/* hgGoldGapGl - Put chromosome .agp and .gl files into browser database.. */ /* Copyright (C) 2013 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "portable.h" #include "linefile.h" #include "dystring.h" #include "hash.h" #include "options.h" #include "agpFrag.h" #include "agpGap.h" #include "jksql.h" #include "ntContig.h" #include "glDbRep.h" #include "hdb.h" /* Command line switches. */ char *chrom = NULL; boolean unsplit = FALSE; boolean noLoad = FALSE; /* command line option specifications */ static struct optionSpec optionSpecs[] = { {"chrom", OPTION_STRING}, {"unsplit", OPTION_BOOLEAN}, {"noLoad", OPTION_BOOLEAN}, {NULL, 0} }; void usage() /* Explain usage and exit. */ { errAbort( "hgLoadGap - Load gap table from AGP-style file containing only gaps\n" "usage:\n" " hgLoadGap database dir\n" "options:\n" " -chrom=chrN - just do a single chromosome. Don't delete old tables.\n" " -unsplit - Instead of making chr*_gap tables from .gap files found \n" " in dir, expect dir to be a .gap file and make an \n" " unsplit gap table from its contents.\n" " -noLoad - Don't load the database table (for testing).\n" "example:\n" " hgLoadGap fr1 /cluster/data/fr1\n" " Gap file must be named with .gap extension \n" " This is only needed if gap table needs to be rebuilt,\n" " without changing the gold table.\n" ); } static int maxChromNameSize = 0; char *createGapSplit = "CREATE TABLE %s (\n" " bin smallint not null," " chrom varchar(255) not null, # which chromosome\n" " chromStart int unsigned not null, # start position in chromosome\n" " chromEnd int unsigned not null, # end position in chromosome\n" " ix int not null, # ix of this fragment (useless)\n" " n char(1) not null, # always 'N'\n" " size int unsigned not null, # size of gap\n" " type varchar(255) not null, # contig, clone, fragment, etc.\n" " bridge varchar(255) not null, # yes, no, mrna, bacEndPair, etc.\n" " #Indices\n" " INDEX(bin),\n" " UNIQUE(chromStart)\n" ")\n"; char *createGapUnsplit = "CREATE TABLE %s (\n" " bin smallint not null," " chrom varchar(255) not null, # which chromosome\n" " chromStart int unsigned not null, # start position in chromosome\n" " chromEnd int unsigned not null, # end position in chromosome\n" " ix int not null, # ix of this fragment (useless)\n" " n char(1) not null, # always 'N'\n" " size int unsigned not null, # size of gap\n" " type varchar(255) not null, # contig, clone, fragment, etc.\n" " bridge varchar(255) not null, # yes, no, mrna, bacEndPair, etc.\n" " #Indices\n" " INDEX(chrom(%d), bin),\n" " UNIQUE(chrom(%d), chromStart)\n" ")\n"; void gapFileToTable(struct sqlConnection *conn, char *gapFileName, char *gapTableName) /* Build a single gap table from a single gap file. */ { struct lineFile *lf = lineFileOpen(gapFileName, TRUE); char tabFileName[256]; FILE *tabFile = NULL; char *words[16]; int wordCount; safef(tabFileName, sizeof(tabFileName), "%s.tab", gapTableName); tabFile = mustOpen(tabFileName, "w"); while ((wordCount = lineFileChop(lf, words)) > 0) { if (wordCount < 5) errAbort("Short line %d of %s", lf->lineIx, lf->fileName); if (words[4][0] == 'N' || words[4][0] == 'U') { int len = strlen(words[0]); if (len > maxChromNameSize) { maxChromNameSize = len; if (maxChromNameSize > 254) errAbort("ERROR: chrom name size is over 254(%d) characters: " "'%s'", maxChromNameSize, words[0]); } struct agpGap gap; agpGapStaticLoad(words, &gap); gap.chromStart -= 1; fprintf(tabFile, "%u\t", hFindBin(gap.chromStart, gap.chromEnd)); agpGapTabOut(&gap, tabFile); } } lineFileClose(&lf); fclose(tabFile); if (! noLoad) { struct dyString *ds = dyStringNew(2048); if (unsplit) sqlDyStringPrintf(ds, createGapUnsplit, gapTableName, maxChromNameSize, maxChromNameSize); else sqlDyStringPrintf(ds, createGapSplit, gapTableName); char query[1024]; sqlRemakeTable(conn, gapTableName, ds->string); sqlSafef(query, sizeof(query), "LOAD data local infile '%s' into table %s", tabFileName, gapTableName); sqlUpdate(conn, query); remove(tabFileName); dyStringFree(&ds); } } void makeGap(struct sqlConnection *conn, char *chromDir) /* Read in .gap files in chromDir and use them to create the * gap table for the corresponding chromosome(s). */ { struct fileInfo *fiList, *fi; fiList = listDirX(chromDir, "*.gap", TRUE); for (fi = fiList; fi != NULL; fi = fi->next) { char dir[256], chrom[128], ext[64]; char *ptr; char gapName[128]; char *gapFileName = fi->name; verbose(1, "Processing %s\n", gapFileName); /* Get full path name of .gap file and process it * into table names. */ splitPath(gapFileName, dir, chrom, ext); while ((ptr = strchr(chrom, '.')) != NULL) *ptr = '_'; safef(gapName, sizeof(gapName), "%s_gap", chrom); gapFileToTable(conn, gapFileName, gapName); } } void hgLoadGap(char *database, char *ooDir, char *oneChrom) /* hgLoadGap - Put chromosome .gap files into browser database.. */ { struct sqlConnection *conn = sqlConnect(database); /* target prefix is used in zoo browser */ if (oneChrom != NULL) { if (startsWith("chr", oneChrom)) oneChrom += 3; else if (startsWith("target", oneChrom)) oneChrom += 6; } if (unsplit) gapFileToTable(conn, ooDir, "gap"); else { struct fileInfo *chrFiList, *chrFi; char pathName[512]; boolean gotAny = FALSE; chrFiList = listDirX(ooDir, "*", FALSE); for (chrFi = chrFiList; chrFi != NULL; chrFi = chrFi->next) { if (chrFi->isDir && ((strlen(chrFi->name) <= 2) || startsWith("NA_", chrFi->name))) { if (oneChrom == NULL || sameWord(chrFi->name, oneChrom)) { safef(pathName, sizeof(pathName), "%s/%s", ooDir, chrFi->name); makeGap(conn, pathName); gotAny = TRUE; verbose(2, "done %s\n", chrFi->name); } } } slFreeList(&chrFiList); if (!gotAny) errAbort("No .gap files found"); } sqlDisconnect(&conn); } int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, optionSpecs); if (argc != 3) usage(); chrom = optionVal("chrom", chrom); unsplit = optionExists("unsplit"); noLoad = optionExists("noLoad"); hgLoadGap(argv[1], argv[2], chrom); return 0; }