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 getTestSubset(int numMrnas, int numEsts, char *accList,
char* selectAccFile, char* relName, char* database,
char* outDir)
/* Get the test subset. */
{
struct gbRelease* release;
struct hash* accTbl = hashNew(20);
unsigned types = 0;
/* note, we find mRNAs and ESTs seperately, but extract in one pass, as
* daily updates have both in a single file */
if (numMrnas > 0)
types |= GB_MRNA;
if (numEsts > 0)
types |= GB_EST;
release = loadIndex(relName, types, database);
if (selectAccFile != NULL)
getRequestedAccs(selectAccFile, release, accTbl);
if (numMrnas > 0)
findAccs(numMrnas, GB_MRNA, release, accTbl);
if (numEsts > 0)
findAccs(numEsts, GB_EST, release, accTbl);
copyAccs(release, types, accTbl, outDir);
if (accList != NULL)
{
FILE *accListFh;
struct hashCookie cookie;
struct hashEl* hel;
gbMakeFileDirs(accList);
accListFh = mustOpen(accList, "w");
cookie = hashFirst(accTbl);
while ((hel = hashNext(&cookie)) != NULL)
fprintf(accListFh, "%s\n", hel->name);
carefulClose(&accListFh);
}
hashFree(&accTbl);
gbIndexFree(&release->index);
}
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);
}
