNKNOWN_FMT; -struct coordCols selectCoordCols; -unsigned selectCaOpts = 0; - -unsigned inFmt = UNKNOWN_FMT; -struct coordCols inCoordCols; -unsigned inCaOpts = 0; - -unsigned selectOpts = 0; -boolean useAggregate = FALSE; -boolean nonOverlapping = FALSE; -boolean mergeOutput = FALSE; -boolean idOutput = FALSE; -boolean statsOutput = FALSE; -boolean outputAll = FALSE; -boolean outputBoth = FALSE; -struct overlapCriteria criteria = {0.0, 1.1, 0.0, 1.1, -1}; - -enum recordFmt parseFormatSpec(char *fmt) -/* parse a format specification */ -{ -if (sameString(fmt, "psl")) - return PSL_FMT; -if (sameString(fmt, "pslq")) - return PSLQ_FMT; -if (sameString(fmt, "chain")) - return CHAIN_FMT; -if (sameString(fmt, "chainq")) - return CHAINQ_FMT; -if (sameString(fmt, "genePred")) - return GENEPRED_FMT; -if (sameString(fmt, "bed")) - return BED_FMT; -errAbort("invalid file format: %s", fmt); -return UNKNOWN_FMT; -} - -enum recordFmt getFileFormat(char *path) -/* determine the file format from the specified file extension */ -{ -char *filePath = path; -char filePathBuf[PATH_LEN]; - -if (endsWith(filePath, ".gz") || endsWith(filePath, ".bz2") || endsWith(filePath, ".Z")) - { - /* strip .gz/.bz2/.Z extension */ - splitPath(path, NULL, filePathBuf, NULL); - filePath = filePathBuf; - } -if (endsWith(filePath, ".psl")) - return PSL_FMT; -if (endsWith(filePath, ".chain")) - return CHAIN_FMT; -if (endsWith(filePath, ".genePred") || endsWith(filePath, ".gp")) - return GENEPRED_FMT; -if (endsWith(filePath, ".bed")) - return BED_FMT; -errAbort("can't determine file format of %s", filePath); -return UNKNOWN_FMT; -} - -static struct chromAnnReader *createChromAnnReader(char *fileName, - enum recordFmt fmt, - unsigned caOpts, - struct coordCols *cols) -/* construct a reader. The coordCols spec is only used for tab files */ -{ -switch (fmt) - { - case PSL_FMT: - case PSLQ_FMT: - return chromAnnPslReaderNew(fileName, caOpts); - case CHAIN_FMT: - case CHAINQ_FMT: - return chromAnnChainReaderNew(fileName, caOpts); - case GENEPRED_FMT: - return chromAnnGenePredReaderNew(fileName, caOpts); - case BED_FMT: - return chromAnnBedReaderNew(fileName, caOpts); - case COORD_COLS_FMT: - return chromAnnTabReaderNew(fileName, cols, caOpts); - case UNKNOWN_FMT: - break; - } -assert(FALSE); -return NULL; -} - -static char *getPrintId(struct chromAnn* ca) -/* get id for output, or <unknown> if not known */ -{ -return (ca->name == NULL) ? "<unknown>" : ca->name; -} - -static void outputMerge(struct chromAnn* inCa, FILE *outFh, - struct chromAnnRef *overlappingRecs) -/* output for the -mergeOutput option; pairs of inRec and overlap */ -{ -struct chromAnnRef *selectCaRef; -for (selectCaRef = overlappingRecs; selectCaRef != NULL; selectCaRef = selectCaRef->next) - { - struct chromAnn *selectCa = selectCaRef->ref; - inCa->recWrite(inCa, outFh, '\t'); - selectCa->recWrite(selectCa, outFh, '\n'); - } -} - -static void outputIds(struct chromAnn* inCa, FILE *outFh, - struct chromAnnRef *overlappingRecs) -/* output for the -idOutput option; pairs of inRec and overlap ids */ -{ -struct chromAnnRef *selectCaRef; -for (selectCaRef = overlappingRecs; selectCaRef != NULL; selectCaRef = selectCaRef->next) - { - struct chromAnn *selectCa = selectCaRef->ref; - fprintf(outFh, "%s\t%s\n", getPrintId(inCa), getPrintId(selectCa)); - } -} - -/* format string for stats output */ -static char *statsFmt = "%s\t%s\t%0.3g\t%0.3g\t%d\t%0.3g\t%d\t%d\n"; - -static void outputStats(struct chromAnn* inCa, FILE *outFh, - struct chromAnnRef *overlappingRecs) -/* output for the -statOutput option; pairs of inRec and overlap ids */ -{ -if (overlappingRecs == NULL) - { - // -statsOutputAll and nothing overlapping - fprintf(outFh, statsFmt, getPrintId(inCa), "", 0.0, 0.0, 0, 0.0, inCa->totalSize, 0); - } -struct chromAnnRef *selectCaRef; -for (selectCaRef = overlappingRecs; selectCaRef != NULL; selectCaRef = selectCaRef->next) - { - struct chromAnn *selectCa = selectCaRef->ref; - unsigned overBases = selectOverlapBases(inCa, selectCa); - fprintf(outFh, statsFmt, getPrintId(inCa), getPrintId(selectCa), - selectFracOverlap(inCa, overBases), selectFracOverlap(selectCa, overBases), overBases, - selectFracSimilarity(inCa, selectCa, overBases), - inCa->totalSize, selectCa->totalSize); - } -} - -static void outputStatsSelNotUsed(FILE *outFh) -/* output stats for select chromAnns that were not used */ -{ -struct chromAnnMapIter iter = selectTableFirst(); -struct chromAnn *selCa; -while ((selCa = chromAnnMapIterNext(&iter)) != NULL) - { - if (!selCa->used) - fprintf(outFh, statsFmt, "", getPrintId(selCa), 0.0, 0.0, 0, 0.0, 0, selCa->totalSize); - } -} - -static void doItemOverlap(struct chromAnn* inCa, FILE *outFh, FILE *dropFh) -/* Do individual item overlap process of chromAnn object given the criteria, - * and if so output */ -{ -struct chromAnnRef *overlappingRecs = NULL; -struct chromAnnRef **overlappingRecsPtr = NULL; /* used to indicate if recs should be collected */ -if (mergeOutput || idOutput || statsOutput) - overlappingRecsPtr = &overlappingRecs; - -boolean overlaps = selectIsOverlapped(selectOpts, inCa, &criteria, overlappingRecsPtr); -if (overlappingRecsPtr != NULL) - slSort(overlappingRecsPtr, chromAnnRefLocCmp); -if (((nonOverlapping) ? !overlaps : overlaps) || outputAll) - { - if (mergeOutput) - outputMerge(inCa, outFh, overlappingRecs); - else if (idOutput) - outputIds(inCa, outFh, overlappingRecs); - else if (statsOutput) - outputStats(inCa, outFh, overlappingRecs); - else - inCa->recWrite(inCa, outFh, '\n'); - } -else if (dropFh != NULL) - { - if (idOutput) - fprintf(dropFh, "%s\n", getPrintId(inCa)); - else - inCa->recWrite(inCa, dropFh, '\n'); - } - -slFreeList(&overlappingRecs); -} - -static void doItemOverlaps(struct chromAnnReader* inCar, FILE *outFh, FILE *dropFh) -/* Do individual item overlap processings */ -{ -struct chromAnn *inCa; -while ((inCa = inCar->caRead(inCar)) != NULL) - { - doItemOverlap(inCa, outFh, dropFh); - chromAnnFree(&inCa); - } -} - - -static void doAggregateOverlap(struct chromAnn* inCa, FILE *outFh, FILE *dropFh) -/* Do aggreate overlap process of chromAnn object given the criteria, - * and if so output */ -{ -struct overlapAggStats stats = selectAggregateOverlap(selectOpts, inCa); -boolean