int main(int argc, char *argv[])
/* Process command line. */
{
cgiSpoof(&argc, argv);
if (argc != 3)
usage();
doTarget = !cgiBoolean("query");
noHead = (cgiBoolean("nohead") || cgiBoolean("noHead"));
maxPile = cgiOptionalInt("maxPile", maxPile);
minPile = cgiOptionalInt("minPile", minPile);
pslUnpile(argv[1], argv[2]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
cgiSpoof(&argc, argv);
if (argc < 2)
usage();
recurse = cgiBoolean("r");
suffix = cgiOptionalString("suffix");
wildCard = cgiOptionalString("wild");
nonz = cgiBoolean("nonz");
catDir(argc-1, argv+1);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
cgiSpoof(&argc, argv);
textField = cgiUsualString("textField", textField);
fileComment = cgiUsualString("comment", fileComment);
picky = cgiBoolean("picky");
makeMain = cgiBoolean("main");
positiveOnly = cgiBoolean("positive");
if (argc != 3)
usage();
autoXml(argv[1], argv[2]);
return 0;
}
void checkArguments()
/** setup our parameters depending on whether we've been called as a
cgi script or from the command line */
{
hgTest = cgiBoolean("hgTest");
numTests = cgiOptionalInt("numTests",0);
origDb = cgiOptionalString("origDb");
origGenome = cgiOptionalString("origGenome");
newGenome = cgiOptionalString("newGenome");
position = cgiOptionalString("position");
chrom = cgiOptionalString("chrom");
chromStart = cgiOptionalInt("chromStart", -1);
chromEnd = cgiOptionalInt("chromEnd", -1);
calledSelf = cgiBoolean("calledSelf");
/* if we're testing we don't need to worry about UI errors */
if(hgTest)
return;
/* parse the position string and make sure that it makes sense */
if (position != NULL && position[0] != 0)
{
parsePosition(cloneString(position), &chrom, &chromStart, &chromEnd);
}
if (chromStart > chromEnd)
{
webAbort("Error:", "Start of range is greater than end. %d > %d", chromStart, chromEnd);
}
/* convert the genomes requested to hgN format */
if(origGenome != NULL)
origGenome = ccFreezeDbConversion(NULL, origGenome, organism);
if(newGenome != NULL)
newGenome = ccFreezeDbConversion(NULL, newGenome, organism);
/* make sure that we've got valid arguments */
if((newGenome == NULL || origGenome == NULL || chrom == NULL || chromStart == -1 || chromEnd == -1) && (calledSelf))
webAbort("Error:", "Missing some inputs.");
if( origGenome != NULL && sameString(origGenome, newGenome))
{
struct dyString *warning = newDyString(1024);
dyStringPrintf(warning, "Did you really want to convert from %s to %s (the same genome)?",
ccFreezeDbConversion(origGenome, NULL, organism), \
ccFreezeDbConversion(newGenome, NULL, organism));
appendWarningMsg(warning->string);
dyStringFree(&warning);
}
}
void outputSeq(DNA *dna, int dnaSize,
boolean hiliteRange, long startRange, long endRange,
FILE *out)
/* Write out sequence. */
{
struct dfm dfm;
int i;
char *seq = dna;
int size = dnaSize;
if (cgiBoolean("translate"))
{
int utr5 = 0;
int maxProtSize = (dnaSize+2)/3;
char *prot = needMem(maxProtSize + 1);
if (cgiVarExists("utr5"))
utr5 = cgiInt("utr5")-1;
startRange -= utr5;
endRange -= utr5;
startRange /= 3;
endRange /= 3;
dna += utr5;
seq = prot;
for (size = 0; size < maxProtSize; ++size)
{
if ((*prot++ = lookupCodon(dna)) == 0)
break;
dna += 3;
}
*prot = 0;
}
initDfm(&dfm, 10, 50, TRUE, hiliteRange, startRange, endRange, out);
for (i=0; i<size; ++i)
dfmOut(&dfm, seq[i]);
}
void initRegPlotOutput(struct dyString *script, char *fileName)
/* Init eithe a pdf or bitmap device. */
{
if(cgiBoolean("pdf"))
dyStringPrintf(script, "pdf(file='%s', width=6, height=6);\n", fileName);
else
dyStringPrintf(script, "bitmap('%s', width=3, height=3, res=200);\n", fileName);
}
void makePlotLink(char *type, char *fileName)
/* Write out an image or pdf link depending on pdf or image. */
{
if(cgiBoolean("pdf"))
dyStringPrintf(html, "<a href='%s'>%s</a><br>\n",
fileName, type);
else
dyStringPrintf(html, "<img src='%s'><br>\n", fileName);
}
int main(int argc, char *argv[])
/* Process command line. */
{
cgiSpoof(&argc, argv);
zeroOk = cgiBoolean("zeroOk");
if (argc < 2)
usage();
return endsInLf(argc-1, argv+1);
}
int main(int argc, char *argv[])
/* Process command line. */
{
cgiSpoof(&argc, argv);
ver = cgiBoolean("ver");
if (argc < 2)
usage();
agpCloneList(argc-1, argv+1);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
cgiSpoof(&argc, argv);
stretch = cgiBoolean("stretch");
if (argc != 4)
usage();
uniqSize(argv[1], argv[2], argv[3], cgiOptionalString("altFile"));
return 0;
}
void doMiddle()
/* Write middle part of .html. */
{
DNA *targetDna;
char *chrom;
int tStart, tEnd;
struct xaAli *xa;
int bothStart, bothEnd;
char cbCosmidName[256];
char *s;
/* Get input variables from CGI. */
char *qOrganism = cgiString("qOrganism");
char *tOrganism = cgiString("tOrganism");
char *query = cgiString("query");
char *target = cgiString("target");
char *strandString = cgiString("strand");
char strand = strandString[0];
