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;
}
示例#2
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;
}
示例#3
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);
}
示例#4
0
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;
}
示例#6
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;
}
示例#7
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;
}