src/hg/instinct/hgBamBam/hgBamBam.c 1.2
1.2 2010/05/26 05:20:33 jsanborn
updated
Index: src/hg/instinct/hgBamBam/hgBamBam.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/instinct/hgBamBam/hgBamBam.c,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 1000000 -r1.1 -r1.2
--- src/hg/instinct/hgBamBam/hgBamBam.c 25 May 2010 20:22:45 -0000 1.1
+++ src/hg/instinct/hgBamBam/hgBamBam.c 26 May 2010 05:20:33 -0000 1.2
@@ -1,222 +1,311 @@
/* hgBamBam */
#include "common.h"
#include "bed.h"
#include "cart.h"
#include "linefile.h"
#include "genoLay.h"
#include "hash.h"
#include "hCommon.h"
#include "hdb.h"
#include "hPrint.h"
#include "htmshell.h"
#include "hui.h"
#include "trackLayout.h"
#include "web.h"
#include "json.h"
#include "hgBamBam.h"
static char const rcsid[] = "$Id$";
/* ---- Global variables. ---- */
struct cart *cart; /* This holds cgi and other variables between clicks. */
struct hash *oldVars; /* Old cart hash. */
#define FLOAT_NULL -9999
char *db = "pdata";
char *localDb = "localDb";
void usage()
/* Explain usage and exit. */
{
errAbort(
"hgBamBam\n"
"usage:\n"
" hgBamBam\n"
);
}
/****** BEGIN HELPER FUNCTIONS *******/
struct bed *getBed(struct sqlConnection *conn, char *tableName, char *pos, int nField,
float *retMaxVal)
{
/* get the data from the database */
char **row = NULL;
char query[512];
query[0] = '\0';
if (!pos)
safef(query, sizeof(query), "select * from %s", tableName);
else
{
char *chrom = NULL;
int start = 0;
int stop = 0;
if (!hgParseChromRange(NULL, pos, &chrom, &start, &stop))
return NULL;
safef(query, sizeof(query),
"select * from %s where chrom = '%s' and chromStart<%d and chromEnd>%d",
tableName, chrom, stop, start);
}
struct sqlResult *sr = sqlGetResult(conn, query);
struct bed *tuple = NULL;
struct bed *tupleList = NULL;
float val, maxVal = -1;
/* all copy number tracks are bed 4 */
while ((row = sqlNextRow(sr)) != NULL)
{
tuple = bedLoadN(row+1, nField);
slAddHead(&tupleList, tuple);
-
val = sqlFloat(tuple->name);
if (val > maxVal)
maxVal = val;
}
*retMaxVal = maxVal;
slReverse(&tupleList);
sqlFreeResult(&sr);
return tupleList;
}
+struct breaks *getBreaks(struct sqlConnection *conn, char *tableName, char *pos, boolean intra)
+{
+/* get the data from the database */
+char **row = NULL;
+char query[512];
+query[0] = '\0';
+
+if (!pos)
+ {
+ if (intra)
+ safef(query, sizeof(query), "select * from %s where chrom = chrom2", tableName);
+ else
+ safef(query, sizeof(query), "select * from %s", tableName);
+ }
+else
+ {
+ char *chrom = NULL;
+ int start = 0;
+ int stop = 0;
+ if (!hgParseChromRange(NULL, pos, &chrom, &start, &stop))
+ return NULL;
+
+ if (intra)
+ safef(query, sizeof(query),
+ "select * from %s where chrom = chrom2 and chrom = '%s' and chromStart<%d and chromEnd>%d",
+ tableName, chrom, stop, start);
+ else
+ safef(query, sizeof(query),
+ "select * from %s where chrom = '%s' and chromStart<%d and chromEnd>%d",
+ tableName, chrom, stop, start);
+ }
+
+struct sqlResult *sr = sqlGetResult(conn, query);
+struct breaks *br, *brList = NULL;
+
+/* all copy number tracks are bed 4 */
+while ((row = sqlNextRow(sr)) != NULL)
+ {
+ AllocVar(br);
+
+ br->chrom = cloneString(row[0]);
+ br->chromStart = atoi(row[1]);
+ br->chromEnd = atoi(row[2]);
+ strcpy(br->strand, row[3]);
+ br->chrom2 = cloneString(row[4]);
+ br->chromStart2 = atoi(row[5]);
+ br->chromEnd2 = atoi(row[6]);
+ strcpy(br->strand2, row[7]);
+ br->support = atoi(row[8]);
+ br->qual = atof(row[9]);
+
+ slAddHead(&brList, br);
+ }
+slReverse(&brList);
+sqlFreeResult(&sr);
+return brList;
+}
+
+
/****** END HELPER FUNCTIONS *******/
float drawCopy(struct sqlConnection *conn, struct json *js,
char *pos, int width, int height, char *name, char *suffix,
float maxVal, float medVal, Color col)
{
char tableName[256];
safef(tableName, sizeof(tableName), "%s_%s", name, suffix);
float tmpMax = 0;
