void checkMrnaPartition(struct gbSelect* select)
/* Check an mRNA partition. For genbank, check all ESTs against
* this mRNA partation. */
{
struct hashCookie cookie;
struct hashEl* hel;
gbReleaseLoadProcessed(select);
struct gbSelect* prevSelect = gbProcessedGetPrevRel(select);
if (prevSelect != NULL)
gbReleaseLoadProcessed(prevSelect);
gbVerbEnter(2, "checking %s", gbSelectDesc(select));
cookie = hashFirst(select->release->entryTbl);
while ((hel = hashNext(&cookie)) != NULL)
checkOrgCat(hel->val, prevSelect);
gbVerbLeave(2, "checking %s", gbSelectDesc(select));
if (select->release->srcDb == GB_GENBANK)
checkEstPartitions(select->release);
gbReleaseUnload(select->release);
if (prevSelect != NULL)
{
gbReleaseUnload(prevSelect->release);
freeMem(prevSelect);
}
}
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;
}
struct gbAlignInfo gbAlignGet(struct gbSelect* select,
struct gbSelect* prevSelect)
/* Build files to align in the work directory. If this is not a full release,
* or there is no previously aligned release, prevSelect should be NULL.
*/
{
struct gbAlignInfo alignInfo;
gbVerbEnter(1, "gbAlignGet: %s", gbSelectDesc(select));
if (prevSelect != NULL)
prevSelect->orgCats = select->orgCats;
/* load the required entry data */
gbReleaseLoadProcessed(select);
if (prevSelect != NULL)
{
gbReleaseLoadProcessed(prevSelect);
gbReleaseLoadAligned(prevSelect);
}
/* select entries to align */
gbVerbEnter(2, "selecting seqs to align");
alignInfo = gbAlignFindNeedAligned(select, prevSelect);
gbVerbLeave(2, "selecting seqs to align");
if (alignInfo.migrate.accTotalCnt > 0)
gbVerbMsg(1, "gbAlignGet: %d %s entries, %d alignments will be migrated",
alignInfo.migrate.accTotalCnt, gbFmtSelect(select->type),
alignInfo.migrate.recTotalCnt);
/* create fasta with sequences to align if not empty */
if (alignInfo.align.accTotalCnt > 0)
{
gbVerbMsg(1, "gbAlignGet: %d %s sequences will be align",
alignInfo.align.accTotalCnt, gbFmtSelect(select->type));
copySelectedFasta(select);
}
/* leave calling cards */
if (select->orgCats & GB_NATIVE)
markAligns(select, GB_NATIVE);
if (select->orgCats & GB_XENO)
markAligns(select, GB_XENO);
/* print before releasing memory */
gbVerbLeave(1, "gbAlignGet: %s", gbSelectDesc(select));
/* unload entries to free memory */
gbReleaseUnload(select->release);
if (prevSelect != NULL)
gbReleaseUnload(prevSelect->release);
return alignInfo;
}
void gbAlignInstall(struct gbSelect* select, struct gbSelect* prevSelect)
/* Install alignments, optionally migrating unchanged ones from a previous
* release. This does one update, accPrefix and either native or xeno */
{
char nativeAlignIdx[PATH_LEN], xenoAlignIdx[PATH_LEN];
struct gbAlignInfo alignInfo;
gbVerbEnter(1, "gbAlignInstall: %s", gbSelectDesc(select));
/* load required entry date */
gbReleaseLoadProcessed(select);
if (prevSelect != NULL)
{
gbReleaseLoadProcessed(prevSelect);
gbReleaseLoadAligned(prevSelect);
}
/* mark entries and updates to migrate or align */
alignInfo = gbAlignFindNeedAligned(select, prevSelect);
/* Process each category */
if (select->orgCats & GB_NATIVE)
installOrgCatAligned(select, GB_NATIVE, prevSelect, &alignInfo,
nativeAlignIdx);
if (select->orgCats & GB_XENO)
installOrgCatAligned(select, GB_XENO, prevSelect, &alignInfo,
xenoAlignIdx);
/* now indices can be renamed, not completely atomic, but good enough */
if (select->orgCats & GB_NATIVE)
gbOutputRename(nativeAlignIdx, NULL);
if (select->orgCats & GB_XENO)
gbOutputRename(xenoAlignIdx, NULL);
/* print message before memory is freed */
gbVerbLeave(1, "gbAlignInstall: %s", gbSelectDesc(select));
/* unload entries to free memory */
gbReleaseUnload(select->release);
if (prevSelect != NULL)
gbReleaseUnload(prevSelect->release);
}
void checkEstPartition(struct gbRelease* mrnaRelease,
struct gbSelect* select)
/* Check an EST partition */
{
struct hashCookie cookie;
struct hashEl* hel;
gbVerbEnter(2, "checking %s", gbSelectDesc(select));
gbReleaseLoadProcessed(select);
struct gbSelect* prevSelect = gbProcessedGetPrevRel(select);
if (prevSelect != NULL)
gbReleaseLoadProcessed(prevSelect);
cookie = hashFirst(select->release->entryTbl);
while ((hel = hashNext(&cookie)) != NULL)
checkEst(mrnaRelease, hel->val, prevSelect);
gbReleaseUnload(select->release);
if (prevSelect != NULL)
{
gbReleaseUnload(prevSelect->release);
freeMem(prevSelect);
}
gbVerbLeave(2, "checking %s", gbSelectDesc(select));
}
static void chkGbRelease(struct gbSelect* select,
struct metaDataTbls* metaDataTbls)
/* Check a partation of gbRelease */
{
gbVerbEnter(1, "check: %s", gbSelectDesc(select));
/* load required entry date */
gbReleaseLoadProcessed(select);
gbReleaseLoadAligned(select);
chkGbIndex(select, metaDataTbls);
/* unload entries to free memory */
gbReleaseUnload(select->release);
gbVerbLeave(1, "check: %s", gbSelectDesc(select));
}
void doLoadPartition(struct gbSelect* select)
/* Do work of syncing the database with the state in the genbank respository for
* a given partition. */
{
gbVerbEnter(2, "load for %s", gbSelectDesc(select));
/* load required entry date */
gbReleaseLoadProcessed(select);
gbReleaseLoadAligned(select);
databaseUpdate(select);
gbVerbLeave(2, "load for %s", gbSelectDesc(select));
/* unload entries to free memory */
gbReleaseUnload(select->release);
}
static void testLoad(struct gbSelect* select, unsigned flags)
/* do load testing of part of a release */
{
char desc[512];
struct stepInfo info;
select->type = (flags & DO_MRNA) ? GB_MRNA : GB_EST;
safef(desc, sizeof(desc), "%s %s",
((flags & DO_PROCESSED) ? "processed" : "aligned"),
gbSelectDesc(select));
info = beginStep(select->release->index, select->release, desc);
if (flags & DO_PROCESSED)
gbReleaseLoadProcessed(select);
else
{
select->orgCats = GB_NATIVE|GB_XENO;
gbReleaseLoadAligned(select);
}
endStep(select->release->index, &info);
select->type = 0;
}