void doHgdpGeo(struct trackDb *tdb, char *item)
/* Show details page for HGDP SNP with population allele frequencies
* plotted on a world map. */
{
struct sqlConnection *conn = hAllocConn(database);
char query[512];
struct sqlResult *sr;
char **row;
int start = cartInt(cart, "o");
genericHeader(tdb, item);
int hasBin=1;
sqlSafef(query, sizeof(query),
"select * from %s where name = '%s' and chrom = '%s' and chromStart = %d",
tdb->table, item, seqName, start);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) == NULL)
errAbort("doHgdpGeo: no match in %s for %s at %s:%d", tdb->table, item, seqName, start);
struct hgdpGeo *geo = hgdpGeoLoad(row+hasBin);
sqlFreeResult(&sr);
printCustomUrl(tdb, item, TRUE);
bedPrintPos((struct bed *)geo, 4, tdb);
printf("<B>Ancestral Allele:</B> %c<BR>\n", geo->ancestralAllele);
printf("<B>Derived Allele:</B> %c<BR>\n", geo->derivedAllele);
printOtherSnpMappings(tdb->table, item, start, conn, hasBin);
printf("<BR>\n");
printf("<TABLE><TR><TD>\n");
hgdpGeoFreqTable(geo);
printf("</TD><TD valign=top>\n");
hgdpGeoImg(geo);
printf("</TD></TR></TABLE>\n");
printTrackHtml(tdb);
hFreeConn(&conn);
}
void doFlyreg(struct trackDb *tdb, char *item)
/* flyreg.org: Drosophila DNase I Footprint db. */
{
struct dyString *query = newDyString(256);
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr = NULL;
char **row;
int start = cartInt(cart, "o");
int end = cartInt(cart, "t");
char fullTable[HDB_MAX_TABLE_STRING];
boolean hasBin = FALSE;
char *motifTable = "flyregMotif";
struct dnaMotif *motif = NULL;
boolean isVersion2 = sameString(tdb->table, "flyreg2");
genericHeader(tdb, item);
if (!hFindSplitTable(database, seqName, tdb->table, fullTable, sizeof fullTable, &hasBin))
errAbort("track %s not found", tdb->table);
sqlDyStringPrintf(query, "select * from %s where chrom = '%s' and ",
fullTable, seqName);
hAddBinToQuery(start, end, query);
sqlDyStringPrintf(query, "chromStart = %d and name = '%s'", start, item);
sr = sqlGetResult(conn, query->string);
if ((row = sqlNextRow(sr)) != NULL)
{
struct flyreg2 fr;
if (isVersion2)
flyreg2StaticLoad(row+hasBin, &fr);
else
flyregStaticLoad(row+hasBin, (struct flyreg *)(&fr));
printf("<B>Factor:</B> %s<BR>\n", fr.name);
printf("<B>Target:</B> %s<BR>\n", fr.target);
if (isVersion2)
printf("<B>Footprint ID:</B> %06d<BR>\n", fr.fpid);
printf("<B>PubMed ID:</B> <A HREF=\"");
printEntrezPubMedUidUrl(stdout, fr.pmid);
printf("\" TARGET=_BLANK>%d</A><BR>\n", fr.pmid);
bedPrintPos((struct bed *)(&fr), 3, tdb);
if (hTableExists(database, motifTable))
{
motif = loadDnaMotif(item, motifTable);
if (motif != NULL)
motifHitSection(NULL, motif);
}
}
else
errAbort("query returned no results: \"%s\"", query->string);
dyStringFree(&query);
sqlFreeResult(&sr);
hFreeConn(&conn);
if (motif != NULL)
webNewSection("%s",tdb->longLabel);
printTrackHtml(tdb);
}
static void bigBedClick(char *fileName, struct trackDb *tdb,
char *item, int start, int end, int bedSize)
/* Handle click in generic bigBed track. */
{
boolean showUrl = FALSE;
char *chrom = cartString(cart, "c");
/* Open BigWig file and get interval list. */
struct bbiFile *bbi = bigBedFileOpen(fileName);
struct lm *lm = lmInit(0);
int ivStart = start, ivEnd = end;
if (start == end)
{
// item is an insertion; expand the search range from 0 bases to 2 so we catch it:
ivStart = max(0, start-1);
ivEnd++;
}
struct bigBedInterval *bbList = bigBedIntervalQuery(bbi, chrom, ivStart, ivEnd, 0, lm);
/* Get bedSize if it's not already defined. */
if (bedSize == 0)
{
bedSize = bbi->definedFieldCount;