boolean showSym = cgiBoolean("symbols");
boolean gotClickPos = cgiVarExists("clickPos");
double clickPos;
if (gotClickPos) clickPos = cgiDouble("clickPos");
strcpy(cbCosmidName, query);
if ((s = strrchr(cbCosmidName, '.')) != NULL)
*s = 0;
/* Get xaAli. */
xa = getOneXaAli(qOrganism, query);
printf("<H2>Alignment of <I>C. briggsae</I> %s:%d-%d and <I>C. elegans</I> %s</H2>\n",
cbCosmidName, xa->qStart, xa->qEnd, target);
htmlParagraph("<I>C. briggsae</I> appears on top. Coding regions in <I>C. elegans</I> are in upper case.");
/* Get display window. */
if (!wormParseChromRange(target, &chrom, &tStart, &tEnd))
errAbort("Target %s isn't formatted correctly", target);
/* Figure out intersection of display window and xeno-alignment */
bothStart = max(xa->tStart, tStart);
bothEnd = min(xa->tEnd, tEnd);
/* Get upper-cased-exon target DNA. */
targetDna = wormChromPartExonsUpper(chrom, bothStart, bothEnd - bothStart);
upcCorresponding(targetDna, bothEnd - bothStart, xa->tSym, bothStart - xa->tStart);
printf("<TT><PRE>");
showTargetRange(xa, bothStart - xa->tStart, bothEnd-bothStart, strand, showSym);
printf("</TT></PRE>");
}
int main(int argc, char *argv[])
/* Process command line. */
{
cgiSpoof(&argc, argv);
clTest = cgiBoolean("test");
clDots = cgiOptionalInt("dots", clDots);
if (argc != 9)
usage();
proteinDB = argv[8];
hgRefSeqMrna(argv[1], argv[2], argv[3], argv[4], argv[5], argv[6], argv[7]);
return 0;
}
int main(int argc, char *argv[])
{
cgiSpoof(&argc, argv);
if(argc == 1)
usage();
else
{
suffix = cgiUsualString("suffix", "pairs.sample.norm");
doAll = cgiBoolean("doAll");
avgTranscriptomeExps();
}
return 0;
}
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 doMiddle(struct cart *theCart)
/* Write header and body of html page. */
{
char *userSeq;
char *db, *organism;
boolean clearUserSeq = cgiBoolean("Clear");
cart = theCart;
dnaUtilOpen();
orgChange = sameOk(cgiOptionalString("changeInfo"),"orgChange");
if (orgChange)
{
cgiVarSet("db", hDefaultDbForGenome(cgiOptionalString("org")));
}
getDbAndGenome(cart, &db, &organism, oldVars);
char *oldDb = cloneString(db);
findClosestServer(&db, &organism);
/* Get sequence - from userSeq variable, or if
* that is empty from a file. */
if (clearUserSeq)
{
cartSetString(cart, "userSeq", "");
cartSetString(cart, "seqFile", "");
}
userSeq = cartUsualString(cart, "userSeq", "");
if (isEmpty(userSeq))
{
userSeq = cartOptionalString(cart, "seqFile");
}
if (isEmpty(userSeq) || orgChange)
{
cartWebStart(theCart, db, "%s BLAT Search", trackHubSkipHubName(organism));
if (differentString(oldDb, db))
printf("<HR><P><EM><B>Note:</B> BLAT search is not available for %s %s; "
"defaulting to %s %s</EM></P><HR>\n",
hGenome(oldDb), hFreezeDate(oldDb), organism, hFreezeDate(db));
askForSeq(organism,db);
cartWebEnd();
}
else
{
blatSeq(skipLeadingSpaces(userSeq), organism);
}
}
void loadDatabase(char *database, char *track, char *tabName)
/* Load up database from tab-file. */
{
struct sqlConnection *conn = sqlConnect(database);
struct dyString *dy = newDyString(1024);
if (!cgiBoolean("add"))
{
sqlDyStringPrintf(dy, createString, track);
sqlRemakeTable(conn, track, dy->string);
dyStringClear(dy);
}
sqlDyStringPrintf(dy, "load data local infile '%s' into table %s",
tabName, track);
sqlUpdate(conn, dy->string);
dyStringFree(&dy);
sqlDisconnect(&conn);
}
int main(int argc, char *argv[])
{
struct altGraphX *agList = NULL;
int cassetteCount = 0;
float minConfidence = 0;
char *bedFileName = NULL;
char *faFile = NULL;
FILE *faOut = NULL;
FILE *bedOut = NULL;
boolean mrnaFilter = FALSE;
float estPrior = 0.0;
int minSize = 0;
if(argc < 4)
usage();
cgiSpoof(&argc, argv);
warn("Loading graphs.");
agList = altGraphXLoadAll(argv[1]);
bedFileName = cgiOptionalString("bedFile");
minConfidence = cgiDouble("minConf");
db = cgiString("db");
faFile = cgiOptionalString("faFile");
estPrior = cgiOptionalDouble("estPrior", 10);
minSize = cgiOptionalInt("minSize", 0);
mrnaFilter = cgiBoolean("mrnaFilter");
if(mrnaFilter)
loadMrnaHash();
warn("Counting cassette exons from %d clusters above confidence: %f", slCount(agList), minConfidence);
if(bedFileName != NULL)
{
bedOut = mustOpen(bedFileName, "w");
printCommandState(argc, argv, bedOut);
fprintf(bedOut, "track name=cass_conf-%4.2f_est-%3.2f description=\"spliceStats minConf=%4.2f estPrior=%3.2f minSize=%d\"\n",
minConfidence, estPrior, minConfidence, estPrior, minSize);
}
if(faFile != NULL)
faOut = mustOpen(faFile, "w");
cassetteCount = countCassetteExons(agList, minConfidence, faOut,bedOut );
carefulClose(&faOut);
carefulClose(&bedOut);
warn("%d cassette exons out of %d clusters in %s", cassetteCount, slCount(agList), argv[1]);
altGraphXFreeList(&agList);
return 0;
}
void submitUrl(struct sqlConnection *conn)
/* Submit validated manifest if it is not already in process. Show
* progress once it is in progress. */
{
/* Parse email and URL out of CGI vars. Do a tiny bit of error checking. */
