void altSummary(char *db, char *agxFileName, char *summaryOutName, char *htmlOutName, char *htmlFramesOutName)
/* Look through a bunch of splice sites and output some statistics and links. */
{
struct altGraphX *agList = NULL, *ag = NULL;
struct altSpliceSite *aSpliceList = NULL, *aSplice=NULL;
char *RDataName = optionVal("RData", NULL);
char *bedName = optionVal("bedName", NULL);
FILE *htmlOut = NULL;
FILE *htmlFramesOut = NULL;
FILE *summaryOut = NULL;
int altSpliceSites = 0, altSpliceLoci = 0, totalSpliceSites = 0;
warn("Loading splicing graphs.");
agList = altGraphXLoadAll(agxFileName);
htmlFramesOut = mustOpen(htmlFramesOutName, "w");
htmlOut = mustOpen(htmlOutName, "w");
summaryOut = mustOpen(summaryOutName, "w");
if(RDataName != NULL)
{
char buff[256];
safef(buff, sizeof(buff), "%s.control", RDataName);
RDataCont = mustOpen(buff, "w");
outputRHeader(RDataCont);
safef(buff, sizeof(buff), "%s.alt", RDataName);
RData = mustOpen(buff, "w");
outputRHeader(RData);
}
if(bedName != NULL)
{
openBedFiles(bedName);
}
writeOutFrames(htmlFramesOut, htmlOutName, db);
carefulClose(&htmlFramesOut);
warn("Examining splicing graphs.");
fprintf(htmlOut, "<html>\n<body bgcolor=\"#FFF9D2\"><b>Alt-Splice List</b>\n"
"<table border=1><tr><th>Name (count)</th><th>Type</th><th>Size</th></tr>\n");
for(ag=agList; ag != NULL; ag=ag->next)
{
lookForAltSplicing(db, ag, &aSpliceList, &altSpliceSites, &altSpliceLoci, &totalSpliceSites);
for(aSplice=aSpliceList; aSplice != NULL; aSplice= aSplice->next)
{
altSpliceSiteOutput(aSplice, summaryOut, '\t', '\n');
htmlLinkOut(db, aSplice, htmlOut);
if(bedViewOutFile != NULL)
bedViewOut(aSplice, bedViewOutFile);
}
altSpliceSiteFreeList(&aSpliceList);
}
warn("\nDone.");
fprintf(htmlOut,"</body></html>\n");
warn("%d altSpliced sites in %d alt-spliced loci out of %d total loci.",
altSpliceSites, altSpliceLoci, slCount(agList));
printSpliceTypeInfo(altSpliceLoci);
altGraphXFreeList(&agList);
if(RData != NULL)
{
carefulClose(&RData);
carefulClose(&RDataCont);
}
carefulClose(&htmlOut);
carefulClose(&summaryOut);
}
void pickIntrons()
/** Top level routine, actually picks the introns. */
{
char *htmlFileName=NULL, *htmlFrameFileName=NULL;
char *bedFileName=NULL, *orthoBedFileName=NULL;
FILE *htmlOut=NULL, *htmlFrameOut=NULL;
FILE *bedOut=NULL, *orthoBedOut=NULL;
char *orthoEvalFile = NULL;
char *db = NULL;
struct orthoEval *ev=NULL, *evList = NULL;
struct intronEv *iv=NULL, *ivList = NULL;
int maxPicks = optionInt("numPicks", 100);
int i=0;
boolean isRefSeq=FALSE, isMgcBad=FALSE;
struct hash *posHash = newHash(12), *agxHash = newHash(12);
struct bed *bed = NULL;
char buff[256];
htmlFileName = optionVal("htmlFile", NULL);
htmlFrameFileName = optionVal("htmlFrameFile", "frame.html");
orthoEvalFile = optionVal("orthoEvalFile", NULL);
db = optionVal("db", NULL);
bedFileName = optionVal("bedOutFile", NULL);
orthoBedFileName = optionVal("orthoBedOut", NULL);
if(htmlFileName == NULL || orthoEvalFile == NULL || db == NULL ||
bedFileName == NULL || orthoBedFileName == NULL )
errAbort("Missing parameters. Use -help for usage.");
warn("Loading orthoEvals.");
evList = orthoEvalLoadAll(orthoEvalFile);
warn("Creating intron records");
for(ev = evList; ev != NULL; ev = ev->next)
{
for(i=0; i<ev->numIntrons; i++)
{
occassionalDot();
iv = intronIvForEv(ev, i);
slAddHead(&ivList, iv);
}
}
warn("\nDone");
warn("Sorting");
slSort(&ivList, intronEvalCmp);
warn("Done.");
htmlOut = mustOpen(htmlFileName, "w");
bedOut = mustOpen(bedFileName, "w");
htmlFrameOut = mustOpen(htmlFrameFileName, "w");
orthoBedOut = mustOpen(orthoBedFileName, "w");
i=0;
fprintf(htmlOut, "<html><body><table border=1><tr><th>Num</th><th>Mouse Acc.</th><th>Score</th><th>TS Pick</th></tr>\n");
warn("Filtering");
safef(buff, sizeof(buff), "tmp");
for(iv = ivList; iv != NULL && maxPicks > 0; iv = iv->next)
{
if(isUniqueCoordAndAgx(db, iv, posHash, agxHash) && iv->support == 0 && !isOverlappedByRefSeq(db, iv) &&
! isOverlappedByEst(db, iv) && ! isOverlappedByMRna(db, iv))
{
boolean twinScan = (coordOverlappedByTable(db, iv->chrom, iv->e1S, iv->e1E, "mgcTSExpPcr") &&
coordOverlappedByTable(db, iv->chrom, iv->e2S, iv->e2E, "mgcTSExpPcr"));
bed = bedForIv(iv);
if(sameString(buff, "tmp"))
safef(buff, sizeof(buff), "%s:%d-%d", bed->chrom, bed->chromStart-50, bed->chromEnd+50);
// isMgcBad = isOverlappedByMgcBad(iv);
fprintf(htmlOut, "<tr><td>%d</td><td><a target=\"browser\" "
"href=\"http://mgc.cse.ucsc.edu/cgi-bin/hgTracks?db=hg15&position=%s:%d-%d\"> "
"%s </a></td><td>%d</td><td>%s</td></tr>\n",
++i,bed->chrom, bed->chromStart-50, bed->chromEnd+50, bed->name, bed->score,
twinScan ? "yes" : "no");
bedTabOutN(bed, 12, bedOut);
bedTabOutN(iv->ev->orthoBed, 12, orthoBedOut);
bedFree(&bed);
maxPicks--;
}
}
writeOutFrames(htmlFrameOut, htmlFileName, db, bedFileName, buff);
fprintf(htmlOut, "</table></body></html>\n");
carefulClose(&bedOut);
carefulClose(&htmlOut);
carefulClose(&htmlFrameOut);
carefulClose(&orthoBedOut);
warn("Done.");
hashFree(&posHash);
hashFree(&agxHash);
}
