b3c00af4551a848e3f6b83ed1e5fb41e12f039a1
braney
Wed Feb 4 13:08:58 2015 -0800
add hgc and hgTables support for bigGenePred in custom tracks. #13861
diff --git src/hg/hgc/hgc.c src/hg/hgc/hgc.c
index 9b6ba86..bd93822 100644
--- src/hg/hgc/hgc.c
+++ src/hg/hgc/hgc.c
@@ -8029,57 +8029,75 @@
int rowOffset = hOffsetPastBin(database, seqName, table);
sqlSafef(query, sizeof(query), "select * from %s where name = \"%s\"", table, geneName);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
gp = genePredLoad(row+rowOffset);
slAddHead(&gpList, gp);
}
sqlFreeResult(&sr);
hFreeConn(&conn);
return gpList;
}
-struct genePred *getGenePredForPositionBigBed(char *table, char *geneName)
-/* find the genePred to the current gene using a bigGenePred */
+struct genePred *getGenePredForPositionBigGene(struct trackDb *tdb, char *geneName)
+/* Find the genePred to the current gene using a bigGenePred. */
{
-struct trackDb *tdb = hubConnectAddHubForTrackAndFindTdb( database, table, NULL, trackHash);
-struct bbiFile *bbi;
char *fileName = cloneString(trackDbSetting(tdb, "bigDataUrl"));
-bbi = bigBedFileOpen(fileName);
+struct bbiFile *bbi = bigBedFileOpen(fileName);
struct lm *lm = lmInit(0);
struct bigBedInterval *bb, *bbList = bigBedIntervalQuery(bbi, seqName, winStart, winEnd, 0, lm);
struct genePred *gpList = NULL;
for (bb = bbList; bb != NULL; bb = bb->next)
{
struct genePred *gp = genePredFromBigGenePred(seqName, bb);
if (sameString(gp->name, geneName))
slAddHead(&gpList, gp);
}
lmCleanup(&lm);
return gpList;
}
+static struct trackDb *getCustomTrackTdb(char *table)
+/* Find the trackDb structure for a custom track table. */
+{
+struct customTrack *ctList = getCtList();
+struct customTrack *ct = NULL;
+for (ct = ctList; ct != NULL; ct = ct->next)
+ if (sameString(table, ct->tdb->track))
+ return ct->tdb;
+return NULL;
+}
+
static struct genePred *getGenePredForPosition(char *table, char *geneName)
+/* Build a genePred list for the given table and gene name. */
{
struct genePred *gpList = NULL;
-if (isHubTrack(table))
- gpList = getGenePredForPositionBigBed(table, geneName);
+if (isCustomTrack(table))
+ {
+ struct trackDb *tdb = getCustomTrackTdb(table);
+ gpList = getGenePredForPositionBigGene(tdb, geneName);
+ }
+else if (isHubTrack(table))
+ {
+ struct trackDb *tdb = hubConnectAddHubForTrackAndFindTdb( database, table, NULL, trackHash);
+ gpList = getGenePredForPositionBigGene(tdb, geneName);
+ }
else
gpList = getGenePredForPositionSql(table, geneName);
return gpList;
}
void htcTranslatedPredMRna(char *geneName)
/* Translate virtual mRNA defined by genePred to protein and display it. */
{
char *table = cartString(cart, "table");
struct genePred *gp = NULL;
char protName[256];
char *prot = NULL;
cartHtmlStart("Protein Translation from Genome");
@@ -8364,73 +8382,87 @@
s = gp->exonStarts[exonIx];
e = gp->exonEnds[exonIx];
if (s < seqStart) s = seqStart;
if (e > seqEnd) e = seqEnd;
if ((size = e - s) > 0)
{
s -= startOffset;
if (s < 0 || s + size > seq->size)
errAbort("Out of range! %d-%d not in %d-%d", s, s+size, 0, size);
toUpperN(seq->dna + s, size);
}
}
}
-static struct bed *getBedsFromBigBedRange(char *table, char *geneName)
+static struct bed *getBedsFromBigBedRange(struct trackDb *tdb, char *geneName)
/* get a list of beds from a bigBed in the current range */
{
