a44421a79fb36cc2036fe116b97ea3bc9590cd0c braney Fri Dec 2 09:34:39 2011 -0800 removed rcsid (#295) diff --git src/hg/agpAllToFaFile/agpAllToFaFile.c src/hg/agpAllToFaFile/agpAllToFaFile.c index e3d98ad..e465eda 100644 --- src/hg/agpAllToFaFile/agpAllToFaFile.c +++ src/hg/agpAllToFaFile/agpAllToFaFile.c @@ -1,211 +1,210 @@ /* agpAllToFaFile - Convert a .agp file to a .fa file containing all sequences*/ #include "common.h" #include "linefile.h" #include "hash.h" #include "options.h" #include "fa.h" #include "agpFrag.h" #include "agpGap.h" -static char const rcsid[] = "$Id: agpAllToFaFile.c,v 1.9 2005/07/22 18:14:24 galt Exp $"; boolean doSort = FALSE; void usage() /* Explain usage and exit. */ { errAbort( "agpAllToFaFile - Convert all sequences in an .agp file to a .fa file \n" "usage:\n" " agpAllToFaFile in.agp in.fa out.fa\n" " options:\n" " -sizes=out - save chrom sizes in out.sizes and gap sizes in out.gaps\n" " -sort - preserve the in.agp chrom order\n" ); } char *chromSizeFile = NULL; /* file for chrom sizes */ char *chromGapSizeFile = NULL; /* file for chrom gap sizes */ void agpAllToFaFile(char *agpFile, char *faIn, char *faOut) /* agpAllToFaFile - Convert a .agp file to a .fa file. */ { struct lineFile *lf = lineFileOpen(agpFile, TRUE); /* input AGP file */ FILE *fIn, *fOut; /* input and output fasta file */ FILE *fSizes = NULL; /* output file w/ chrom sizes */ FILE *fGapSizes = NULL; /* output file w/ chrom gap sizes */ char *line, *words[16]; int lineSize, wordCount; int lastPos = 0; struct agpFrag *agpList = NULL, *agp; struct hash *chromHash = newHash(0); struct hash *chromSizeHash = newHash(0); struct hash *chromGapSizeHash = newHash(0); struct hash *fragHash = newHash(17); char *seqName = ""; DNA *dna = NULL; struct dnaSeq *seq; struct hashCookie cookie; struct hashEl *hel; int gap; /* count of gap bases for a chrom */ struct slName *chromNames = NULL, *chromName=NULL; /* read in AGP file, constructing hash of chrom agp lists */ verbose(1, "Reading %s\n", agpFile); while (lineFileNext(lf, &line, &lineSize)) { if (line[0] == '#' || line[0] == '\n') continue; wordCount = chopLine(line, words); if (wordCount < 5) errAbort("Bad line %d of %s\n", lf->lineIx, lf->fileName); if (words[4][0] != 'N' && words[4][0] != 'U') { /* not a gap */ lineFileExpectWords(lf, 9, wordCount); seqName = words[0]; agp = agpFragLoad(words); // file is 1-based but agpFragLoad() now assumes 0-based: agp->chromStart -= 1; agp->fragStart -= 1; if (!hashFindVal(chromHash, seqName)) lastPos = 0; if (agp->chromStart != lastPos) errAbort("Start doesn't match previous end line %d of %s\n", lf->lineIx, lf->fileName); if (agp->chromEnd - agp->chromStart != agp->fragEnd - agp->fragStart) errAbort("Sizes don't match in %s and %s line %d of %s\n", agp->chrom, agp->frag, lf->lineIx, lf->fileName); if (!hashFindVal(chromHash, seqName)) { if (agpList) slReverse(&agpList); /* new chrom */ AllocVar(agpList); /* add to hashes of chrom agp lists and sizes */ hashAdd(chromHash, seqName, agpList); hashAddInt(chromSizeHash, seqName, agp->chromEnd); if (doSort) slNameAddHead(&chromNames, seqName); } slAddHead(&agpList, agp); lastPos = agp->chromEnd; } else { /* gap */ gap = lineFileNeedNum(lf, words, 5); if (hashLookup(chromGapSizeHash, seqName) != NULL) { gap += hashIntVal(chromGapSizeHash, seqName); hashRemove(chromGapSizeHash, seqName); } hashAddInt(chromGapSizeHash, seqName, gap); lastPos = lineFileNeedNum(lf, words, 2); } if (hashLookup(chromSizeHash, seqName) != NULL) hashRemove(chromSizeHash, seqName); hashAddInt(chromSizeHash, seqName, lastPos); } if (agpList) slReverse(&agpList); /* read in input fasta file */ verbose(1, "Reading %s\n", faIn); fIn = mustOpen(faIn, "r"); while (faReadMixedNext(fIn, TRUE, "bogus", TRUE, NULL, &seq)) hashAdd(fragHash, seq->name, seq); /* set up output files */ verbose(1, "Writing %s\n", faOut); fOut = mustOpen(faOut, "w"); if (chromSizeFile != NULL) { verbose(1, "Writing %s\n", chromSizeFile); fSizes = mustOpen(chromSizeFile, "w"); fGapSizes = mustOpen(chromGapSizeFile, "w"); } if (doSort) { slReverse(&chromNames); chromName=chromNames; } else cookie = hashFirst(chromHash); /* traverse hash, writing out sequence records */ while (TRUE) { if (doSort) { if (chromName == NULL) break; hel = hashLookup(chromHash, chromName->name); } else { if ((hel = hashNext(&cookie)) == NULL) break; } seqName = (char *)hel->name; agpList = (struct agpFrag *)hel->val; lastPos = hashIntVal(chromSizeHash, seqName); if (lastPos == 0) errAbort("%s not found\n", seqName); if (fSizes != NULL) { fprintf(fSizes, "%s\t%d\n", seqName, lastPos); if (hashLookup(chromGapSizeHash, seqName)) { gap = hashIntVal(chromGapSizeHash, seqName); fprintf(fGapSizes, "%s\t%d\n", seqName, gap); } } dna = needLargeMem(lastPos+1); memset(dna, 'n', lastPos); dna[lastPos] = 0; for (agp = agpList->next; agp != NULL; agp = agp->next) { int size; verbose(2,"%s\n", agp->frag); seq = hashFindVal(fragHash, agp->frag); if (seq == NULL) errAbort("Couldn't find %s in %s", agp->frag, faIn); size = agp->fragEnd - agp->fragStart; memcpy(dna + agp->chromStart, seq->dna + agp->fragStart, size); if (agp->strand[0] == '-') reverseComplement(dna + agp->chromStart, size); } verbose(2,"Writing sequence %s, %d bases to %s\n", seqName, lastPos, faOut); faWriteNext(fOut, seqName, dna, lastPos); freeMem(dna); if (doSort) chromName=chromName->next; } if (doSort) slNameFreeList(&chromNames); } int main(int argc, char *argv[]) /* Process command line. */ { char *sizeFileBase = NULL; optionHash(&argc, argv); if (argc != 4) usage(); sizeFileBase = optionVal("sizes", sizeFileBase); if (sizeFileBase != NULL) { chromSizeFile = addSuffix(cloneString(sizeFileBase), ".sizes"); chromGapSizeFile = addSuffix(cloneString(sizeFileBase), ".gaps"); } if (optionExists("sort")) doSort = TRUE; agpAllToFaFile(argv[1], argv[2], argv[3]); return 0; }