static char *getCds(struct sqlConnection *conn, char *acc)
/* get CDS for an NM, results should be freed */
{
char query[128];
sqlSafef(query, sizeof(query), "SELECT cds.name FROM gbCdnaInfo,cds WHERE (gbCdnaInfo.acc = \"%s\") AND (gbCdnaInfo.cds = cds.id)", acc);
return sqlNeedQuickString(conn, query);
}
char *spDescription(struct sqlConnection *conn, char *acc)
/* Return protein description. FreeMem this when done. */
{
char query[256];
safef(query, sizeof(query),
"select val from description where acc = '%s'", acc);
return sqlNeedQuickString(conn, query);
}
char *spRefCite(struct sqlConnection *conn, int refId)
/* Get journal/page/etc of reference. */
{
char query[256];
safef(query, sizeof(query),
"select cite from reference where id=%d", refId);
return sqlNeedQuickString(conn, query);
}
char *spFeatureClassName(struct sqlConnection *conn, int featureClass)
/* Return name associated with featureClass. */
{
char query[256];
safef(query, sizeof(query),
"select val from featureClass where id=%d", featureClass);
return sqlNeedQuickString(conn, query);
}
char *spAccToId(struct sqlConnection *conn, char *acc)
/* Convert primary accession to SwissProt ID (which will
* often look something like HXA1_HUMAN. */
{
char query[256];
safef(query, sizeof(query), "select val from displayId where acc = '%s'",
acc);
return sqlNeedQuickString(conn, query);
}
char *spAnnDate(struct sqlConnection *conn, char *acc)
/* Return annotation last update date in YYYY-MM-DD format. FreeMem
* this when done. */
{
char query[256];
safef(query, sizeof(query),
"select annDate from info where acc = '%s'", acc);
return sqlNeedQuickString(conn, query);
}
char *spTaxonToBinomial(struct sqlConnection *conn, int taxon)
/* Return Latin binomial name associated with taxon. */
{
char query[256];
if (taxon <= 0)
errAbort("Bad taxon id %d\n", taxon);
safef(query, sizeof(query),
"select binomial from taxon where id = %d", taxon);
return sqlNeedQuickString(conn, query);
}
char *spFeatureTypeName(struct sqlConnection *conn, int featureType)
/* Return name associated with featureType */
{
if (featureType == 0)
return cloneString("n/a");
else
{
char query[256];
safef(query, sizeof(query),
"select val from featureType where id=%d", featureType);
return sqlNeedQuickString(conn, query);
}
}
char *spLookupPrimaryAcc(struct sqlConnection *conn,
char *anyAcc) /* Primary or secondary accession. */
/* This will return the primary accession. It's ok to pass in
* either a primary or secondary accession. */
{
char query[256];
if (spIsPrimaryAcc(conn, anyAcc))
return cloneString(anyAcc);
else
{
safef(query, sizeof(query),
"select acc from otherAcc where val = '%s'", anyAcc);
return sqlNeedQuickString(conn, query);
}
}
static void processProtSeq(FILE *fh, struct sqlConnection *conn, struct refSeqVerInfo *rsvi, struct hash *doneProts)
/* get an protein sequence, which already includes version in name. Don't duplicate NPs */
{
char query[128];
sqlSafef(query, sizeof(query), "SELECT protAcc FROM refLink WHERE mrnaAcc = \"%s\"", rsvi->acc);
char *protAcc = sqlNeedQuickString(conn, query);
if (isNotEmpty(protAcc) && hashLookup(doneProts, protAcc) == NULL)
{
struct dnaSeq *seq = hGenBankGetPepC(conn, protAcc, NULL);
if (seq == NULL)
errAbort("failed to get %s from database", protAcc);
faWriteNext(fh, seq->name, seq->dna, seq->size);
dnaSeqFree(&seq);
hashAdd(doneProts, protAcc, NULL);
}
freeMem(protAcc);
}
