struct hash *loadAndWeighTce(char *fileName, struct hash *refToPepHash,
struct hash *pepToRefHash)
/* Load transcript cds evidence from file into hash of
* txCdsInfo. */
{
/* Read all tce's in file into list and hash of txCdsInfo. */
struct txCdsInfo *tx, *txList = NULL;
struct lineFile *lf = lineFileOpen(fileName, TRUE);
struct hash *hash = hashNew(18);
char *row[CDSEVIDENCE_NUM_COLS];
while (lineFileRow(lf, row))
{
/* Convert row to cdsEvidence structure. */
struct cdsEvidence *cds = cdsEvidenceLoad(row);
char *acc = txAccFromTempName(cds->name);
tx = hashFindVal(hash, cds->name);
if (tx == NULL)
{
AllocVar(tx);
hashAddSaveName(hash, cds->name, tx, &tx->name);
slAddHead(&txList, tx);
}
/* Track whether it's refSeq, and the associated protein. */
char *refSeqAcc = NULL, *refPepAcc = NULL;
refPepAcc = hashFindVal(refToPepHash, acc);
refSeqAcc = hashFindVal(pepToRefHash, acc);
if (refPepAcc != NULL && refSeqAcc == NULL)
refSeqAcc = acc;
if (refSeqAcc != NULL && refPepAcc == NULL)
refPepAcc = acc;
/* If we are refSeq, bump our score for matches to our own
* bits by a huge factor. */
if (refPepAcc != NULL && startsWith("RefPep", cds->source)
&& sameString(cds->accession, refPepAcc))
cds->score += refSeqWeight;
if (refSeqAcc != NULL && startsWith("RefSeq", cds->source)
&& sameString(cds->accession, refSeqAcc))
cds->score += refSeqWeight + 100;
/* If we are CCDS then that's great too. */
if (sameString("ccds", cds->source))
cds->score += ccdsWeight;
/* If we are txCdsPredict bump weight too. Only RefSeq and txCdsPredict
* can actually possibly make it over real threshold. */
if (sameString("txCdsPredict", cds->source))
cds->score += txCdsPredictWeight;
slAddHead(&tx->cdsList, cds);
}
lineFileClose(&lf);
slReverse(&txList);
/* Sort all cdsLists by score. */
for (tx = txList; tx != NULL; tx = tx->next)
slSort(&tx->cdsList, cdsEvidenceCmpScore);
return hash;
}
void showCdsEvidence(char *geneName, struct trackDb *tdb, char *evTable)
/* Print out stuff from cdsEvidence table. */
{
struct sqlConnection *conn = hAllocConn(database);
double bestScore = 0;
if (sqlTableExists(conn, evTable))
{
webNewSection("CDS Prediction Information");
char query[512];
sqlSafef(query, sizeof(query),
"select count(*) from %s where name='%s'", evTable, geneName);
if (sqlQuickNum(conn, query) > 0)
{
sqlSafef(query, sizeof(query),
"select * from %s where name='%s' order by score desc", evTable, geneName);
struct sqlResult *sr = sqlGetResult(conn, query);
char **row;
webPrintLinkTableStart();
webPrintLabelCell("ORF<BR>size");
webPrintLabelCell("start in<BR>transcript");
webPrintLabelCell("end in<BR>transcript");
webPrintLabelCell("source");
webPrintLabelCell("accession");
webPrintLabelCell("ad-hoc<BR>score");
webPrintLabelCell("start<BR>codon");
webPrintLabelCell("end<BR>codon");
webPrintLabelCell("piece<BR>count");
webPrintLabelCell("piece list");
webPrintLabelCell("frame");
webPrintLinkTableNewRow();
while ((row = sqlNextRow(sr)) != NULL)
{
struct cdsEvidence *ev = cdsEvidenceLoad(row);
webPrintIntCell(ev->end - ev->start);
int i;
webPrintIntCell(ev->start+1);
webPrintIntCell(ev->end);
webPrintLinkCell(ev->source);
webPrintLinkCell(ev->accession);
webPrintLinkCellRightStart();
printf("%3.2f", ev->score);
bestScore = max(ev->score, bestScore);
webPrintLinkCellEnd();
webPrintLinkCell(ev->startComplete ? "yes" : "no");
webPrintLinkCell(ev->endComplete ? "yes" : "no");
webPrintIntCell(ev->cdsCount);
webPrintLinkCellRightStart();
for (i=0; i<ev->cdsCount; ++i)
{
int start = ev->cdsStarts[i];
int end = start + ev->cdsSizes[i];
printf("%d-%d ", start+1, end);
}
webPrintLinkCellEnd();
webPrintLinkCellRightStart();
for (i=0; i<ev->cdsCount; ++i)
{
if (i>0) printf(",");
printf("%d", ev->cdsStarts[i]%3 + 1);
}
webPrintLinkCellEnd();
webPrintLinkTableNewRow();
}
sqlFreeResult(&sr);
webPrintLinkTableEnd();
printf("This table shows CDS predictions for this transcript from a number of "
"sources including alignments against UniProtKB proteins, alignments against Genbank "
"mRNAs with CDS regions annotated by the sequence submitter, and "
"Victor Solovyev's bestorf program. Each prediction is assigned an ad-hoc score "
"score is based on several factors including the quality of "
"any associated alignments, the quality of the source, and the length of the "
"prediction. For RefSeq transcripts with annotated CDSs the ad-hoc score "
"is over a million unless there are severe problems mapping the mRNA to the "
"genome. In other cases the score generally ranges from 0 to 50,000. "
"The highest scoring prediction in this table is used to define the CDS "
"boundaries for this transcript.<P>If no score is 2000 or more, the transcript "
"is considered non-coding. In cases where the CDS is subject to "
"nonsense-mediated decay the CDS is removed. The CDS is also removed "
"from transcripts when evidence points to it being in an artifact of an "
"incompletely processed transcript. Specifically if the CDS is entirely "
"enclosed in the 3' UTR or an intron of a refSeq or other high quality "
"transcript, the CDS is removed.");
}
else
{
printf("no significant CDS prediction found, likely %s is noncoding",
geneName);
}
}
hFreeConn(&conn);
}