char *url = trimSpaces(cgiString("url"));
if (!stringIn("://", url))
errAbort("%s doesn't seem to be a valid URL, no '://'", url);
/* Do some reality checks that email and URL actually exist. */
edwMustGetUserFromEmail(conn, userEmail);
int sd = netUrlMustOpenPastHeader(url);
close(sd);
edwAddSubmitJob(conn, userEmail, url, cgiBoolean("update"));
/* Give the system a half second to react and then put up status info about submission */
sleep1000(1000);
monitorSubmission(conn);
}
void doMatrixPlot(struct dyString *script,
char *skipPSet, char *tableName, char *type,
boolean linesOnly)
/* Print out a matrix plot for a particular table. */
{
struct tempName plotFile;
struct dyString *query = newDyString(256);
struct dMatrix *dM = NULL;
char title[256];
safef(title, sizeof(title), "%s - %s", altEvent->geneName, type);
if(cgiBoolean("pdf"))
makeTempName(&plotFile, "sp", ".pdf");
else
makeTempName(&plotFile, "sp", ".png");
touchBlank(plotFile.forCgi);
makePlotLink(type, plotFile.forCgi);
//dyStringPrintf(html, "<img src='%s'><br>\n", plotFile.forCgi);
constructQueryForEvent(query, skipPSet, tableName);
dM = dataFromTable(tableName, query->string);
plotMatrixRows(dM, script, title, plotFile.forCgi, type, linesOnly) ;
}
void intronSizes(char *database, char *table)
/* intronSizes - Output list of intron sizes.. */
{
struct dyString *query = newDyString(1024);
struct sqlConnection *conn;
struct sqlResult *sr;
char **row;
struct genePred *gp;
int rowOffset;
struct bed *bedList = NULL, *bed = NULL;
hSetDb(database);
rowOffset = hOffsetPastBin(NULL, table);
conn = hAllocConn(database);
sqlDyStringPrintf(query, "select * from %s", table);
if (chromName != NULL)
dyStringPrintf(query, " where chrom = '%s'", chromName);
if (cgiBoolean("withUtr"))
{
dyStringPrintf(query, " %s txStart != cdsStart",
(chromName == NULL ? "where" : "and"));
}
sr = sqlGetResult(conn, query->string);
while ((row = sqlNextRow(sr)) != NULL)
{
gp = genePredLoad(row+rowOffset);
genePredIntrons(gp, &bedList);
slReverse(&bedList);
for (bed = bedList ; bed != NULL ; bed=bed->next)
bedTabOutN(bed,6, stdout);
bedFreeList(&bedList);
genePredFree(&gp);
}
sqlFreeResult(&sr);
hFreeConn(&conn);
}
void intronEnds(char *database, char *table)
/* intronEnds - Gather stats on intron ends.. */
{
struct dyString *query = newDyString(1024);
struct sqlConnection *conn;
struct sqlResult *sr;
char **row;
struct genePred *gp;
int total = 0;
int gtag = 0;
int gcag = 0;
int atac = 0;
int ctac = 0;
DNA ends[4];
int exonIx, txStart;
struct dnaSeq *seq;
int rowOffset;
char strand;
rowOffset = hOffsetPastBin(database, NULL, table);
conn = hAllocConn(database);
sqlDyStringPrintf(query, "select * from %s", table);
if (chromName != NULL)
dyStringPrintf(query, " where chrom = '%s'", chromName);
if (cgiBoolean("withUtr"))
{
dyStringPrintf(query, " %s txStart != cdsStart",
(chromName == NULL ? "where" : "and"));
}
sr = sqlGetResult(conn, query->string);
while ((row = sqlNextRow(sr)) != NULL)
{
gp = genePredLoad(row+rowOffset);
strand = gp->strand[0];
txStart = gp->txStart;
seq = hDnaFromSeq(database, gp->chrom, txStart, gp->txEnd, dnaLower);
for (exonIx=1; exonIx < gp->exonCount; ++exonIx)
{
++total;
memcpy(ends, seq->dna + gp->exonEnds[exonIx-1] - txStart, 2);
memcpy(ends+2, seq->dna + gp->exonStarts[exonIx] - txStart - 2, 2);
if (strand == '-')
reverseComplement(ends, 4);
if (ends[0] == 'g' && ends[1] == 't' && ends[2] == 'a' && ends[3] == 'g')
++gtag;
if (ends[0] == 'g' && ends[1] == 'c' && ends[2] == 'a' && ends[3] == 'g')
++gcag;
if (ends[0] == 'a' && ends[1] == 't' && ends[2] == 'a' && ends[3] == 'c')
++atac;
if (ends[0] == 'c' && ends[1] == 't' && ends[2] == 'a' && ends[3] == 'c')
++ctac;
}
freeDnaSeq(&seq);
genePredFree(&gp);
}
sqlFreeResult(&sr);
hFreeConn(&conn);
printf("gt/ag %d (%4.2f)\n", gtag, 100.0*gtag/total);
printf("gc/ag %d (%4.2f)\n", gcag, 100.0*gcag/total);
printf("at/ac %d (%4.2f)\n", atac, 100.0*atac/total);
printf("ct/ac %d (%4.2f)\n", ctac, 100.0*ctac/total);
printf("Total %d\n", total);
}
void doMiddle()
{
char *seqName;
boolean intronsLowerCase = TRUE;
boolean intronsParenthesized = FALSE;
boolean hiliteNear = FALSE;
int startRange = 0;
int endRange = 0;
boolean gotRange = FALSE;
struct dnaSeq *cdnaSeq;
boolean isChromRange = FALSE;
DNA *dna;
char *translation = NULL;
seqName = cgiString("geneName");
seqName = trimSpaces(seqName);
if (cgiVarExists("intronsLowerCase"))
intronsLowerCase = cgiBoolean("intronsLowerCase");
if (cgiVarExists("intronsParenthesized"))
intronsParenthesized = cgiBoolean("intronsParenthesized");
if (cgiVarExists("startRange") && cgiVarExists("endRange" ))
{
startRange = cgiInt("startRange");
endRange = cgiInt("endRange");
gotRange = TRUE;
}
if (cgiVarExists("hiliteNear"))
{
hiliteNear = TRUE;
}
fprintf(stdout, "<P><TT>\n");
/* The logic here is a little complex to optimize speed.