showUrl = TRUE;
}
char *scoreFilter = cartOrTdbString(cart, tdb, "scoreFilter", NULL);
int minScore = 0;
if (scoreFilter)
minScore = atoi(scoreFilter);
/* Find particular item in list - matching start, and item if possible. */
boolean found = FALSE;
boolean firstTime = TRUE;
struct bigBedInterval *bb;
for (bb = bbList; bb != NULL; bb = bb->next)
{
if (!(bb->start == start && bb->end == end))
continue;
if (bedSize > 3)
{
char *name = cloneFirstWordByTab(bb->rest);
boolean match = sameString(name, item);
freez(&name);
if (!match)
continue;
}
found = TRUE;
if (firstTime)
printf("<BR>\n");
int seq1Seq2Fields = 0;
// check for seq1 and seq2 in columns 7+8 (eg, pairedTagAlign)
boolean seq1Seq2 = sameOk(trackDbSetting(tdb, BASE_COLOR_USE_SEQUENCE), "seq1Seq2");
if (seq1Seq2 && bedSize == 6)
seq1Seq2Fields = 2;
char *fields[bedSize+seq1Seq2Fields];
char startBuf[16], endBuf[16];
char *rest = cloneString(bb->rest);
int bbFieldCount = bigBedIntervalToRow(bb, chrom, startBuf, endBuf, fields,
bedSize+seq1Seq2Fields);
if (bbFieldCount != bedSize+seq1Seq2Fields)
{
errAbort("Disagreement between trackDb field count (%d) and %s fieldCount (%d)",
bedSize, fileName, bbFieldCount);
}
struct bed *bed = bedLoadN(fields, bedSize);
if (bedSize >= 6 && scoreFilter && bed->score < minScore)
continue;
if (showUrl && (bedSize >= 4))
printCustomUrl(tdb, item, TRUE);
bedPrintPos(bed, bedSize, tdb);
// display seq1 and seq2
if (seq1Seq2 && bedSize+seq1Seq2Fields == 8)
printf("<table><tr><th>Sequence 1</th><th>Sequence 2</th></tr>"
"<tr><td> %s </td><td> %s </td></tr></table>", fields[6], fields[7]);
else if (isNotEmpty(rest))
{
char *restFields[256];
int restCount = chopTabs(rest, restFields);
int restBedFields = bedSize - 3;
if (restCount > restBedFields)
{
if (0 == extraFieldsPrint(tdb,NULL,restFields + restBedFields,restCount - restBedFields))
{
int i;
char label[20];
safef(label, sizeof(label), "nonBedFieldsLabel");
printf("<B>%s </B>",
trackDbSettingOrDefault(tdb, label, "Non-BED fields:"));
for (i = restBedFields; i < restCount; i++)
printf("%s%s", (i > 0 ? "\t" : ""), restFields[i]);
printf("<BR>\n");
}
}
}
if (isCustomTrack(tdb->track))
{
time_t timep = bbiUpdateTime(bbi);
printBbiUpdateTime(&timep);
}
}
if (!found)
{
printf("No item %s starting at %d\n", emptyForNull(item), start);
}
lmCleanup(&lm);
bbiFileClose(&bbi);
}
void doGvf(struct trackDb *tdb, char *item)
/* Show details for variants represented as GVF, stored in a bed8Attrs table */
{
struct sqlConnection *conn = hAllocConn(database);
int start = cartInt(cart, "o");
char query[1024];
sqlSafef(query, sizeof(query),
"select * from %s where name = '%s' and chrom = '%s' and chromStart = %d",
tdb->table, item, seqName, start);
struct sqlResult *sr = sqlGetResult(conn, query);
char **row;
if ((row = sqlNextRow(sr)) == NULL)
errAbort("doGvfDetails: can't find item '%s' in %s at %s:%d", item, database, seqName, start);
int rowOffset = hOffsetPastBin(database, seqName, tdb->table);
struct bed8Attrs *ba = bed8AttrsLoad(row+rowOffset);
bedPrintPos((struct bed *)ba, 3, tdb);
int i = 0;
// Note: this loop modifies ba->attrVals[i], assuming we won't use them again:
for (i = 0; i < ba->attrCount; i++)
{
// The ID is the bed8Attrs name and has already been displayed:
if (sameString(ba->attrTags[i], "ID"))
continue;
cgiDecode(ba->attrVals[i], ba->attrVals[i], strlen(ba->attrVals[i]));
char *tag = ba->attrTags[i];
// User-defined keywords used in dbVar's GVF:
if (sameString(tag, "var_type")) // This one isn't anymore, but I add it back (hg18.txt).
