void checkSgdSync(char *downloadDir)
/* checkSgdSync - Make sure that genes and sequence are in sync for
* SGD yeast database. */
{
struct hash *chromHash;
char path[PATH_LEN];
safef(path, sizeof(path), "%s/%s", downloadDir, "chromosomes");
chromHash = loadChroms(path);
safef(path, sizeof(path), "%s/%s",
downloadDir, gffFile);
checkGff(path, chromHash);
}
int main(int argc, char *argv[])
/* read ContigLocFilter, writing to individual chrom tables */
{
struct hashCookie cookie;
struct hashEl *hel;
char *chromName;
if (argc != 3)
usage();
snpDb = argv[1];
contigGroup = argv[2];
hSetDb(snpDb);
/* check for needed tables */
if(!hTableExistsDb(snpDb, "ContigLocFilter"))
errAbort("no ContigLocFilter table in %s\n", snpDb);
if(!hTableExistsDb(snpDb, "ContigInfo"))
errAbort("no ContigInfo table in %s\n", snpDb);
chromHash = loadChroms(contigGroup);
if (chromHash == NULL)
{
verbose(1, "couldn't get chrom info\n");
return 1;
}
writeSplitTables();
verbose(1, "closing files...\n");
cookie = hashFirst(chromHash);
while (hel = hashNext(&cookie))
fclose(hel->val);
verbose(1, "creating tables...\n");
cookie = hashFirst(chromHash);
while ((chromName = hashNextName(&cookie)) != NULL)
createTable(chromName);
verbose(1, "loading database...\n");
cookie = hashFirst(chromHash);
while ((chromName = hashNextName(&cookie)) != NULL)
{
verbose(1, "chrom = %s\n", chromName);
loadDatabase(chromName);
}
return 0;
}
int main(int argc, char *argv[])
{
char *snpDb = NULL;
char *snpTableName = NULL;
struct hashCookie cookie;
char *chromName = NULL;
if (argc != 3)
usage();
snpDb = argv[1];
hSetDb(snpDb);
snpTableName = argv[2];
/* check that tables exist */
if (!hTableExists(snpTableName))
errAbort("no %s table in %s\n", snpTableName, snpDb);
if (!hTableExists("chromInfo"))
errAbort("no chromInfo table in %s\n", snpDb);
loadChroms();
getSnps(snpTableName);
verbose(1, "creating tables...\n");
cookie = hashFirst(chromHash);
while ((chromName = hashNextName(&cookie)) != NULL)
createTable(chromName);
verbose(1, "loading database...\n");
cookie = hashFirst(chromHash);
while ((chromName = hashNextName(&cookie)) != NULL)
{
verbose(1, "chrom = %s\n", chromName);
loadDatabase(chromName);
}
return 0;
}