* If we can decide what type of thing the name refers to by
* simply looking at the name we do. Otherwise we have to
* search the database in various ways until we get a hit. */
if (wormIsNamelessCluster(seqName))
{
isChromRange = TRUE;
}
else if (wormIsChromRange(seqName))
{
isChromRange = TRUE;
}
else if (getWormGeneDna(seqName, &dna, TRUE))
{
if (cgiBoolean("litLink"))
{
char nameBuf[64];
char *geneName = NULL;
char *productName = NULL;
char *coding;
int transSize;
struct wormCdnaInfo info;
printf("<H3>Information and Links for %s</H3>\n", seqName);
if (wormInfoForGene(seqName, &info))
{
if (info.description)
printf("<P>%s</P>\n", info.description);
geneName = info.gene;
productName = info.product;
}
else
{
if (wormIsGeneName(seqName))
geneName = seqName;
else if (wormGeneForOrf(seqName, nameBuf, sizeof(nameBuf)))
geneName = nameBuf;
}
coding = cloneUpperOnly(dna);
transSize = 1 + (strlen(coding)+2)/3;
translation = needMem(1+strlen(coding)/3);
dnaTranslateSome(coding, translation, transSize);
freez(&coding);
if (geneName)
{
printf("<A HREF=\"http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?form=4&db=m"
"&term=C+elegans+%s&dispmax=50&relentrezdate=No+Limit\">", geneName);
printf("PubMed search on gene: </A>%s<BR>\n", geneName);
}
if (productName)
{
char *encoded = cgiEncode(productName);
printf("<A HREF=\"http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?form=4&db=m"
"&term=%s&dispmax=50&relentrezdate=No+Limit\">", encoded);
printf("PubMed search on product:</A> %s<BR>\n", productName);
freeMem(encoded);
}
/* Process name to get rid of isoform letter for Proteome. */
if (geneName)
strcpy(nameBuf, geneName);
else
{
strcpy(nameBuf, seqName);
#ifdef NEVER
/* Sometimes Proteome requires the letter after the orf name
* in alt-spliced cases, sometimes it can't handle it.... */
nameLen = strlen(nameBuf);
if (wormIsOrfName(nameBuf) && isalpha(nameBuf[nameLen-1]))
{
char *dotPos = strrchr(nameBuf, '.');
if (dotPos != NULL && isdigit(dotPos[1]))
nameBuf[nameLen-1] = 0;
}
#endif /* NEVER */
}
printf("<A HREF=\"http://www.wormbase.org/db/seq/sequence?name=%s;class=Sequence\">", seqName);
printf("WormBase link on:</A> %s<BR>\n", seqName);
printf("<A HREF=\"http://www.proteome.com/databases/WormPD/reports/%s.html\">", nameBuf);
printf("Proteome link on:</A> %s<BR>\n<BR>\n", nameBuf);
printf("<A HREF=#DNA>Genomic DNA Sequence</A><BR>\n");
if (hiliteNear)
printf("<A HREF=\"#CLICKED\">Shortcut to where you clicked in gene</A><BR>");
printf("<A HREF=#protein>Translated Protein Sequence</A><BR>\n");
htmlHorizontalLine();
printf("<A NAME=DNA></A>");
printf("<H3>%s Genomic DNA sequence</H3>", seqName);
}
if (!intronsLowerCase)
tolowers(dna);
if (hiliteNear)
{
if (!gotRange)
{
double nearPos = cgiDouble("hiliteNear");
int rad = 5;
int dnaSize = strlen(dna);
long mid = (int)(dnaSize * nearPos);
startRange = mid - rad;
if (startRange < 0) startRange = 0;
endRange = mid + rad;
if (endRange >= dnaSize) endRange = dnaSize - 1;
}
}
outputSeq(dna, strlen(dna), hiliteNear, startRange, endRange, stdout);
freez(&dna);
}
else if (wormCdnaSeq(seqName, &cdnaSeq, NULL))
{
outputSeq(cdnaSeq->dna, cdnaSeq->size, FALSE, 0, 0, stdout);
}
else
{
isChromRange = TRUE;
}
if (isChromRange)
{
char *chromId;
int start, end;
char strand = '+';
int size;
if (!wormGeneRange(seqName, &chromId, &strand, &start, &end))
errAbort("Can't find %s",seqName);
size = end - start;
if (intronsLowerCase)
dna = wormChromPartExonsUpper(chromId, start, size);
else
{
dna = wormChromPart(chromId, start, size);
touppers(dna);
}
if (cgiVarExists("strand"))
strand = cgiString("strand")[0];
if (strand == '-')
reverseComplement(dna, size);
outputSeq(dna, size, FALSE, 0, 0, stdout);
}
if (translation != NULL)
{
htmlHorizontalLine();
printf("<A NAME=protein></A>");
printf("<H3>Translated Protein of %s</H3>\n", seqName);
outputSeq(translation, strlen(translation), FALSE, 0, 0, stdout);
freez(&translation);
}
fprintf(stdout, "</TT></P>\n");
}
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);
}
}
}
static void hgSeqConcatRegionsDb(char *db, char *chrom, int chromSize, char strand, char *name,
int rCount, unsigned *rStarts, unsigned *rSizes,
boolean *exonFlags, boolean *cdsFlags)
/* Concatenate and print out dna for a series of regions. */
{
// Note: this code use to generate different sequence ids if the global
// database in hdb was different than the db parameter. This functionality
// has been removed since the global database was removed and it didn't
// appear to be used.