tag = "Variant type";
else if (sameString(tag, "clinical_int"))
tag = "Clinical interpretation";
else if (sameString(tag, "var_origin"))
tag = "Variant origin";
else if (islower(tag[0]))
// Uppercase for nice display, assuming user doesn't care which keywords are
// user-defined vs. GVF standard:
tag[0] = toupper(tag[0]);
// GVF standard Start_range and End_range tags (1-based coords):
if (sameString(tag, "Start_range") || sameString(tag, "End_range"))
{
char *copy = cloneString(ba->attrVals[i]);
char *words[3];
int wordCount = chopCommas(copy, words);
if (wordCount == 2 &&
(sameString(".", words[0]) || isInteger(words[0])) &&
(sameString(".", words[1]) || isInteger(words[1])))
{
boolean isStartRange = sameString(tag, "Start_range");
char *rangeStart = words[0], *rangeEnd = words[1];
if (sameString(".", rangeStart))
rangeStart = "unknown";
if (sameString(".", rangeEnd))
rangeEnd = "unknown";
if (isStartRange)
printf("<B>Start range</B>: outer start %s, inner start %s<BR>\n",
rangeStart, rangeEnd);
else
printf("<B>End range</B>: inner end %s, outer end %s<BR>\n",
rangeStart, rangeEnd);
}
else
// not formatted as expected, just print as-is:
printf("<B>%s</B>: %s<BR>\n", tag, htmlEncode(ba->attrVals[i]));
}
// Parent sounds like mom or dad (as in var_origin)... tweak it too:
else if (sameString(tag, "Parent"))
{
printf("<B>Variant region:</B> "
"<A HREF=\"http://www.ncbi.nlm.nih.gov/dbvar/variants/%s/\" "
"TARGET=_BLANK>%s</A><BR>\n", ba->attrVals[i], htmlEncode(ba->attrVals[i]));
}
else if (sameString(tag, "Name"))
{
char *url = trackDbSetting(tdb, "url");
// Show the Name only if it hasn't already appeared in the URL:
if (url == NULL || !stringIn("$$", url))
printf("<B>%s</B>: %s<BR>\n", tag, htmlEncode(ba->attrVals[i]));
}
else if (sameWord(tag, "Phenotype_id") && startsWith("HPO:HP:", ba->attrVals[i]))
{
subChar(tag, '_', ' ');
printf("<B>%s</B>: <A HREF=\"http://www.berkeleybop.org/obo/%s\" "
"TARGET=_BLANK>%s</A><BR>\n", tag, ba->attrVals[i]+strlen("HPO:"),
htmlEncode(ba->attrVals[i]));
}
else
{
subChar(tag, '_', ' ');
printf("<B>%s</B>: %s<BR>\n", tag, htmlEncode(ba->attrVals[i]));
}
}
sqlFreeResult(&sr);
hFreeConn(&conn);
/* printTrackHtml is done in genericClickHandlerPlus. */
}
