boolean bedPassFilters(struct bed *bed, struct altGraphX *ag, int cassetteEdge)
{
int minFlankingNum = cgiUsualInt("minFlankingNum", 2);
int minFlankingSize = cgiUsualInt("minFlankingSize", 0);
boolean mrnaFilter = cgiBoolean("mrnaFilter");
boolean passed = TRUE;
int i =0;
for(i = 0; i<bed->blockCount; i++)
{
if(bed->expIds[i] != cassetteEdge)
{
passed &= passFilter(bed, i, ag, minFlankingNum, minFlankingSize, mrnaFilter);
}
}
return passed;
}
void resetVars()
/* Reset vars except for position and database. */
{
static char *except[] = {"db", "position", NULL};
char *cookieName = hUserCookie();
int sessionId = cgiUsualInt(cartSessionVarName(), 0);
char *hguidString = findCookieData(cookieName);
int userId = (hguidString == NULL ? 0 : atoi(hguidString));
struct cart *oldCart = cartNew(userId, sessionId, NULL, NULL);
cartRemoveExcept(oldCart, except);
cartCheckout(&oldCart);
cgiVarExcludeExcept(except);
}
void faNcbiToUcsc(char *inFile, char *out)
/* faNcbiToUcsc - Convert FA file from NCBI to UCSC format.. */
{
struct lineFile *lf = lineFileOpen(inFile, TRUE);
char outName[512];
char *line;
boolean split = cgiBoolean("split");
boolean ntLast = cgiBoolean("ntLast");
boolean encode = cgiBoolean("encode");
struct dnaSeq seq;
FILE *f = NULL;
char *wordBefore = cgiUsualString("wordBefore", "gb");
int wordIx = cgiUsualInt("wordIx", -1);
char *e = NULL;
char *nt = NULL;
ZeroVar(&seq);
if (split)
makeDir(out);
else
f = mustOpen(out, "w");
while (lineFileNext(lf, &line, NULL))
{
if (line[0] == '>')
{
if (ntLast || encode)
{
nt = NULL;
if (ntLast)
{
e = NULL;
nt = stringIn("NT_", line);
if (nt == NULL)
nt = stringIn("NG_", line);
if (nt == NULL)
nt = stringIn("NC_", line);
if (nt == NULL)
errAbort("Expecting NT_ NG_ or NC_in '%s'", line);
e = strchr(nt, '|');
if (e != NULL) *e = 0;
e = strchr(nt, ' ');
if (e != NULL) *e = 0;
}
else
{
nt = stringIn("|EN", line);
if (nt == NULL)
errAbort("Expecting EN in %s", line);
nt++;
nt = firstWordInLine(nt);
}
if (split)
{
sprintf(outName, "%s/%s.fa", out, nt);
carefulClose(&f);
f = mustOpen(outName, "w");
}
fprintf(f, ">%s\n", nt);
}
else
{
char *words[32];
int wordCount, i;
char *accession = NULL;
wordCount = chopString(line+1, "|", words, ArraySize(words));
if (wordIx >= 0)
{
if (wordIx >= wordCount)
errAbort("Sorry only %d words", wordCount);
accession = words[wordIx];
}
else
{
for (i=0; i<wordCount-1; ++i)
{
if (sameString(words[i], wordBefore))
{
accession = words[i+1];
break;
}
}
if (accession == NULL)
errAbort("Couldn't find '%s' line %d of %s",
wordBefore, lf->lineIx, lf->fileName);
}
chopSuffix(accession);
fprintf(f, ">%s\n", accession);
}
}
else
{
fprintf(f, "%s\n", line);
}
}
}
void wikiPlot()
/* wikiPlot - Quick plots of maps vs. each other. */
{
boolean gotDir = cgiVarExists("contigDir");
double step;
contigDir = cgiUsualString("contigDir", contigDir);
mapX = cgiUsualString("mapX", mapX);
mapY = cgiUsualString("mapY", mapY);
pix = cgiUsualInt("pix", pix);
xOff = cgiUsualDouble("xOff", xOff);
yOff = cgiUsualDouble("yOff", yOff);
zoom = cgiUsualDouble("zoom", zoom);
step = 0.1 * 1/zoom;
if (cgiVarExists("boxOut"))
{
double invZoom = 1.0/zoom;
double xCen = xOff + invZoom*0.5;
double yCen = yOff + invZoom*0.5;
zoom /= 2;
invZoom = 1.0/zoom;
xOff = xCen - invZoom*0.5;
yOff = yCen - invZoom*0.5;
}
else if (cgiVarExists("boxUp"))
yOff -= step;
else if (cgiVarExists("boxDown"))
yOff += step;
else if (cgiVarExists("boxLeft"))
xOff -= step;
else if (cgiVarExists("boxRight"))
xOff += step;
else if (cgiVarExists("boxUpLeft"))
{
yOff -= step;
xOff -= step;
}
else if (cgiVarExists("boxUpRight"))
{
yOff -= step;
xOff += step;
}
else if (cgiVarExists("boxDownLeft"))
{
yOff += step;
xOff -= step;
}
else if (cgiVarExists("boxDownRight"))
{
yOff += step;
xOff += step;
}
else if (cgiVarExists("unzoom"))
{
xOff = yOff = -0.05;
zoom = 0.9;
}
printf("<FORM ACTION=\"../cgi-bin/wikiPlot\" METHOD=\"GET\">\n");
printf("<TABLE BORDER=0 WIDTH=\"100%%\">\n");
printf("<TR>\n");
printf("<TD WIDTH=\"78%%\">\n");
printf("<B>Wiki Plotter</B><BR>\n");
printf("<B>Contig: </B>");
cgiMakeTextVar("contigDir", contigDir, 0);
if (gotDir)
{
cgiMakeButton("refresh", "refresh");
}
else
cgiMakeButton("submit", "submit");
printf("<BR>\n");
printf("<B>Map X: </B>");
cgiMakeTextVar("mapX", mapX, 12);
printf("<B>Map Y: </B>");
cgiMakeTextVar("mapY", mapY, 12);
printf("<B>Pixels: </B>");
cgiMakeIntVar("pix", pix, 4);
printf("</TD>\n");
printf("<TD WIDTH=\"22%%\">\n");
if (gotDir)
printBox();
printf("</TD>\n");
printf("</TR>\n");
printf("</TABLE>\n");
if (gotDir)
{
char xFile[512], yFile[512];
struct hash *xHash = NULL, *yHash = NULL;
struct clonePos *xList = NULL, *yList = NULL;
sprintf(xFile, "%s/%s", contigDir, mapX);
sprintf(yFile, "%s/%s", contigDir, mapY);
loadMaps(xFile, yFile, &xList, &yList, &xHash, &yHash);
makePlot(xList, yList, yHash);
}
/* Save hidden vars. */
{
char buf[256];
sprintf(buf, "%f", zoom);
cgiMakeHiddenVar("zoom", buf);
sprintf(buf, "%f", xOff);
cgiMakeHiddenVar("xOff", buf);
sprintf(buf, "%f", yOff);
cgiMakeHiddenVar("yOff", buf);
}
printf("</FORM>\n");
}