struct dnaSeq *rSeq = NULL;
struct dnaSeq *cSeq = NULL;
char recName[256];
int seqStart, seqEnd;
int offset, cSize;
int i;
boolean isRc = (strand == '-') || cgiBoolean("hgSeq.revComp");
boolean maskRep = cgiBoolean("hgSeq.maskRepeats");
int padding5 = cgiOptionalInt("hgSeq.padding5", 0);
int padding3 = cgiOptionalInt("hgSeq.padding3", 0);
char *casing = cgiString("hgSeq.casing");
char *repMasking = cgiString("hgSeq.repMasking");
char *granularity = cgiOptionalString("hgSeq.granularity");
boolean concatRegions = granularity && sameString("gene", granularity);
if (rCount < 1)
return;
/* Don't support padding if granularity is gene (i.e. concat'ing all). */
if (concatRegions)
{
padding5 = padding3 = 0;
}
i = rCount - 1;
seqStart = rStarts[0] - (isRc ? padding3 : padding5);
seqEnd = rStarts[i] + rSizes[i] + (isRc ? padding5 : padding3);
/* Padding might push us off the edge of the chrom; if so, truncate: */
if (seqStart < 0)
{
if (isRc)
padding3 += seqStart;
else
padding5 += seqStart;
seqStart = 0;
}
/* if we know the chromSize, don't pad out beyond it */
if ((chromSize > 0) && (seqEnd > chromSize))
{
if (isRc)
padding5 += (chromSize - seqEnd);
else
padding3 += (chromSize - seqEnd);
seqEnd = chromSize;
}
if (seqEnd <= seqStart)
{
printf("# Null range for %s_%s (range=%s:%d-%d 5'pad=%d 3'pad=%d) (may indicate a query-side insert)\n",
db,
name,
chrom, seqStart+1, seqEnd,
padding5, padding3);
return;
}
if (maskRep)
{
rSeq = hDnaFromSeq(db, chrom, seqStart, seqEnd, dnaMixed);
if (sameString(repMasking, "N"))
lowerToN(rSeq->dna, strlen(rSeq->dna));
if (!sameString(casing, "upper"))
tolowers(rSeq->dna);
}
else if (sameString(casing, "upper"))
rSeq = hDnaFromSeq(db, chrom, seqStart, seqEnd, dnaUpper);
else
rSeq = hDnaFromSeq(db, chrom, seqStart, seqEnd, dnaLower);
/* Handle casing and compute size of concatenated sequence */
cSize = 0;
for (i=0; i < rCount; i++)
{
if ((sameString(casing, "exon") && exonFlags[i]) ||
(sameString(casing, "cds") && cdsFlags[i]))
{
int rStart = rStarts[i] - seqStart;
toUpperN(rSeq->dna+rStart, rSizes[i]);
}
cSize += rSizes[i];
}
cSize += (padding5 + padding3);
AllocVar(cSeq);
cSeq->dna = needLargeMem(cSize+1);
cSeq->size = cSize;
offset = 0;
for (i=0; i < rCount; i++)
{
int start = rStarts[i] - seqStart;
int size = rSizes[i];
if (i == 0)
{
start -= (isRc ? padding3 : padding5);
assert(start == 0);
size += (isRc ? padding3 : padding5);
}
if (i == rCount-1)
{
size += (isRc ? padding5 : padding3);
}
memcpy(cSeq->dna+offset, rSeq->dna+start, size);
offset += size;
}
assert(offset == cSeq->size);
cSeq->dna[offset] = 0;
freeDnaSeq(&rSeq);
if (isRc)
reverseComplement(cSeq->dna, cSeq->size);
safef(recName, sizeof(recName),
"%s_%s range=%s:%d-%d 5'pad=%d 3'pad=%d "
"strand=%c repeatMasking=%s",
db,
name,
chrom, seqStart+1, seqEnd,
padding5, padding3,
(isRc ? '-' : '+'),
(maskRep ? repMasking : "none"));
faWriteNext(stdout, recName, cSeq->dna, cSeq->size);
freeDnaSeq(&cSeq);
}
void blatSeq(char *userSeq, char *organism)
/* Blat sequence user pasted in. */
{
FILE *f;
struct dnaSeq *seqList = NULL, *seq;
struct tempName pslTn, faTn;
int maxSingleSize, maxTotalSize, maxSeqCount;
int minSingleSize = minMatchShown;
char *genome, *db;
char *type = cgiString("type");
char *seqLetters = cloneString(userSeq);
struct serverTable *serve;
int conn;
int oneSize, totalSize = 0, seqCount = 0;
boolean isTx = FALSE;
