struct gbRelease* loadIndex(char* relName, unsigned types, char* database)
/* load processed section of index for release */
{
struct gbIndex* index = gbIndexNew(database, NULL);
struct gbSelect select;
ZeroVar(&select);
select.release = gbIndexMustFindRelease(index, relName);
if (types & GB_MRNA)
{
select.type = GB_MRNA;
gbReleaseLoadProcessed(&select);
}
if ((types & GB_EST) && (select.release->srcDb == GB_GENBANK))
{
struct slName* prefixes, *prefix;
select.type = GB_EST;
prefixes = gbReleaseGetAccPrefixes(select.release, GB_PROCESSED, GB_EST);
for (prefix = prefixes; prefix != NULL; prefix = prefix->next)
{
select.accPrefix = prefix->name;
gbReleaseLoadProcessed(&select);
}
select.accPrefix = NULL;
slFreeList(&prefixes);
}
return select.release;
}
int main(int argc, char* argv[])
{
char *relName, *updateName, *typeAccPrefix, *database, *sep;
struct gbIndex* index;
struct gbSelect select;
struct gbSelect* prevSelect = NULL;
struct gbAlignInfo alignInfo;
boolean noMigrate;
ZeroVar(&select);
optionInit(&argc, argv, optionSpecs);
if (argc != 5)
usage();
maxFaSize = optionInt("fasize", -1);
workDir = optionVal("workdir", "work/align");
noMigrate = optionExists("noMigrate");
createPolyASizes = optionExists("polyASizes");
gbVerbInit(optionInt("verbose", 0));
relName = argv[1];
updateName = argv[2];
typeAccPrefix = argv[3];
database = argv[4];
/* parse typeAccPrefix */
sep = strchr(typeAccPrefix, '.');
if (sep != NULL)
*sep = '\0';
select.type = gbParseType(typeAccPrefix);
if (sep != NULL)
{
select.accPrefix = sep+1;
*sep = '.';
}
select.orgCats = gbParseOrgCat(optionVal("orgCats", "native,xeno"));
index = gbIndexNew(database, NULL);
select.release = gbIndexMustFindRelease(index, relName);
select.update = gbReleaseMustFindUpdate(select.release, updateName);
gbVerbMsg(0, "gbAlignGet: %s/%s/%s/%s", select.release->name,
select.release->genome->database, select.update->name,
typeAccPrefix);
/* Get the release to migrate, if applicable */
if (!noMigrate)
prevSelect = gbAlignGetMigrateRel(&select);
alignInfo = gbAlignGet(&select, prevSelect);
/* always print stats */
fprintf(stderr, "gbAlignGet: %s/%s/%s/%s: align=%d, migrate=%d\n",
select.release->name, select.release->genome->database,
select.update->name, typeAccPrefix,
alignInfo.align.accTotalCnt, alignInfo.migrate.accTotalCnt);
gbIndexFree(&index);
/* print alignment and migrate count, which is read by the driver program */
printf("alignCnt: %d %d\n", alignInfo.align.accTotalCnt, alignInfo.migrate.accTotalCnt);
return 0;
}
int main(int argc, char* argv[])
{
char *relName, *updateName, *typeAccPrefix, *database, *sep;
struct gbIndex* index;
struct gbSelect select;
struct gbSelect* prevSelect = NULL;
boolean noMigrate;
ZeroVar(&select);
optionInit(&argc, argv, optionSpecs);
if (argc != 5)
usage();
gWorkDir = optionVal("workdir", "work/align");
gSortTmp = optionVal("sortTmp", NULL);
noMigrate = optionExists("noMigrate");
gbVerbInit(optionInt("verbose", 0));
relName = argv[1];
updateName = argv[2];
typeAccPrefix = argv[3];
database = argv[4];
/* parse typeAccPrefix */
sep = strchr(typeAccPrefix, '.');
if (sep != NULL)
*sep = '\0';
select.type = gbParseType(typeAccPrefix);
if (sep != NULL)
{
select.accPrefix = sep+1;
*sep = '.';
}
index = gbIndexNew(database, NULL);
select.release = gbIndexMustFindRelease(index, relName);
select.update = gbReleaseMustFindUpdate(select.release, updateName);
select.orgCats = gbParseOrgCat(optionVal("orgCats", "native,xeno"));
gbVerbMsg(0, "gbAlignInstall: %s/%s/%s/%s", select.release->name,
