src/hg/hgc/encodeClick.c 1.16
1.16 2010/05/17 02:30:20 kent
Working on details pages for DNase Clusters and Txn Factor ChIP tracks.
Index: src/hg/hgc/encodeClick.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgc/encodeClick.c,v
retrieving revision 1.15
retrieving revision 1.16
diff -b -B -U 1000000 -r1.15 -r1.16
--- src/hg/hgc/encodeClick.c 11 May 2010 01:43:28 -0000 1.15
+++ src/hg/hgc/encodeClick.c 17 May 2010 02:30:20 -0000 1.16
@@ -1,152 +1,204 @@
/* Handle details page for ENCODE tracks. */
#include "common.h"
#include "cart.h"
#include "hgc.h"
#include "hCommon.h"
#include "hgColors.h"
#include "customTrack.h"
#include "web.h"
#include "encode/encodePeak.h"
+static boolean pairInList(struct slPair *pair, struct slPair *list)
+/* Return TRUE if pair is in list. */
+{
+struct slPair *el;
+for (el = list; el != NULL; el = el->next)
+ if (sameString(pair->name, el->name) && sameString(pair->val, el->val))
+ return TRUE;
+return FALSE;
+}
+
+static boolean selGroupListMatch(struct trackDb *tdb, struct slPair *selGroupList)
+/* Return TRUE if tdb has match to every item in selGroupList */
+{
+char *subGroups = trackDbSetting(tdb, "subGroups");
+if (subGroups == NULL)
+ return FALSE;
+struct slPair *groupList = slPairFromString(subGroups);
+struct slPair *selGroup;
+for (selGroup = selGroupList; selGroup != NULL; selGroup = selGroup->next)
+ {
+ if (!pairInList(selGroup, groupList))
+ return FALSE;
+ }
+return TRUE;
+}
+
+static void rAddMatching(struct trackDb *tdb, struct slPair *selGroupList, struct slName **pList)
+/* Add track and any descendents that match selGroupList to pList */
+{
+if (selGroupListMatch(tdb, selGroupList))
+ slNameAddHead(pList, tdb->track);
+struct trackDb *sub;
+for (sub = tdb->subtracks; sub != NULL; sub = sub->next)
+ rAddMatching(sub, selGroupList, pList);
+}
+
+struct slName *encodeFindMatchingSubtracks(struct slName *inTrackList, struct slPair *selGroupList)
+/* Look at a list of tracks, and their descendents for tracks with groups that match all
+ * name/value pairs in selGroupList */
+{
+struct slName *matchList = NULL;
+struct slName *inTrack;
+for (inTrack = inTrackList; inTrack != NULL; inTrack = inTrack->next)
+ {
+ struct trackDb *tdb = hashFindVal(trackHash, inTrack->name);
+ if (tdb == NULL)
+ errAbort("Can't find track %s which is in inputTracks", inTrack->name);
+ rAddMatching(tdb, selGroupList, &matchList);
+ }
+return matchList;
+}
+
void doEncodePeak(struct trackDb *tdb, struct customTrack *ct)
/* details for encodePeak type tracks. */
{
struct sqlConnection *conn;
struct sqlResult *sr;
enum encodePeakType peakType;
char **row;
char *db;
char *table = tdb->table;
char *chrom = cartString(cart,"c");
int start = cgiInt("o");
int end = cgiInt("t");
int rowOffset;
/* connect to DB */
if (ct)
{
db = CUSTOM_TRASH;
table = ct->dbTableName;
}
else
db = database;
conn = hAllocConn(db);
peakType = encodePeakInferTypeFromTable(db, table, tdb->type);
if (peakType == 0)
errAbort("unrecognized peak type from table %s", tdb->table);
genericHeader(tdb, NULL);
sr = hOrderedRangeQuery(conn, table, chrom, start, end,
NULL, &rowOffset);
while((row = sqlNextRow(sr)) != NULL)
{
char **rowPastOffset = row + rowOffset;
if ((sqlUnsigned(rowPastOffset[1]) != start) || (sqlUnsigned(rowPastOffset[2]) != end))
continue;
float signal = -1;
float pValue = -1;
float qValue = -1;
/* Name */
if (rowPastOffset[3][0] != '.')