boolean isTxTx = FALSE;
boolean txTxBoth = FALSE;
struct gfOutput *gvo;
boolean qIsProt = FALSE;
enum gfType qType, tType;
struct hash *tFileCache = gfFileCacheNew();
boolean feelingLucky = cgiBoolean("Lucky");
getDbAndGenome(cart, &db, &genome, oldVars);
if(!feelingLucky)
cartWebStart(cart, db, "%s BLAT Results", trackHubSkipHubName(organism));
/* Load user sequence and figure out if it is DNA or protein. */
if (sameWord(type, "DNA"))
{
seqList = faSeqListFromMemText(seqLetters, TRUE);
uToT(seqList);
isTx = FALSE;
}
else if (sameWord(type, "translated RNA") || sameWord(type, "translated DNA"))
{
seqList = faSeqListFromMemText(seqLetters, TRUE);
uToT(seqList);
isTx = TRUE;
isTxTx = TRUE;
txTxBoth = sameWord(type, "translated DNA");
}
else if (sameWord(type, "protein"))
{
seqList = faSeqListFromMemText(seqLetters, FALSE);
isTx = TRUE;
qIsProt = TRUE;
}
else
{
seqList = faSeqListFromMemTextRaw(seqLetters);
isTx = !seqIsDna(seqList);
if (!isTx)
{
for (seq = seqList; seq != NULL; seq = seq->next)
{
seq->size = dnaFilteredSize(seq->dna);
dnaFilter(seq->dna, seq->dna);
toLowerN(seq->dna, seq->size);
subChar(seq->dna, 'u', 't');
}
}
else
{
for (seq = seqList; seq != NULL; seq = seq->next)
{
seq->size = aaFilteredSize(seq->dna);
aaFilter(seq->dna, seq->dna);
toUpperN(seq->dna, seq->size);
}
qIsProt = TRUE;
}
}
if (seqList != NULL && seqList->name[0] == 0)
{
freeMem(seqList->name);
seqList->name = cloneString("YourSeq");
}
trimUniq(seqList);
/* If feeling lucky only do the first on. */
if(feelingLucky && seqList != NULL)
{
seqList->next = NULL;
}
/* Figure out size allowed. */
maxSingleSize = (isTx ? 10000 : 75000);
maxTotalSize = maxSingleSize * 2.5;
#ifdef LOWELAB
maxSeqCount = 200;
#else
maxSeqCount = 25;
#endif
/* Create temporary file to store sequence. */
trashDirFile(&faTn, "hgSs", "hgSs", ".fa");
faWriteAll(faTn.forCgi, seqList);
/* Create a temporary .psl file with the alignments against genome. */
trashDirFile(&pslTn, "hgSs", "hgSs", ".pslx");
f = mustOpen(pslTn.forCgi, "w");
gvo = gfOutputPsl(0, qIsProt, FALSE, f, FALSE, TRUE);
serve = findServer(db, isTx);
/* Write header for extended (possibly protein) psl file. */
if (isTx)
{
if (isTxTx)
{
qType = gftDnaX;
tType = gftDnaX;
}
else
{
qType = gftProt;
tType = gftDnaX;
}
}
else
{
qType = gftDna;
tType = gftDna;
}
pslxWriteHead(f, qType, tType);
if (qType == gftProt)
{
minSingleSize = 14;
}
else if (qType == gftDnaX)
{
minSingleSize = 36;
}
/* Loop through each sequence. */
for (seq = seqList; seq != NULL; seq = seq->next)
{
printf(" "); fflush(stdout); /* prevent apache cgi timeout by outputting something */
oneSize = realSeqSize(seq, !isTx);
if ((seqCount&1) == 0) // Call bot delay every 2nd time starting with first time
hgBotDelay();
if (++seqCount > maxSeqCount)
{
warn("More than 25 input sequences, stopping at %s.",
seq->name);
break;
}
if (oneSize > maxSingleSize)
{
warn("Sequence %s is %d letters long (max is %d), skipping",
seq->name, oneSize, maxSingleSize);
continue;
}
if (oneSize < minSingleSize)
{
warn("Warning: Sequence %s is only %d letters long (%d is the recommended minimum)",
seq->name, oneSize, minSingleSize);
// we could use "continue;" here to actually enforce skipping,
// but let's give the short sequence a chance, it might work.
// minimum possible length = tileSize+stepSize, so mpl=16 for dna stepSize=5, mpl=10 for protein.