select.release->genome->database, select.update->name,
typeAccPrefix);
/* Get the release to migrate, if applicable */
if (!noMigrate)
prevSelect = gbAlignGetMigrateRel(&select);
gbAlignInstall(&select, prevSelect);
/* must go to stderr to be logged */
gbVerbMsg(0, "gbAlignInstall: complete");
gbIndexFree(&index);
return 0;
}
void gbProcessedCheck()
/* do processed sanity checks on newest genbank/refseq releases */
{
struct gbIndex* index = gbIndexNew(NULL, gGbRoot);
struct gbSelect* partitions, *select;
/* get mRNA data only, ESTs are compared against mRNAs for type change */
partitions = gbIndexGetPartitions(index, GB_PROCESSED, GB_GENBANK|GB_REFSEQ,
NULL, GB_MRNA, GB_NATIVE|GB_XENO, NULL);
for (select = partitions; select != NULL; select = select->next)
checkMrnaPartition(select);
gbIndexFree(&index);
}
int main(int argc, char* argv[])
{
int argi;
char* dumpFile = NULL;
unsigned flags = 0;
char* database, *accPrefix;
struct gbIndex* index;
struct stepInfo runInfo;
gbVerbInit(0);
optionInit(&argc, argv, optionSpecs);
if (argc < 2)
usage();
if (optionExists("processed"))
flags |= DO_PROCESSED;
if (optionExists("aligned"))
flags |= DO_PROCESSED|DO_ALIGNED;
if (optionExists("mrna"))
flags |= DO_MRNA;
if (optionExists("est"))
flags |= DO_EST;
dumpFile = optionVal("dump", NULL);
database = optionVal("db", NULL);
accPrefix = optionVal("accPrefix", NULL);
if ((flags & DO_ALIGNED) && (database == NULL))
errAbort("must specify -db with -aligned");
if (!(flags & (DO_MRNA|DO_EST)))
errAbort("must specify at least one of -mrna or -est");
if (!(flags & (DO_ALIGNED|DO_PROCESSED)))
errAbort("must specify at least one of -processed or -aligned");
index = gbIndexNew(database, NULL);
runInfo = beginStep(index, NULL, "loading index files");
for (argi = 1; argi < argc; argi++)
testRelLoad(index, gbIndexMustFindRelease(index, argv[argi]),
database, flags, accPrefix);
if (dumpFile != NULL)
{
FILE* dumpOut = mustOpen(dumpFile, "w");
gbIndexDump(index, dumpOut);
if (fclose(dumpOut) != 0)
errnoAbort("close of dumpfile");
}
endStep(index, &runInfo);
gbIndexFree(&index);
return 0;
}
static void gbSanity(char* database)
/* Run sanity checks */
{
struct gbIndex* index = gbIndexNew(database, NULL);
struct sqlConnection *conn;
struct gbRelease* release;
gbErrorSetDb(database);
int checkedSetCnt = 0;
if (gOptions.relRestrict == NULL)
{
int releaseCnt = 0;
/* Check each partition of the genbank/refseq using the newest aligned
* release */
release = newestReleaseWithAligns(index, database, GB_GENBANK);
if (release != NULL)
{
releaseCnt++;
checkedSetCnt += releaseSanity(release, database);
}
release = newestReleaseWithAligns(index, database, GB_REFSEQ);
if (release != NULL)
{
releaseCnt++;
checkedSetCnt += releaseSanity(release, database);
}
if (releaseCnt == 0)
errAbort("Error: No RefSeq or Genbank alignments for %s\n"
"have updates been enabled?", database);
}
else
{
release = gbIndexMustFindRelease(index, gOptions.relRestrict);
checkedSetCnt += releaseSanity(release, database);
}
if (checkedSetCnt == 0)
errAbort("Error: no alignment data was checked");
verbose(1, "%d alignment sets checked\n", checkedSetCnt);
gbIndexFree(&index);
/* check of uniqueStr ids */
conn = hAllocConn(database);
checkGbCdnaInfoStrKeys(conn);
hFreeConn(&conn);
}
void checkEstPartitions(struct gbRelease* mrnaRelease)
/* Check EST partitions, this compares against mRNA entries
* for changed type. Separate gbIndex objects are used so EST
* partitions can be unloaded.