printf("<B>Name:</B> %s<BR>\n", rowPastOffset[3]);
/* Position */
printf("<B>Position:</B> "
"<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">%s:%d-%d</a><BR>\n",
hgTracksPathAndSettings(), database, chrom, start+1, end, chrom, start+1, end);
/* Print peak base */
if ((peakType == narrowPeak) || (peakType == encodePeak))
{
int peak = sqlSigned(rowPastOffset[9]);
if (peak > -1)
printf("<B>Peak point:</B> %d<BR>\n", start + peak + 1); // one based
}
/* Strand, score */
if (rowPastOffset[5][0] != '.')
printf("<B>Strand:</B> %c<BR>\n", rowPastOffset[5][0]);
printf("<B>Score:</B> %d<BR>\n", sqlUnsigned(rowPastOffset[4]));
/* signalVal, pVal */
if (peakType != gappedPeak)
{
signal = sqlFloat(rowPastOffset[6]);
pValue = sqlFloat(rowPastOffset[7]);
qValue = sqlFloat(rowPastOffset[8]);
}
else
{
signal = sqlFloat(rowPastOffset[12]);
pValue = sqlFloat(rowPastOffset[13]);
qValue = sqlFloat(rowPastOffset[14]);
}
if (signal >= 0)
printf("<B>Signal value:</B> %.3f<BR>\n", signal);
if (pValue >= 0)
printf("<B>P-value (-log10):</B> %.3f<BR>\n", pValue);
if (qValue >= 0)
printf("<B>Q-value (FDR): </B> %.3f<BR>\n", qValue);
}
sqlFreeResult(&sr);
hFreeConn(&conn);
}
int encodeFiveCInterCmp(const void *va, const void *vb)
/* reverse sort on bed nine's reserved field which in this */
/* case is the where the strength of the interaction is stored */
{
const struct bed *a = *((struct bed **)va);
const struct bed *b = *((struct bed **)vb);
return b->itemRgb - a->itemRgb;
}
void doEncodeFiveC(struct sqlConnection *conn, struct trackDb *tdb)
/* Print details for 5C track */
{
char *interTable = trackDbRequiredSetting(tdb, "interTable");
char *interTableKind = trackDbRequiredSetting(tdb, "interTableKind");
char **row;
char *chrom = cartString(cart,"c");
int start = cgiInt("o");
int end = cgiInt("t");
int rowOffset;
int outCount = 0;
struct sqlResult *sr;
struct bed *interList = NULL, *inter;
genericHeader(tdb, NULL);
sr = hOrderedRangeQuery(conn, interTable, chrom, start, end, NULL, &rowOffset);
printf("<B>Position:</B> "
"<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">%s:%d-%d</a><BR>\n",
hgTracksPathAndSettings(), database, chrom, start+1, end, chrom, start+1, end);
while ((row = sqlNextRow(sr)) != NULL)
{
inter = bedLoadN(row + rowOffset, 9);
slAddHead(&interList, inter);
}
slSort(&interList, encodeFiveCInterCmp);
webNewSection("Top %s interations", interTableKind);
webPrintLinkTableStart();
webPrintLabelCell("Position");
webPrintLabelCell("5C signal");
webPrintLabelCell("Distance");
webPrintLinkTableNewRow();
for (inter = interList; inter != NULL; inter = inter->next)
{
char s[1024];
int distance = 0;
safef(s, sizeof(s), "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">%s:%d-%d</A>",
hgTracksPathAndSettings(), database, chrom, inter->thickStart+1, inter->thickEnd, chrom, inter->thickStart+1, inter->thickEnd);
webPrintLinkCell(s);
safef(s, sizeof(s), "%d", inter->itemRgb);
webPrintLinkCell(s);
if (start > inter->thickStart)
distance = inter->thickEnd - start;
else
distance = inter->thickStart - end;
safef(s, sizeof(s), "%d", distance);
webPrintLinkCell(s);
if (++outCount == 50)
break;
if (inter->next != NULL)
webPrintLinkTableNewRow();
}
webPrintLinkTableEnd();
sqlFreeResult(&sr);
}