if (qIsProt && oneSize < 1) // protein does not tolerate oneSize==0
continue;
}
totalSize += oneSize;
if (totalSize > maxTotalSize)
{
warn("Sequence %s would take us over the %d letter limit, stopping here.",
seq->name, maxTotalSize);
break;
}
conn = gfConnect(serve->host, serve->port);
if (isTx)
{
gvo->reportTargetStrand = TRUE;
if (isTxTx)
{
gfAlignTransTrans(&conn, serve->nibDir, seq, FALSE, 5,
tFileCache, gvo, !txTxBoth);
if (txTxBoth)
{
reverseComplement(seq->dna, seq->size);
conn = gfConnect(serve->host, serve->port);
gfAlignTransTrans(&conn, serve->nibDir, seq, TRUE, 5,
tFileCache, gvo, FALSE);
}
}
else
{
gfAlignTrans(&conn, serve->nibDir, seq, 5, tFileCache, gvo);
}
}
else
{
gfAlignStrand(&conn, serve->nibDir, seq, FALSE, minMatchShown, tFileCache, gvo);
reverseComplement(seq->dna, seq->size);
conn = gfConnect(serve->host, serve->port);
gfAlignStrand(&conn, serve->nibDir, seq, TRUE, minMatchShown, tFileCache, gvo);
}
gfOutputQuery(gvo, f);
}
carefulClose(&f);
showAliPlaces(pslTn.forCgi, faTn.forCgi, serve->db, qType, tType,
organism, feelingLucky);
if(!feelingLucky)
cartWebEnd();
gfFileCacheFree(&tFileCache);
}
int hgSeqBed(char *db, struct hTableInfo *hti, struct bed *bedList)
/* Print out dna sequence from the given database of all items in bedList.
* hti describes the bed-compatibility level of bedList items.
* Returns number of FASTA records printed out. */
{
struct bed *bedItem;
char itemName[128];
boolean isRc;
int count;
unsigned *starts = NULL;
unsigned *sizes = NULL;
boolean *exonFlags = NULL;
boolean *cdsFlags = NULL;
int i, rowCount, totalCount;
boolean promoter = cgiBoolean("hgSeq.promoter");
boolean intron = cgiBoolean("hgSeq.intron");
boolean utrExon5 = cgiBoolean("hgSeq.utrExon5");
boolean utrIntron5 = utrExon5 && intron;
boolean cdsExon = cgiBoolean("hgSeq.cdsExon");
boolean cdsIntron = cdsExon && intron;
boolean utrExon3 = cgiBoolean("hgSeq.utrExon3");
boolean utrIntron3 = utrExon3 && intron;
boolean downstream = cgiBoolean("hgSeq.downstream");
int promoterSize = cgiOptionalInt("hgSeq.promoterSize", 0);
int downstreamSize = cgiOptionalInt("hgSeq.downstreamSize", 0);
char *granularity = cgiOptionalString("hgSeq.granularity");
boolean concatRegions = granularity && sameString("gene", granularity);
boolean concatAdjacent = (cgiBooleanDefined("hgSeq.splitCDSUTR") &&
(! cgiBoolean("hgSeq.splitCDSUTR")));
boolean isCDS, doIntron;
boolean canDoUTR, canDoIntrons;
/* catch a special case: introns selected, but no exons -> include all introns
* instead of qualifying intron with exon flags. */
if (intron && !(utrExon5 || cdsExon || utrExon3))
{
utrIntron5 = cdsIntron = utrIntron3 = TRUE;
}
canDoUTR = hti->hasCDS;
canDoIntrons = hti->hasBlocks;
rowCount = totalCount = 0;
for (bedItem = bedList; bedItem != NULL; bedItem = bedItem->next)
{
if (bedItem->blockCount == 0) /* An intersection may have made hti unreliable. */
canDoIntrons = FALSE;
rowCount++;
int chromSize = hgSeqChromSize(db, bedItem->chrom);
// bed: translate relative starts to absolute starts
for (i=0; i < bedItem->blockCount; i++)
{
bedItem->chromStarts[i] += bedItem->chromStart;
}
isRc = (bedItem->strand[0] == '-');
// here's the max # of feature regions:
if (canDoIntrons)
count = 4 + (2 * bedItem->blockCount);
else
count = 5;
maxStartsOffset = count-1;
starts = needMem(sizeof(unsigned) * count);
sizes = needMem(sizeof(unsigned) * count);
exonFlags = needMem(sizeof(boolean) * count);
cdsFlags = needMem(sizeof(boolean) * count);
// build up a list of selected regions
count = 0;
if (!isRc && promoter && (promoterSize > 0))
{
addFeature(&count, starts, sizes, exonFlags, cdsFlags,
(bedItem->chromStart - promoterSize), promoterSize,
FALSE, FALSE, chromSize);
}
else if (isRc && downstream && (downstreamSize > 0))
{
addFeature(&count, starts, sizes, exonFlags, cdsFlags,
(bedItem->chromStart - downstreamSize), downstreamSize,
FALSE, FALSE, chromSize);
}
if (canDoIntrons && canDoUTR)
{
for (i=0; i < bedItem->blockCount; i++)
{
if ((bedItem->chromStarts[i] + bedItem->blockSizes[i]) <=
bedItem->thickStart)
{
if ((!isRc && utrExon5) || (isRc && utrExon3))
{
addFeature(&count, starts, sizes, exonFlags, cdsFlags,
bedItem->chromStarts[i], bedItem->blockSizes[i],
TRUE, FALSE, chromSize);
}
if (((!isRc && utrIntron5) || (isRc && utrIntron3)) &&
(i < bedItem->blockCount - 1))
{