-struct trackDb *tdb = hubConnectAddHubForTrackAndFindTdb( database, table, NULL, trackHash);
struct bbiFile *bbi;
char *fileName = cloneString(trackDbSetting(tdb, "bigDataUrl"));
bbi = bigBedFileOpen(fileName);
struct lm *lm = lmInit(0);
struct bigBedInterval *bb, *bbList = bigBedIntervalQuery(bbi, seqName, winStart, winEnd, 0, lm);
struct bed *bedList = NULL;
char *bedRow[32];
char startBuf[16], endBuf[16];
for (bb = bbList; bb != NULL; bb = bb->next)
{
bigBedIntervalToRow(bb, seqName, startBuf, endBuf, bedRow, ArraySize(bedRow));
struct bed *bed = bedLoadN(bedRow, 12);
if (sameString(bed->name, geneName))
slAddHead(&bedList, bed);
}
lmCleanup(&lm);
return bedList;
}
+static int getSeqForBigGene(struct trackDb *tdb, char *geneName)
+/* Output sequence for a gene in a bigGenePred file. */
+{
+struct hTableInfo *hti;
+AllocVar(hti);
+hti->hasCDS = TRUE;
+hti->hasBlocks = TRUE;
+hti->rootName = tdb->table;
+
+struct bed *bedList = getBedsFromBigBedRange(tdb, geneName);
+int itemCount = hgSeqBed(database, hti, bedList);
+freez(&hti);
+bedFreeList(&bedList);
+return itemCount;
+}
+
void htcDnaNearGene( char *geneName)
/* Fetch DNA near a gene. */
{
char *table = cartString(cart, "o");
int itemCount;
char *quotedItem = makeQuotedString(geneName, '\'');
puts("");
+struct trackDb *tdb = NULL;
+
if (isHubTrack(table))
{
- struct hTableInfo *hti;
- AllocVar(hti);
- hti->hasCDS = TRUE;
- hti->hasBlocks = TRUE;
- hti->rootName = table;
-
- struct bed *bedList = getBedsFromBigBedRange(table, geneName);
- itemCount = hgSeqBed(database, hti, bedList);
- freez(&hti);
- bedFreeList(&bedList);
+ tdb = hubConnectAddHubForTrackAndFindTdb( database, table, NULL, trackHash);
+ itemCount = getSeqForBigGene(tdb, geneName);
+ }
+else if (isCustomTrack(table))
+ {
+ tdb = getCustomTrackTdb(table);
+ itemCount = getSeqForBigGene(tdb, geneName);
}
else
{
char constraints[256];
safef(constraints, sizeof(constraints), "name = %s", quotedItem);
itemCount = hgSeqItemsInRange(database, table, seqName, winStart, winEnd, constraints);
}
if (itemCount == 0)
printf("\n# No results returned from query.\n\n");
puts("");
freeMem(quotedItem);
}
void htcTrackHtml(struct trackDb *tdb)
/* Handle click to display track html */
@@ -20465,31 +20497,31 @@
for (ct = ctList; ct != NULL; ct = ct->next)
if (sameString(trackId, ct->tdb->track))
break;
if (ct == NULL)
errAbort("Couldn't find '%s' in '%s'", trackId, fileName);
type = ct->tdb->type;
cartWebStart(cart, database, "Custom Track: %s", ct->tdb->shortLabel);
itemName = skipLeadingSpaces(fileItem);
printf("%s
\n", ct->tdb->longLabel);
if (sameWord(type, "array"))
doExpRatio(ct->tdb, fileItem, ct);
else if (sameWord(type, "encodePeak"))
doEncodePeak(ct->tdb, ct, fileName);
else if (sameWord(type, "bigWig"))
bigWigCustomClick(ct->tdb);
-else if (sameWord(type, "bigBed"))
+else if (sameWord(type, "bigBed") || sameWord(type, "bigGenePred"))
bigBedCustomClick(ct->tdb);
#ifdef USE_BAM
else if (sameWord(type, "bam"))
doBamDetails(ct->tdb, itemName);
#endif//def USE_BAM
#ifdef USE_TABIX
else if (sameWord(type, "vcfTabix"))
doVcfTabixDetails(ct->tdb, itemName);
#endif//def USE_TABIX
else if (sameWord(type, "vcf"))
doVcfDetails(ct->tdb, itemName);
else if (sameWord(type, "makeItems"))
doMakeItemsDetails(ct, fileName); // fileName is first word, which is, go figure, id
else if (ct->wiggle)
{