void getAccMrna(char *acc, struct sqlConnection *conn, FILE *outFa)
/* get mrna for an accession */
{
HGID seqId;
char *faSeq;
struct dnaSeq *dna;
boolean cdsOk = TRUE;
char accBuf[512];
struct genbankCds cds;
faSeq = hGetSeqAndId(conn, acc, &seqId);
if (faSeq == NULL)
{
fprintf(stderr, "%s\tsequence not in database\n", acc);
return;
}
dna = faFromMemText(faSeq);
if (cdsUpper || peptides)
cdsOk = getCds(conn, acc, dna->size, !cdsUpperAll, &cds);
if (cdsOk && cdsUpper)
upperCaseCds(dna, &cds);
if ((cdsOk || cdsUpperAll) && inclVer)
{
int ver = getVersion(conn, acc);
safef(accBuf, sizeof(accBuf), "%s.%d", acc, ver);
acc = accBuf;
}
if ((cdsOk || cdsUpperAll))
{
if (peptides)
writePeptide(outFa, acc, dna, &cds);
else
faWriteNext(outFa, acc, dna->dna, dna->size);
}
dnaSeqFree(&dna);
}
void doRefGeneProteinSequence(struct sqlConnection *conn, struct bed *bedList)
/* Fetch refGene proteins corresponding to names in bedList. */
{
struct hash *uniqHash = newHash(18);
struct hash *protHash = newHash(18);
struct sqlResult *sr;
char **row;
struct bed *bed;
/* Get translation from mRNA to protein from refLink table. */
sr = sqlGetResult(conn, "NOSQLINJ select mrnaAcc,protAcc from refLink");
while ((row = sqlNextRow(sr)) != NULL)
{
char *protAcc = row[1];
if (protAcc != NULL && protAcc[0] != 0)
hashAdd(protHash, row[0], lmCloneString(protHash->lm, protAcc));
}
sqlFreeResult(&sr);
boolean gotResults = FALSE;
for (bed = bedList; bed != NULL; bed = bed->next)
{
char *protAcc = hashFindVal(protHash, bed->name);
if (protAcc != NULL && !hashLookup(uniqHash, protAcc))
{
char *fa = hGetSeqAndId(conn, protAcc, NULL);
hashAdd(uniqHash, protAcc, NULL);
if (fa != NULL)
hPrintf("%s", fa);
freez(&fa);
gotResults = TRUE;
}
}
if (!gotResults)
hPrintf(NO_RESULTS);
hashFree(&protHash);
hashFree(&uniqHash);
}
void doRefGeneMrnaSequence(struct sqlConnection *conn, struct bed *bedList)
/* Fetch refGene mRNA sequence. */
{
struct hash *uniqHash = newHash(18);
struct bed *bed;
boolean gotResults = FALSE;
for (bed = bedList; bed != NULL; bed = bed->next)
{
if (!hashLookup(uniqHash, bed->name))
{
char *fa = hGetSeqAndId(conn, bed->name, NULL);
hashAdd(uniqHash, bed->name, NULL);
if (fa != NULL)
hPrintf("%s", fa);
freez(&fa);
gotResults = TRUE;
}
}
if (!gotResults)
hPrintf(NO_RESULTS);
hashFree(&uniqHash);
}