overlaps; -if (criteria.threshold <= 0.0) - overlaps = (stats.inOverlap > 0.0); /* any overlap */ -else - overlaps = (stats.inOverlap >= criteria.threshold); -if (((nonOverlapping) ? !overlaps : overlaps) || outputAll) - { - if (idOutput) - fprintf(outFh, "%s\n", getPrintId(inCa)); - else if (statsOutput) - fprintf(outFh, "%s\t%0.3g\t%d\t%d\n", getPrintId(inCa), - stats.inOverlap, stats.inOverBases, stats.inBases); - else - inCa->recWrite(inCa, outFh, '\n'); - } -else if (dropFh != NULL) - { - if (idOutput) - fprintf(dropFh, "%s\n", getPrintId(inCa)); - else - inCa->recWrite(inCa, dropFh, '\n'); - } -} - -static void doAggregateOverlaps(struct chromAnnReader* inCar, FILE *outFh, FILE *dropFh) -/* Do aggreate overlap processing */ -{ -struct chromAnn *inCa; -while ((inCa = inCar->caRead(inCar)) != NULL) - { - doAggregateOverlap(inCa, outFh, dropFh); - chromAnnFree(&inCa); - } -} - -void loadSelectTable(char *selectFile) -/* load the select table from a file */ -{ -struct chromAnnReader *selCar = createChromAnnReader(selectFile, selectFmt, selectCaOpts, &selectCoordCols); -selectTableAddRecords(selCar); -selCar->carFree(&selCar); -} - -void overlapSelect(char *selectFile, char *inFile, char *outFile, char *dropFile) -/* select records based on overlap of chromosome ranges */ -{ -struct chromAnnReader *inCar - = createChromAnnReader(inFile, inFmt, inCaOpts, &inCoordCols); -loadSelectTable(selectFile); -FILE *outFh = mustOpen(outFile, "w"); -FILE *dropFh = NULL; -if (dropFile != NULL) - dropFh = mustOpen(dropFile, "w"); -if (idOutput) - { - if (useAggregate) - fputs("#inId\n", outFh); - else - fputs("#inId\t" "selectId\n", outFh); - } -if (statsOutput) - { - if (useAggregate) - fputs("#inId\t" "inOverlap\t" "inOverBases\t" "inBases\n", outFh); - else - fputs("#inId\t" "selectId\t" "inOverlap\t" "selectOverlap\t" "overBases\t" "similarity\t" "inBases\t" "selectBases\n", outFh); - } - -if (useAggregate) - doAggregateOverlaps(inCar, outFh, dropFh); -else - doItemOverlaps(inCar, outFh, dropFh); - -inCar->carFree(&inCar); -if (statsOutput && outputBoth) - outputStatsSelNotUsed(outFh); - -carefulClose(&outFh); -carefulClose(&dropFh); -/* enable for memory analysis */ -#if 0 -selectTableFree(); -#endif -} - -void usage(char *msg) -/* usage message and abort */ -{ -static char *usageMsg = -#include "usage.msg" - ; -errAbort("%s: %s", msg, usageMsg); -} - -/* entry */ -int main(int argc, char** argv) -{ -char *selectFile, *inFile, *outFile, *dropFile; -optionInit(&argc, argv, optionSpecs); -if (argc != 4) - usage("wrong # args"); -selectFile = argv[1]; -inFile = argv[2]; -outFile = argv[3]; - -/* select file options */ -if (optionExists("selectFmt") && optionExists("selectCoordCols")) - errAbort("can't specify both -selectFmt and -selectCoordCols"); - -if (optionExists("selectFmt")) - selectFmt = parseFormatSpec(optionVal("selectFmt", NULL)); -else if (optionExists("selectCoordCols")) - { - selectCoordCols = coordColsParseSpec("selectCoordCols", - optionVal("selectCoordCols", NULL)); - selectFmt = COORD_COLS_FMT; - } -else - selectFmt = getFileFormat(selectFile); - -if (optionExists("selectCds")) - selectCaOpts |= chromAnnCds; -if (optionExists("selectRange")) - selectCaOpts |= chromAnnRange; -if ((selectFmt == PSLQ_FMT) || (selectFmt == CHAINQ_FMT)) - selectCaOpts |= chromAnnUseQSide; - -/* in file options */ -if (optionExists("inFmt") && optionExists("inCoordCols")) - errAbort("can't specify both -inFmt and -inCoordCols"); -if (optionExists("inFmt")) - inFmt = parseFormatSpec(optionVal("inFmt", NULL)); -else if (optionExists("inCoordCols")) - { - inCoordCols = coordColsParseSpec("inCoordCols", - optionVal("inCoordCols", NULL)); - inFmt = COORD_COLS_FMT; - } -else - inFmt = getFileFormat(inFile); - -inCaOpts = chromAnnSaveLines; // need lines for output -if (optionExists("inCds")) - inCaOpts |= chromAnnCds; -if (optionExists("inRange")) - inCaOpts |= chromAnnRange; -if ((inFmt == PSLQ_FMT) || (inFmt == CHAINQ_FMT)) - inCaOpts |= chromAnnUseQSide; - -/* select options */ -useAggregate = optionExists("aggregate"); -nonOverlapping = optionExists("nonOverlapping"); -if (optionExists("strand") && optionExists("oppositeStrand")) - errAbort("can only specify one of -strand and -oppositeStrand"); -if (optionExists("strand")) - selectOpts |= selStrand; -if (optionExists("oppositeStrand")) - selectOpts |= selOppositeStrand; -if (optionExists("excludeSelf") && (optionExists("idMatch"))) - errAbort("can't specify both -excludeSelf and -idMatch"); -if (optionExists("excludeSelf")) - selectOpts |= selExcludeSelf; -if (optionExists("idMatch")) - selectOpts |= selIdMatch; - -criteria.threshold = optionFloat("overlapThreshold", 0.0); -criteria.thresholdCeil = optionFloat("overlapThresholdCeil", 1.1); -criteria.similarity = optionFloat("overlapSimilarity", 0.0); -criteria.similarityCeil = optionFloat("overlapSimilarityCeil", 1.1); -criteria.bases = optionInt("overlapBases", -1); - -/* output options */ -mergeOutput = optionExists("mergeOutput"); -idOutput = optionExists("idOutput"); -statsOutput = optionExists("statsOutput") || optionExists("statsOutputAll") || optionExists("statsOutputBoth"); -if ((mergeOutput + idOutput + statsOutput) > 1) - errAbort("can only specify one of -mergeOutput, -idOutput, -statsOutput, -statsOutputAll, or -statsOutputBoth"); -outputAll = optionExists("statsOutputAll"); -outputBoth = optionExists("statsOutputBoth"); -if (outputBoth) - outputAll = TRUE; -if (mergeOutput) - { - if (nonOverlapping) - errAbort("can't use -mergeOutput with -nonOverlapping"); - if (useAggregate) - errAbort("can't use -mergeOutput with -aggregate"); - if ((selectFmt == CHAIN_FMT) || (selectFmt == CHAINQ_FMT) - || (inFmt == CHAIN_FMT) || (inFmt == CHAINQ_FMT)) - if (useAggregate) - errAbort("can't use -mergeOutput with chains"); - selectCaOpts |= chromAnnSaveLines; - } -dropFile = optionVal("dropped", NULL); - -/* check for options incompatible with aggregate mode */ -if (useAggregate) - { - int i; - for (i = 0; aggIncompatible[i] != NULL; i++) - { - if (optionExists(aggIncompatible[i])) - errAbort("-%s is not allowed -aggregate", aggIncompatible[i]); - } - } - -overlapSelect(selectFile, inFile, outFile, dropFile); -return 0; -}