struct estOrientInfo *estOrientInfoLoadWhere(struct sqlConnection *conn, char *table, char *where)
/* Load all estOrientInfo from table that satisfy where clause. The
* where clause may be NULL in which case whole table is loaded
* Dispose of this with estOrientInfoFreeList(). */
{
struct estOrientInfo *list = NULL, *el;
struct dyString *query = dyStringNew(256);
struct sqlResult *sr;
char **row;
sqlDyStringPrintf(query, "select * from %s", table);
if (where != NULL)
dyStringPrintf(query, " where %s", where);
sr = sqlGetResult(conn, query->string);
int off = sqlFieldColumn(sr, "bin") + 1; // offset of data; function returns -1 if no bin
while ((row = sqlNextRow(sr)) != NULL)
{
el = estOrientInfoLoad(row+off);
slAddHead(&list, el);
}
slReverse(&list);
sqlFreeResult(&sr);
dyStringFree(&query);
return list;
}
static void processOIFile(struct sqlConnection *conn, struct gbSelect* select,
struct gbStatusTbl* statusTbl, char* oiPath)
/* Parse a psl file looking for accessions to add to the database. */
{
char *row[EST_ORIENT_INFO_NUM_COLS];
struct lineFile *oiLf = gzLineFileOpen(oiPath);
while (lineFileNextRow(oiLf, row, EST_ORIENT_INFO_NUM_COLS))
{
struct estOrientInfo* oi = estOrientInfoLoad(row);
processOI(conn, select, statusTbl, oi, oiLf);
estOrientInfoFree(&oi);
}
gzLineFileClose(&oiLf);
}
struct estOrientInfo *estOrientInfoLoadAll(char *fileName)
/* Load all estOrientInfo from a tab-separated file.
* Dispose of this with estOrientInfoFreeList(). */
{
struct estOrientInfo *list = NULL, *el;
struct lineFile *lf = lineFileOpen(fileName, TRUE);
char *row[9];
while (lineFileRow(lf, row))
{
el = estOrientInfoLoad(row);
slAddHead(&list, el);
}
lineFileClose(&lf);
slReverse(&list);
return list;
}
static void processOrgCatOi(struct gbSelect* select, unsigned orgCat)
/* process files in an update an organism category. OIs are only available
* for native, however this follow the structure of the PSL code */
{
char inOi[PATH_LEN], *row[EST_ORIENT_INFO_NUM_COLS];
struct lineFile* inOiLf;
unsigned orgCatsHold = select->orgCats;
select->orgCats = orgCat;
gbAlignedGetPath(select, "oi.gz", NULL, inOi);
inOiLf = gzLineFileOpen(inOi);
while (lineFileNextRowTab(inOiLf, row, EST_ORIENT_INFO_NUM_COLS))
{
struct estOrientInfo* oi = estOrientInfoLoad(row);
processOi(select, oi);
estOrientInfoFree(&oi);
}
gzLineFileClose(&inOiLf);
select->orgCats = orgCatsHold;
}
struct hash *readEstInfo(char *fileName)
/* Read in EST info from file. */
{
struct lineFile *lf = lineFileOpen(fileName, TRUE);
char *row[9];
struct hash *hash = newHash(20);
while (lineFileRow(lf, row))
{
struct estOrientInfo *ei = estOrientInfoLoad(row), *oldEi;
oldEi = hashFindVal(hash, ei->name);
if (oldEi != NULL)
{
if (scoreEi(ei, NULL) < scoreEi(oldEi, NULL))
{
estOrientInfoFree(&ei);
continue;
}
}
hashAdd(hash, ei->name, ei);
}
return hash;
}
void migrateOrientInfos(struct migrateAligns* migrate, FILE* outOiFh)
/* Migrate estOrientInfo records */
{
char inOi[PATH_LEN];
struct lineFile* inOiLf;
char *row[EST_ORIENT_INFO_NUM_COLS];
gbAlignedGetPath(migrate->prevSelect, "oi.gz", NULL, inOi);
if (fileExists(inOi))
{
gbVerbEnter(2, "migrating from %s", inOi);
inOiLf = gzLineFileOpen(inOi);
while (lineFileNextRowTab(inOiLf, row, ArraySize(row)))
{
struct estOrientInfo *oi = estOrientInfoLoad(row);
migrateOrientInfo(migrate, oi, inOi, outOiFh);
estOrientInfoFree(&oi);
}
gzLineFileClose(&inOiLf);
gbVerbLeave(2, "migrating from %s", inOi);
}
}
void copyOrientInfos(struct gbSelect* select, FILE* outOiFh,
struct recCounts* recCounts)
/* Copy an OI file from the work directory, if it exists, count alignments
* for index. */
{
char inOi[PATH_LEN];
struct lineFile* inOiLf;
char *row[EST_ORIENT_INFO_NUM_COLS];
gbAlignedGetPath(select, "oi", gWorkDir, inOi);
if (fileExists(inOi))
{
gbVerbEnter(2, "installing from %s", inOi);
inOiLf = gzLineFileOpen(inOi);
while (lineFileNextRowTab(inOiLf, row, ArraySize(row)))
{
struct estOrientInfo *oi = estOrientInfoLoad(row);
copyOrientInfo(select, oi, inOi, outOiFh, recCounts);
estOrientInfoFree(&oi);
}
gzLineFileClose(&inOiLf);
gbVerbLeave(2, "installing from %s", inOi);
}
}
