void convertPslFileRow(struct sqlConnection *conn, char **row, FILE *genePredFh)
/* A row from the PSL file, getting CDS */
{
struct psl *psl = pslLoad(row);
struct genbankCds cds = getCds(conn, psl);
convertPsl(psl, &cds, genePredFh);
pslFree(&psl);
}
void retroShowCdnaAli(char *mappedId)
/* Show alignment for accession, mostly ripped off from htcCdnaAli */
{
char *track = cartString(cart, "aliTable");
struct trackDb *tdb = hashMustFindVal(trackHash, track);
char *table = cartString(cart, "table");
int start = cartInt(cart, "o");
struct sqlConnection *conn = hAllocConn(database);
struct sqlConnection *defDbConn = NULL;
struct mappingInfo *mi = mappingInfoNew(conn, table, mappedId);
struct genbankCds cds = getCds(conn, mi);
struct psl *psl;
struct dnaSeq *rnaSeq = NULL;
char *spec = trackDbRequiredSetting(tdb, BASE_COLOR_USE_SEQUENCE);
char *specCopy = cloneString(spec);
char *words[3];
int nwords = chopByWhite(specCopy, words, ArraySize(words));
char acc[512];
/* Print start of HTML. */
writeFramesetType();
puts("<HTML>");
printf("<HEAD>\n<TITLE>%s vs Genomic [%s]</TITLE>\n</HEAD>\n\n", mi->seqId, track);
/* Look up alignment and sequence in database. Always get sequence
* from defaultDb */
psl = loadAlign(conn, mi, start);
if (startsWith("August",mi->geneSet))
safef(acc, sizeof(acc), "aug-%s.T1",mi->seqId);
else
safef(acc, sizeof(acc), "%s",mi->seqId);
// value is: extFile seqTbl extFileTbl
if ((nwords != (int)ArraySize(words)) || !sameString(words[0], "extFile"))
errAbort("invalid %s track setting: %s ", BASE_COLOR_USE_SEQUENCE, spec);
char *seqTable = words[1];
char *extTable = words[2];
rnaSeq = hDnaSeqGet(database, acc, seqTable, extTable);
if (rnaSeq == NULL)
{
char *acc = mi->seqId;
rnaSeq = hExtSeq(database, acc);
if (rnaSeq == NULL)
errAbort("can't get mRNA sequence from %s prefix %s for %s from %s mappedId %s",
database, mi->geneSet, acc, track, mappedId);
}
sqlDisconnect(&defDbConn);
showSomeAlignment(psl, rnaSeq, gftDna, 0, rnaSeq->size, NULL, cds.start, cds.end);
pslFree(&psl);
dnaSeqFree(&rnaSeq);
mappingInfoFree(&mi);
hFreeConn(&conn);
}
static void processMetaData(FILE *fh, struct sqlConnection *conn, struct sqlConnection *conn2, struct refSeqVerInfo *rsvi)
/* get meta data for an accession */
{
boolean isCoding = genbankIsRefSeqCodingMRnaAcc(rsvi->acc);
char query[256];
sqlSafef(query, sizeof(query), "SELECT rl.name,rl.product,rl.protAcc,rl.locusLinkId,rs.status FROM refLink rl, refSeqStatus rs WHERE (rl.mrnaAcc = \"%s\") and (rs.mrnaAcc = rl.mrnaAcc)", rsvi->acc);
struct sqlResult *sr = sqlGetResult(conn, query);
char **row = sqlNextRow(sr);
if (row == NULL)
errAbort("no RefLink entry for %s", rsvi->acc);
char buf[32];
char *protAccVer = getProtAccVerIf(conn2, rsvi->acc, row[2], buf, sizeof(buf));
char *cds = isCoding ? getCds(conn2, rsvi->acc) : "";
fprintf(fh, "%s.%d\t%s\t%s\t%s\t%s\t%s\t%s\n", rsvi->acc, rsvi->ver, protAccVer, row[0], row[3], cds, row[1], row[4]);
sqlFreeResult(&sr);
if (isCoding)
freeMem(cds);
}
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);
}
