void refPepList(char *db,
FILE* outFh)
/* list of sequences needing repair */
{
struct sqlConnection *conn = sqlConnect(db);
struct brokenRefPepTbl *brpTbl;
struct hashCookie cookie;
struct hashEl *hel;
struct extFileTbl* extFileTbl = NULL;
if (!checkForRefLink(conn))
{
sqlDisconnect(&conn);
return;
}
extFileTbl = extFileTblLoad(conn);
brpTbl = brokenRefPepTblNew(conn, NULL);
brokenRefPepGetSeqScan(conn, extFileTbl, brpTbl);
brokenRefPepGetMrnas(conn, brpTbl);
extFileTblFree(&extFileTbl);
cookie = hashFirst(brpTbl->protAccHash);
while ((hel = hashNext(&cookie)) != NULL)
{
struct brokenRefPep *brp = hel->val;
fprintf(outFh, "%s\t%s\t%s\n", sqlGetDatabase(conn), brp->protAcc, (brp->mrnaAcc != NULL)? "repair" : "drop");
}
gbVerbMsg(1, "%s: need to repair %d refseq protein gbExtFile entries",
sqlGetDatabase(conn), brpTbl->numToRepair);
gbVerbMsg(1, "%s: need to drop %d refseq protein gbExtFile entries",
sqlGetDatabase(conn), brpTbl->numToDrop);
}
void refPepRepair(char *db,
char *accFile,
boolean dryRun)
/* fix dangling repPep gbSeq entries. */
{
struct sqlConnection *conn = sqlConnect(db);
struct brokenRefPepTbl *brpTbl;
struct extFileTbl* extFileTbl;
struct slName *accs = (accFile == NULL) ? NULL : slNameLoadReal(accFile);
if (!checkForRefLink(conn))
{
sqlDisconnect(&conn);
return;
}
gbVerbMsg(1, "%s: repairing refseq protein gbExtFile entries%s",
sqlGetDatabase(conn), (dryRun? " (dry run)" : ""));
extFileTbl = extFileTblLoad(conn);
brpTbl = brokenRefPepTblNew(conn, accs);
brokenRefPepGetSeqScan(conn, extFileTbl, brpTbl);
brokenRefPepGetMrnas(conn, brpTbl);
fillInFastaOffsets(brpTbl, conn, extFileTbl);
if (brpTbl->numToRepair > 0)
makeRepairs(brpTbl, conn, extFileTbl, dryRun);
else
gbVerbMsg(1, "%s: no refseq proteins to repair", sqlGetDatabase(conn));
brokenRefPepTblFree(&brpTbl);
extFileTblFree(&extFileTbl);
sqlDisconnect(&conn);
slFreeList(&accs);
}
void loadSeqData(struct metaDataTbls* metaDataTbls,
struct gbSelect* select, struct sqlConnection* conn,
boolean checkExtSeqRecs, char* gbdbMapToCurrent)
/* load seq table data, gbCdnaInfo table should be loaded. For
* refseq, refLink should also have been loaded*/
{
struct extFileTbl* extFileTbl;
gbVerbMsg(2, "load gbExtFile table data");
extFileTbl = extFileTblLoad(conn);
/* setup globals */
if (missingExtFileIds == NULL)
{
missingExtFileIds = hashNew(16);
missingExtFiles = hashNew(16);
}
loadSeqCDnaData(metaDataTbls,select, conn, checkExtSeqRecs, gbdbMapToCurrent,
extFileTbl);
if (select->release->srcDb == GB_REFSEQ)
loadSeqPepData(metaDataTbls, conn, checkExtSeqRecs, gbdbMapToCurrent,
extFileTbl);
extFileTblFree(&extFileTbl);
}
static HGID getExtFileId(struct sqlConnection *conn, char* relPath)
/* get the extFile id for a file, prepending the gbdb root dir */
{
char path[PATH_LEN];
path[0] = '\0';
if (gGbdbGenBank[0] != '\0')
{
strcpy(path, gGbdbGenBank);
strcat(path, "/");
}
strcat(path, relPath);
if (extFiles == NULL)
{
gbVerbMsg(4, "loading extFile table");
extFiles = extFileTblLoad(conn);
}
return extFileTblGet(extFiles, conn, path);
}