*/
{
struct gbIndex* estIndex = gbIndexNew(NULL, gGbRoot);
struct gbRelease* estRelease = gbIndexMustFindRelease(estIndex,
mrnaRelease->name);
struct gbSelect* partitions, *select;
partitions = gbIndexGetPartitions(estIndex, GB_PROCESSED, GB_GENBANK,
estRelease->name,
GB_EST, GB_NATIVE|GB_XENO, NULL);
for (select = partitions; select != NULL; select = select->next)
checkEstPartition(mrnaRelease, select);
slFreeList(&partitions);
gbIndexFree(&estIndex);
}
void gbLoadRna(char* reloadList)
/* Sync the database with the state in the genbank respository. */
{
struct gbIndex* index = gbIndexNew(gDatabase, NULL);
struct gbSelect* selectList, *select;
struct sqlConnection* conn;
/* must go through all tables if any reload is selected,
* extFile update is requested, or rebuilding derived */
if ((reloadList != NULL) || gReload)
gOptions.flags |= DBLOAD_BYPASS_GBLOADED;
if (gReload && (gOptions.flags & DBLOAD_DRY_RUN))
errAbort("can't specify both -reload and -dryRun");
gbVerbEnter(1, "gbLoadRna");
conn = hAllocConn(gDatabase);
gbLockDb(conn, NULL);
if (gOptions.flags & DBLOAD_INITIAL)
checkInitialLoad(conn);
/* delete anything on the reload list up front */
if (((gOptions.flags & DBLOAD_DRY_RUN) == 0) && (reloadList != NULL))
{
gbAlignDataInit(gWorkDir, &gOptions, conn);
gbReloadDelete(gDatabase, reloadList, &gOptions, gWorkDir);
}
selectList = dbLoadPartitionsGet(&gOptions, index);
if ((gOptions.flags & DBLOAD_INITIAL) && (selectList == NULL))
errAbort("-initialLoad specified and no sequences were found to load");
/* clean up any ignored entries before setting anything up */
gbVerbEnter(3, "delete ignored");
gbIgnoredDelete(gDatabase, selectList, gForceIgnoreDelete, &gOptions, gWorkDir);
gbVerbLeave(3, "delete ignored");
/* loaded table to track updates that have been processed */
gLoadedTbl = gbLoadedTblNew(conn);
/* load each partition */
for (select = selectList; select != NULL; select = select->next)
loadPartition(select, conn);
/* If we are delaying table load, now is the time */
if ((gOptions.flags & DBLOAD_INITIAL)
&& ((gOptions.flags & DBLOAD_DRY_RUN) == 0))
loadDelayedTables();
/* clean up extFile table if we change references for any seq */
if ((gOptions.flags & DBLOAD_EXT_FILE_UPDATE) && ((gOptions.flags & DBLOAD_DRY_RUN) == 0))
cleanExtFileTable();
/* clean up */
slFreeList(&selectList);
gbMetaDataFree();
gbLoadedTblFree(&gLoadedTbl);
gbUnlockDb(conn, NULL);
hFreeConn(&conn);
/* must go to stderr to be logged */
gbVerbLeave(1, "gbLoadRna");
if (gMaxShrinkageError)
errAbort("Stoping due to maxShrinkage limit being exceeded in one or more\n"
"partitions. Investigate and rerun with -allowLargeDeletes.");
}