struct bed *bed = getBed(conn, tableName, pos, 4, &tmpMax);
if (maxVal == FLOAT_NULL)
maxVal = tmpMax;
struct settings *settings = initSettings(conn, pos, width, height, 0, maxVal);
char *filename = copyNumberGif(conn, bed, settings, suffix, medVal, col);
+if (!filename)
+ return 0.0;
char jsName[256];
safef(jsName, sizeof(jsName), "image_%s", suffix);
jsonAddString(js, jsName, filename);
bedFree(&bed);
return tmpMax;
}
+void drawBreaks(struct sqlConnection *conn, struct json *js,
+ char *pos, int width, char *name, char *suffix)
+{
+char tableName[256];
+safef(tableName, sizeof(tableName), "%s_%s", name, suffix);
+
+int height = DEFAULT_LABEL_HEIGHT;
+struct breaks *breaks = getBreaks(conn, tableName, pos, TRUE); // TRUE = intra
+
+struct settings *settings = initSettings(conn, pos, width, height, 0, 0);
+
+char *filename = breaksGif(conn, breaks, settings);
+if (!filename)
+ return;
+
+jsonAddString(js, suffix, filename);
+jsonAddInt(js, "breaksHeight", settings->height);
+}
+
void drawIdeo(struct sqlConnection *conn, struct json *js,
char *pos, int width)
{
int height = DEFAULT_LABEL_HEIGHT + CYTO_HEIGHT;
struct settings *settings = initSettings(conn, pos, width, height, 0, 0);
char *filename = genomeLabelsGif(conn, settings);
+if (!filename)
+ return;
jsonAddString(js, "ideogram", filename);
}
void drawGenes(struct sqlConnection *conn, struct json *js,
char *pos, int width)
{
int height = DEFAULT_LABEL_HEIGHT;
struct settings *settings = initSettings(conn, pos, width, height, 0, 0);
char *filename = annotationGif(settings, "refGene");
+if (!filename)
+ return;
jsonAddString(js, "genes", filename);
+jsonAddInt(js, "genesHeight", settings->height);
}
void drawScale(struct sqlConnection *conn, struct json *js,
char *pos, int width)
{
int height = DEFAULT_LABEL_HEIGHT;
struct settings *settings = initSettings(conn, pos, width, height, 0, 0);
char *filename = genomeScaleGif(settings);
+if (!filename)
+ return;
jsonAddString(js, "scale", filename);
}
void draw()
{
struct sqlConnection *conn = hAllocConnProfile(localDb, db);
char *pos = cartUsualString(cart, bbPos, NULL);
int width = cartUsualInt(cart, bbWidth, DEFAULT_PLOT_WIDTH);
int height = cartUsualInt(cart, bbHeight, DEFAULT_PLOT_HEIGHT);
char *name = "TCGA_13_0751";
struct json *js = newJson();
float maxVal = FLOAT_NULL;
maxVal = drawCopy(conn, js, pos, width, height, name, "cnv", FLOAT_NULL, 0.8, MG_BLACK);
drawCopy(conn, js, pos, width, height, name, "major", maxVal, 0.5, MG_RED);
drawCopy(conn, js, pos, width, height, name, "minor", maxVal, 0.4, MG_BLUE);
+drawBreaks(conn, js, pos, width, name, "breaks");
+
drawIdeo(conn, js, pos, width);
drawGenes(conn, js, pos, width);
drawScale(conn, js, pos, width);
+hFreeConn(&conn);
+
if (js)
hPrintf("%s\n", js->print(js));
-hFreeConn(&conn);
}
void dispatchRoutines()
/* Look at command variables in cart and figure out which
* page to draw. */
{
/* retrieve cart variables, handle various modes */
char *mode = cartOptionalString(cart, bbMode);
if (!mode)
errAbort("%s is required.", bbMode);
if (sameString(mode, "draw"))
draw();
else
errAbort("Incorrect mode = %s", mode);
cartRemovePrefix(cart, bbPrefix);
}
void hghDoUsualHttp()
/* Wrap html page dispatcher with code that writes out
* HTTP header and write cart back to database. */
{
cartWriteCookie(cart, hUserCookie());
printf("Content-Type:application/x-javascript\r\n\r\n");
/* Dispatch other pages, that actually want to write HTML. */
cartWarnCatcher(dispatchRoutines, cart, jsonEarlyWarningHandler);
cartCheckout(&cart);
}
char *excludeVars[] = {"Submit", "submit", NULL};
int main(int argc, char *argv[])
/* Process command line. */
{
htmlPushEarlyHandlers();
cgiSpoof(&argc, argv);
htmlSetStyle(htmlStyleUndecoratedLink);
oldVars = hashNew(12);
cart = cartForSession(hUserCookie(), excludeVars, oldVars);
hghDoUsualHttp();
return 0;
}