c82562a709708e014040c71cb700e84630c901e3 steve Thu Jan 26 09:43:58 2012 -0800 Modified the warning message diff --git src/hg/liftOver/liftOver.c src/hg/liftOver/liftOver.c index 1b2a924..3081e51 100644 --- src/hg/liftOver/liftOver.c +++ src/hg/liftOver/liftOver.c @@ -1,180 +1,182 @@ /* liftOver - Move annotations from one assembly to another. */ #include "common.h" #include "linefile.h" #include "hash.h" #include "options.h" #include "binRange.h" #include "chain.h" #include "bed.h" #include "genePred.h" #include "sample.h" #include "liftOver.h" int bedPlus = 0; bool fudgeThick = FALSE; bool errorHelp = FALSE; bool multiple = FALSE; bool hasBin = FALSE; bool tabSep = FALSE; char *chainTable = NULL; static struct optionSpec optionSpecs[] = { {"bedPlus", OPTION_INT}, {"chainTable", OPTION_STRING}, {"errorHelp", OPTION_BOOLEAN}, {"fudgeThick", OPTION_BOOLEAN}, {"genePred", OPTION_BOOLEAN}, {"gff", OPTION_BOOLEAN}, {"hasBin", OPTION_BOOLEAN}, {"minBlocks", OPTION_FLOAT}, {"minChainQ", OPTION_INT}, {"minChainT", OPTION_INT}, {"minMatch", OPTION_FLOAT}, {"minSizeQ", OPTION_INT}, {"minSizeT", OPTION_INT}, {"multiple", OPTION_BOOLEAN}, {"positions", OPTION_BOOLEAN}, {"pslT", OPTION_BOOLEAN}, {"sample", OPTION_BOOLEAN}, {"tab", OPTION_BOOLEAN}, {"tabSep", OPTION_BOOLEAN}, {NULL, 0} }; void usage() /* Explain usage and exit. */ { errAbort( "liftOver - Move annotations from one assembly to another\n" "usage:\n" " liftOver oldFile map.chain newFile unMapped\n" "oldFile and newFile are in bed format by default, but can be in GFF and\n" "maybe eventually others with the appropriate flags below.\n" "The map.chain file has the old genome as the target and the new genome\n" "as the query.\n\n" "***********************************************************************\n" "WARNING: liftOver was only designed to work between different\n" - " assemblies of the same organism, it may not do what you want\n" - " if you are lifting between different organisms.\n" + " assemblies of the same organism. It may not do what you want\n" + " if you are lifting between different organisms. If there has\n" + " been a rearrangement in one of the species, the size of the\n" + " region being mapped may change dramatically after mapping.\n" "***********************************************************************\n\n" "options:\n" " -minMatch=0.N Minimum ratio of bases that must remap. Default %3.2f\n" " -gff File is in gff/gtf format. Note that the gff lines are converted\n" " separately. It would be good to have a separate check after this\n" " that the lines that make up a gene model still make a plausible gene\n" " after liftOver\n" " -genePred - File is in genePred format\n" " -sample - File is in sample format\n" " -bedPlus=N - File is bed N+ format\n" " -positions - File is in browser \"position\" format\n" " -hasBin - File has bin value (used only with -bedPlus)\n" " -tab - Separate by tabs rather than space (used only with -bedPlus)\n" " -pslT - File is in psl format, map target side only\n" " -minBlocks=0.N Minimum ratio of alignment blocks or exons that must map\n" " (default %3.2f)\n" " -fudgeThick (bed 12 or 12+ only) If thickStart/thickEnd is not mapped,\n" " use the closest mapped base. Recommended if using \n" " -minBlocks.\n" " -multiple Allow multiple output regions\n" " -minChainT, -minChainQ Minimum chain size in target/query, when mapping\n" " to multiple output regions (default 0, 0)\n" " -minSizeT deprecated synonym for -minChainT (ENCODE compat.)\n" " -minSizeQ Min matching region size in query with -multiple.