int main(int argc, char *argv[])
/* Process command line. */
{
setlinebuf(stdout);
setlinebuf(stderr);
optionInit(&argc, argv, optionSpecs);
boolean drop = optionExists("drop");
gbVerbInit(optionInt("verbose", 0));
if (gbVerbose >= 5)
sqlMonitorEnable(JKSQL_TRACE);
if (drop)
{
if (argc != 2)
usage();
mgcDropTables(argv[1]);
}
else
{
if (argc != 3)
usage();
workDir = optionVal("workdir", "work/load/mgc");
gbMakeDirs(workDir);
allMgcTables = optionExists("allMgcTables");
mgcDbLoad(argv[1], argv[2]);
}
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
char *repairTask, **dbs, *accFile = NULL;;
boolean dryRun;
int ndbs, i;
optionInit(&argc, argv, optionSpecs);
if (argc < 3)
usage("wrong # args");
gbVerbInit(optionInt("verbose", 1));
dryRun = optionExists("dryRun");
accFile = optionVal("accFile", NULL);
repairTask = argv[1];
dbs = argv+2;
ndbs = argc-2;
if (sameString(repairTask, "refPepList"))
{
if (accFile != NULL)
errAbort("-accFile is not valid for refPepList");
for (i = 0; i < ndbs; i++)
refPepList(dbs[i], stdout);
}
else if (sameString(repairTask, "refPepRepair"))
{
for (i = 0; i < ndbs; i++)
refPepRepair(dbs[i], accFile, dryRun);
}
else
errAbort("invalid repairTask: %s", repairTask);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
char *database;
optionInit(&argc, argv, optionSpecs);
if (argc != 2)
usage();
if (optionExists("gbdbCurrent"))
{
char* p;
gGbdbMapToCurrent = optionVal("gbdbCurrent", NULL);
/* trim trailing slashes */
for (p = gGbdbMapToCurrent + (strlen(gGbdbMapToCurrent)-1);
((p > gGbdbMapToCurrent) && (*p == '/')); p--)
*p = '\0';
}
gbVerbInit(optionInt("verbose", 0));
if (gbVerbose >= 5)
sqlMonitorEnable(JKSQL_TRACE);
database = argv[1];
gOptions = dbLoadOptionsParse(database);
testMode = optionExists("test");
gCheckExtSeqRecs = optionExists("checkExtSeqRecs");
gbVerbEnter(0, "gbSanity: begin: %s", database);
gbSanity(database);
gbVerbLeave(0, "gbSanity: completed: %d errors", errorCnt);
return ((errorCnt == 0) ? 0 : 1);
}
int main(int argc, char* argv[])
/* parse command line */
{
int numMrnas;
int numEsts;
char *accList, *selectAccFile;
char *database, *relName, *outDir;
verboseSetLevel(0);
optionInit(&argc, argv, optionSpecs);
if (argc != 4)
usage();
relName = argv[1];
database = argv[2];
outDir = argv[3];
numMrnas = optionInt("numMrnas", 10);
numEsts = optionInt("numEsts", 10);
accList = optionVal("accList", NULL);
selectAccFile = optionVal("selectAcc", NULL);
gbVerbInit(optionInt("verbose", 0));
if (verboseLevel() > 0)
setlinebuf(stderr);
getTestSubset(numMrnas, numEsts, accList, selectAccFile,
relName, database, outDir);
return 0;
}
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;
}
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;
}
int main(int argc, char* argv[])
{
optionInit(&argc, argv, optionSpecs);
if (argc != 1)
usage();
gbVerbInit(optionInt("verbose", 0));
gGbRoot = optionVal("gbRoot", NULL);
gbProcessedCheck();
if (gErrorCnt > 0)
errAbort("%d errors detected in processed entries, most likely need to "
"add to etc/ignore.idx", gErrorCnt);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
boolean drop, move, copy;
struct sigaction sigSpec;
setlinebuf(stdout);
setlinebuf(stderr);
ZeroVar(&sigSpec);
sigSpec.sa_handler = sigStopSignaled;
sigSpec.sa_flags = SA_RESTART;
if (sigaction(SIGUSR1, &sigSpec, NULL) < 0)
errnoAbort("can't set SIGUSR1 handler");
optionInit(&argc, argv, optionSpecs);
drop = optionExists("drop");
move = optionExists("move");
copy = optionExists("copy");
gReload = optionExists("reload");
if (move || copy)
{
if (argc != 3)
usage();
}
else if (argc != 2)
usage();
if ((drop+move+copy) > 1)
errAbort("can only specify one of -drop, -move, or -copy");
gbVerbInit(optionInt("verbose", 0));
if (gbVerbose >= 6)
sqlMonitorEnable(JKSQL_TRACE);
if (drop)
dropAll(argv[1]);
else if (move)
moveAll(argv[1], argv[2]);
else if (copy)
copyAll(argv[1], argv[2]);
else
{
char *reloadList = optionVal("reloadList", NULL);
gDatabase = argv[1];
gOptions = dbLoadOptionsParse(gDatabase);
gForceIgnoreDelete = optionExists("forceIgnoreDelete");
if (optionExists("rebuildDerived"))
gOptions.flags |= DBLOAD_BYPASS_GBLOADED|DBLOAD_REBUILD_DERIVED;
gMaxShrinkage = optionFloat("maxShrinkage", 0.1);
gGbdbGenBank = optionVal("gbdbGenBank", NULL);
if (gGbdbGenBank == NULL)
gGbdbGenBank = gbConfGet(gOptions.conf, "gbdb.genbank");
if (gGbdbGenBank == NULL)
gGbdbGenBank = "/gbdb/genbank";
gWorkDir = optionVal("workdir", "work/load");
if (gOptions.flags & DBLOAD_DRY_RUN)
printf("*** using dry run mode ***\n");
gbLoadRna(reloadList);
}
return 0;
}