int main(int argc, char *argv[])
/* get hapmapOrtho table from overall snpOrtho table */
/* hash in contents of hapmap table */
{
char *database = NULL;
char *hapmapTableName = NULL;
char *snpOrthoTableName = NULL;
struct hash *hapmapHash = NULL;
if (argc != 4)
usage();
database = argv[1];
hapmapTableName = argv[2];
snpOrthoTableName = argv[3];
hSetDb(database);
if (!hTableExists(hapmapTableName))
errAbort("no %s table in %s\n", hapmapTableName, database);
if (!hTableExists(snpOrthoTableName))
errAbort("no %s table in %s\n", snpOrthoTableName, database);
hapmapHash = storeHapmap(hapmapTableName);
processSnps(snpOrthoTableName, hapmapHash);
return 0;
}
int main(int argc, char *argv[])
{
char *snpDb = NULL;
char *oldTableName = NULL;
char *newTableName = NULL;
if (argc != 4)
usage();
snpDb = argv[1];
hSetDb(snpDb);
oldTableName = argv[2];
newTableName = argv[3];
/* check that tables exist */
if (!hTableExists(oldTableName))
errAbort("no %s table in %s\n", oldTableName, snpDb);
if (!hTableExists(newTableName))
errAbort("no %s table in %s\n", newTableName, snpDb);
if (!hTableExists("ContigLoc"))
errAbort("no ContigLoc table in %s\n", snpDb);
if (!hTableExists("MapInfo"))
errAbort("no MapInfo table in %s\n", snpDb);
processSnps(oldTableName, newTableName);
return 0;
}
int main(int argc, char *argv[])
/* work with singly aligning SNPs only */
/* load oldTable subset into list */
/* load newTable subset into hash */
{
char *snpDb = NULL;
struct weightList *oldTableList = NULL;
struct hash *newTableHash = NULL;
char *oldTableName = NULL;
char *newTableName = NULL;
if (argc != 4)
usage();
oneToOne = 0;
oneToTwo = 0;
oneToThree = 0;
twoToTwo = 0;
twoToOne = 0;
twoToThree = 0;
threeToThree = 0;
threeToOne = 0;
threeToTwo = 0;
snpDb = argv[1];
hSetDb(snpDb);
oldTableName = argv[2];
newTableName = argv[3];
// check that tables exist
if (!hTableExists(oldTableName))
errAbort("no %s table in %s\n", oldTableName, snpDb);
if (!hTableExists(newTableName))
errAbort("no %s table in %s\n", newTableName, snpDb);
oldTableList = getTableList(oldTableName);
newTableHash = getTableHash(newTableName);
logFileHandle = mustOpen("snpCompareWeightLog.out", "w");
processSnps(oldTableList, newTableHash);
carefulClose(&logFileHandle);
countFileHandle = mustOpen("snpCompareWeightCounts.out", "w");
fprintf(countFileHandle, "oneToOne = %d\n", oneToOne);
fprintf(countFileHandle, "oneToTwo = %d\n", oneToTwo);
fprintf(countFileHandle, "oneToThree = %d\n", oneToThree);
fprintf(countFileHandle, "twoToTwo = %d\n", twoToTwo);
fprintf(countFileHandle, "twoToOne = %d\n", twoToOne);
fprintf(countFileHandle, "twoToThree = %d\n", twoToThree);
fprintf(countFileHandle, "threeToThree = %d\n", threeToThree);
fprintf(countFileHandle, "threeToOne = %d\n", threeToOne);
fprintf(countFileHandle, "threeToTwo = %d\n", threeToTwo);
carefulClose(&countFileHandle);
return 0;
}
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[])
/* 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;
}