\n" " -chainTable Used with -multiple, format is db.tablename,\n" " to extend chains from net (preserves dups)\n" " -errorHelp Explain error messages\n", LIFTOVER_MINMATCH, LIFTOVER_MINBLOCKS ); } void liftOver(char *oldFile, char *mapFile, double minMatch, double minBlocks, int minSizeT, int minSizeQ, int minChainT, int minChainQ, bool multiple, char *chainTable, char *newFile, char *unmappedFile) /* liftOver - Move annotations from one assembly to another. */ { struct hash *chainHash = newHash(0); /* Old chromosome name keyed, chromMap valued. */ FILE *mapped = mustOpen(newFile, "w"); FILE *unmapped = mustOpen(unmappedFile, "w"); int errCt; if (!fileExists(oldFile)) errAbort("Can't find file: %s\n", oldFile); fprintf(stderr, "Reading liftover chains\n"); readLiftOverMap(mapFile, chainHash); fprintf(stderr, "Mapping coordinates\n"); if (optionExists("gff")) { fprintf(stderr, "WARNING: -gff is not recommended.\nUse 'ldHgGene -out=<file.gp>' and then 'liftOver -genePred <file.gp>'\n"); liftOverGff(oldFile, chainHash, minMatch, minBlocks, mapped, unmapped); } else if (optionExists("genePred")) liftOverGenePred(oldFile, chainHash, minMatch, minBlocks, fudgeThick, mapped, unmapped); else if (optionExists("sample")) liftOverSample(oldFile, chainHash, minMatch, minBlocks, fudgeThick, mapped, unmapped); else if (optionExists("pslT")) liftOverPsl(oldFile, chainHash, minMatch, minBlocks, fudgeThick, mapped, unmapped); else if (optionExists("bedPlus")) liftOverBedPlus(oldFile, chainHash, minMatch, minBlocks, minSizeT, minSizeQ, minChainT, minChainQ, fudgeThick, mapped, unmapped, multiple, chainTable, bedPlus, hasBin, tabSep, &errCt); else if (optionExists("positions")) liftOverPositions(oldFile, chainHash, minMatch, minBlocks, minSizeT, minSizeQ, minChainT, minChainQ, fudgeThick, mapped, unmapped, multiple, chainTable, &errCt); else liftOverBed(oldFile, chainHash, minMatch, minBlocks, minSizeT, minSizeQ, minChainT, minChainQ, fudgeThick, mapped, unmapped, multiple, chainTable, &errCt); if (!optionExists("positions")) /* I guess liftOverPositions closes these files. This is a little akward though. */ { carefulClose(&mapped); carefulClose(&unmapped); } } int main(int argc, char *argv[]) /* Process command line. */ { int minSizeT = 0; int minSizeQ = 0; int minChainT = 0; int minChainQ = 0; double minMatch = LIFTOVER_MINMATCH; double minBlocks = LIFTOVER_MINBLOCKS; optionInit(&argc, argv, optionSpecs); minMatch = optionFloat("minMatch", minMatch); minBlocks = optionFloat("minBlocks", minBlocks); fudgeThick = optionExists("fudgeThick"); multiple = optionExists("multiple"); if ((!multiple) && (optionExists("minSizeT") || optionExists("minSizeQ") || optionExists("minChainT") || optionExists("minChainQ") || optionExists("chainTable"))) errAbort("minSizeT/Q, minChainT/Q and chainTable can only be used with -multiple."); if (optionExists("minSizeT") && optionExists("minChainT")) errAbort("minSizeT is currently a deprecated synonym for minChainT. Can't set both."); minSizeT = optionInt("minSizeT", minChainT); /* note: we're setting minChainT */ minSizeQ = optionInt("minSizeQ", minSizeQ); minChainT = optionInt("minChainT", minChainT); minChainQ = optionInt("minChainQ", minChainQ); bedPlus = optionInt("bedPlus", bedPlus); hasBin = optionExists("hasBin"); tabSep = optionExists("tab") || optionExists("tabSep"); if ((hasBin || tabSep) && !bedPlus) usage(); chainTable = optionVal("chainTable", chainTable); if (optionExists("errorHelp")) errAbort("%s", liftOverErrHelp()); if (argc != 5) usage(); liftOver(argv[1], argv[2], minMatch, minBlocks, minSizeT, minSizeQ, minChainT, minChainQ, multiple, chainTable, argv[3], argv[4]); return 0; }