int main(int argc, char *argv[])
/* hash subsnp_class and var_str from UniVariation */
/* read SNP for univar_id, lookup into univarHash */
/* store univarHash elements in snpHash */
/* read through chrN_snpTmp, rewrite with extensions to individual chrom tables */
{
struct slName *chromList, *chromPtr;
char tableName[64];
if (argc != 2)
usage();
snpDb = argv[1];
hSetDb(snpDb);
/* check for necessary tables */
if(!hTableExistsDb(snpDb, "SNP"))
errAbort("missing SNP table");
if(!hTableExistsDb(snpDb, "UniVariation"))
errAbort("missing UniVariation table");
chromList = hAllChromNamesDb(snpDb);
errorFileHandle = mustOpen("snpClassAndObserved.errors", "w");
univarHash = getUnivarHash();
snpHash = getSNPHash();
for (chromPtr = chromList; chromPtr != NULL; chromPtr = chromPtr->next)
{
safef(tableName, ArraySize(tableName), "%s_snpTmp", chromPtr->name);
if (!hTableExists(tableName)) continue;
verbose(1, "chrom = %s\n", chromPtr->name);
processSnps(chromPtr->name);
}
carefulClose(&errorFileHandle);
for (chromPtr = chromList; chromPtr != NULL; chromPtr = chromPtr->next)
{
safef(tableName, ArraySize(tableName), "%s_snpTmp", chromPtr->name);
if (!hTableExists(tableName)) continue;
recreateDatabaseTable(chromPtr->name);
verbose(1, "loading chrom = %s\n", chromPtr->name);
loadDatabase(chromPtr->name);
}
return 0;
}
int main(int argc, char *argv[])
/* read chrN_snpTmp, lookup in snpFasta, rewrite to individual chrom tables */
{
struct slName *chromList, *chromPtr;
char tableName[64];
if (argc != 2)
usage();
snpDb = argv[1];
hSetDb(snpDb);
chromList = hAllChromNamesDb(snpDb);
if (chromList == NULL)
{
verbose(1, "couldn't get chrom info\n");
return 1;
}
errorFileHandle = mustOpen("snpSNP.errors", "w");
/* read into global hash */
verbose(1, "reading SNP table into hash...\n");
readSNP();
for (chromPtr = chromList; chromPtr != NULL; chromPtr = chromPtr->next)
{
safef(tableName, ArraySize(tableName), "%s_snpTmp", chromPtr->name);
if (!hTableExists(tableName)) continue;
verbose(1, "processing chrom = %s\n", chromPtr->name);
processSnps(chromPtr->name);
}
carefulClose(&errorFileHandle);
for (chromPtr = chromList; chromPtr != NULL; chromPtr = chromPtr->next)
{
safef(tableName, ArraySize(tableName), "%s_snpTmp", chromPtr->name);
if (!hTableExists(tableName)) continue;
recreateDatabaseTable(chromPtr->name);
verbose(1, "loading chrom = %s\n", chromPtr->name);
loadDatabase(chromPtr->name);
}
return 0;
}
int main(int argc, char *argv[])
/* Read chromInfo into hash. */
/* Read ContigLocusIdCondense into hash. */
/* Recreate chrN_snpTmp, adding fxn_classes. */
{
struct slName *chromList, *chromPtr;
char tableName[64];
if (argc != 2)
usage();
snpDb = argv[1];
hSetDb(snpDb);
chromList = hAllChromNamesDb(snpDb);
/* check for needed tables */
if(!hTableExistsDb(snpDb, "ContigLocusIdCondense"))
errAbort("no ContigLocusIdCondense table in %s\n", snpDb);
if(!hTableExistsDb(snpDb, "chromInfo"))
errAbort("no chromInfo table in %s\n", snpDb);
functionHash = createFunctionHash();
for (chromPtr = chromList; chromPtr != NULL; chromPtr = chromPtr->next)
{
safef(tableName, ArraySize(tableName), "%s_snpTmp", chromPtr->name);
if (!hTableExists(tableName)) continue;
verbose(1, "chrom = %s\n", chromPtr->name);
addFunction(chromPtr->name);
}
for (chromPtr = chromList; chromPtr != NULL; chromPtr = chromPtr->next)
{
safef(tableName, ArraySize(tableName), "%s_snpTmp", chromPtr->name);
if (!hTableExists(tableName)) continue;
verbose(1, "loading chrom = %s\n", chromPtr->name);
recreateDatabaseTable(chromPtr->name);
loadDatabase(chromPtr->name);
}
return 0;
}
int main(int argc, char *argv[])
/* hash snpFasta, read through chrN_snpTmp, rewrite with extensions to individual chrom tables */
{
struct slName *chromList, *chromPtr;
char tableName[64];
if (argc != 2)
usage();
snpDb = argv[1];
hSetDb(snpDb);
chromList = hAllChromNamesDb(snpDb);
errorFileHandle = mustOpen("snpMoltype.errors", "w");
multiFastaHash = readFasta("chrMulti");
for (chromPtr = chromList; chromPtr != NULL; chromPtr = chromPtr->next)
{
safef(tableName, ArraySize(tableName), "%s_snpTmp", chromPtr->name);
if (!hTableExists(tableName)) continue;
verbose(1, "chrom = %s\n", chromPtr->name);
chromFastaHash = readFasta(chromPtr->name);
processSnps(chromPtr->name);
}
carefulClose(&errorFileHandle);
for (chromPtr = chromList; chromPtr != NULL; chromPtr = chromPtr->next)
{
safef(tableName, ArraySize(tableName), "%s_snpTmp", chromPtr->name);
if (!hTableExists(tableName)) continue;
recreateDatabaseTable(chromPtr->name);
verbose(1, "loading chrom = %s\n", chromPtr->name);
loadDatabase(chromPtr->name);
}
return 0;
}
int main(int argc, char *argv[])
/* read chrN_snpTmp, handle locType, rewrite to individual chrom tables */
{
struct slName *chromList, *chromPtr;
int expandCount = 0;
if (argc != 3)
usage();
snpDb = argv[1];
contigGroup = argv[2];
hSetDb(snpDb);
chromList = getChromListFromContigInfo(contigGroup);
if (chromList == NULL)
{
verbose(1, "couldn't get chrom info\n");
return 1;
}
errorFileHandle = mustOpen("snpLocType125.errors", "w");
exceptionFileHandle = mustOpen("snpLocType125.exceptions", "w");
for (chromPtr = chromList; chromPtr != NULL; chromPtr = chromPtr->next)
{
verbose(1, "chrom = %s\n", chromPtr->name);
expandCount = expandCount + doLocType(chromPtr->name);
recreateDatabaseTable(chromPtr->name);
loadDatabase(chromPtr->name);
}
if (expandCount > 0)
verbose(1, "need to expand %d alleles\n", expandCount);
carefulClose(&errorFileHandle);
carefulClose(&exceptionFileHandle);
return 0;
}