addFeature(&count, starts, sizes, exonFlags, cdsFlags,
(bedItem->chromStarts[i] +
bedItem->blockSizes[i]),
(bedItem->chromStarts[i+1] -
bedItem->chromStarts[i] -
bedItem->blockSizes[i]),
FALSE, FALSE, chromSize);
}
}
else if (bedItem->chromStarts[i] < bedItem->thickEnd)
{
if ((bedItem->chromStarts[i] < bedItem->thickStart) &&
((bedItem->chromStarts[i] + bedItem->blockSizes[i]) >
bedItem->thickEnd))
{
if ((!isRc && utrExon5) || (isRc && utrExon3))
{
addFeature(&count, starts, sizes, exonFlags, cdsFlags,
bedItem->chromStarts[i],
(bedItem->thickStart -
bedItem->chromStarts[i]),
TRUE, FALSE, chromSize);
}
if (cdsExon)
{
addFeature(&count, starts, sizes, exonFlags, cdsFlags,
bedItem->thickStart,
(bedItem->thickEnd - bedItem->thickStart),
TRUE, TRUE, chromSize);
}
if ((!isRc && utrExon3) || (isRc && utrExon5))
{
addFeature(&count, starts, sizes, exonFlags, cdsFlags,
bedItem->thickEnd,
(bedItem->chromStarts[i] +
bedItem->blockSizes[i] -
bedItem->thickEnd),
TRUE, FALSE, chromSize);
}
}
else if (bedItem->chromStarts[i] < bedItem->thickStart)
{
if ((!isRc && utrExon5) || (isRc && utrExon3))
{
addFeature(&count, starts, sizes, exonFlags, cdsFlags,
bedItem->chromStarts[i],
(bedItem->thickStart -
bedItem->chromStarts[i]),
TRUE, FALSE, chromSize);
}
if (cdsExon)
{
addFeature(&count, starts, sizes, exonFlags, cdsFlags,
bedItem->thickStart,
(bedItem->chromStarts[i] +
bedItem->blockSizes[i] -
bedItem->thickStart),
TRUE, TRUE, chromSize);
}
}
else if ((bedItem->chromStarts[i] + bedItem->blockSizes[i]) >
bedItem->thickEnd)
{
if (cdsExon)
{
addFeature(&count, starts, sizes, exonFlags, cdsFlags,
bedItem->chromStarts[i],
(bedItem->thickEnd -
bedItem->chromStarts[i]),
TRUE, TRUE, chromSize);
}
if ((!isRc && utrExon3) || (isRc && utrExon5))
{
addFeature(&count, starts, sizes, exonFlags, cdsFlags,
bedItem->thickEnd,
(bedItem->chromStarts[i] +
bedItem->blockSizes[i] -
bedItem->thickEnd),
TRUE, FALSE, chromSize);
}
}
else if (cdsExon)
{
addFeature(&count, starts, sizes, exonFlags, cdsFlags,
bedItem->chromStarts[i], bedItem->blockSizes[i],
TRUE, TRUE, chromSize);
}
isCDS = ! ((bedItem->chromStarts[i] + bedItem->blockSizes[i]) >
bedItem->thickEnd);
doIntron = (isCDS ? cdsIntron :
((!isRc) ? utrIntron3 : utrIntron5));
if (doIntron && (i < bedItem->blockCount - 1))
{
addFeature(&count, starts, sizes, exonFlags, cdsFlags,
(bedItem->chromStarts[i] +
bedItem->blockSizes[i]),
(bedItem->chromStarts[i+1] -
bedItem->chromStarts[i] -
bedItem->blockSizes[i]),
FALSE, isCDS, chromSize);
}
}
else
{
if ((!isRc && utrExon3) || (isRc && utrExon5))
{
addFeature(&count, starts, sizes, exonFlags, cdsFlags,
bedItem->chromStarts[i], bedItem->blockSizes[i],
TRUE, FALSE, chromSize);
}
if (((!isRc && utrIntron3) || (isRc && utrIntron5)) &&
(i < bedItem->blockCount - 1))
{
addFeature(&count, starts, sizes, exonFlags, cdsFlags,
(bedItem->chromStarts[i] +
bedItem->blockSizes[i]),
(bedItem->chromStarts[i+1] -
bedItem->chromStarts[i] -
bedItem->blockSizes[i]),
FALSE, FALSE, chromSize);
}
}
}
}
else if (canDoIntrons)
{
for (i=0; i < bedItem->blockCount; i++)
{
if (cdsExon)
{
addFeature(&count, starts, sizes, exonFlags, cdsFlags,
bedItem->chromStarts[i], bedItem->blockSizes[i],
TRUE, FALSE, chromSize);
}
if (cdsIntron && (i < bedItem->blockCount - 1))
{
addFeature(&count, starts, sizes, exonFlags, cdsFlags,
(bedItem->chromStarts[i] + bedItem->blockSizes[i]),
(bedItem->chromStarts[i+1] -
bedItem->chromStarts[i] -
bedItem->blockSizes[i]),
FALSE, FALSE, chromSize);
}
}
}
else if (canDoUTR)
{
if (bedItem->thickStart == 0 && bedItem->thickEnd == 0)
bedItem->thickStart = bedItem->thickEnd = bedItem->chromStart;
if ((!isRc && utrExon5) || (isRc && utrExon3))
{
addFeature(&count, starts, sizes, exonFlags, cdsFlags,
bedItem->chromStart,
(bedItem->thickStart - bedItem->chromStart),
TRUE, FALSE, chromSize);
}
if (cdsExon)
{
addFeature(&count, starts, sizes, exonFlags, cdsFlags,
bedItem->thickStart,
(bedItem->thickEnd - bedItem->thickStart),
TRUE, TRUE, chromSize);
}
if ((!isRc && utrExon3) || (isRc && utrExon5))
{
addFeature(&count, starts, sizes, exonFlags, cdsFlags,
bedItem->thickEnd,
(bedItem->chromEnd - bedItem->thickEnd),
TRUE, FALSE, chromSize);
}
}
else
{
addFeature(&count, starts, sizes, exonFlags, cdsFlags,
bedItem->chromStart,
(bedItem->chromEnd - bedItem->chromStart),
TRUE, FALSE, chromSize);
}
if (!isRc && downstream && (downstreamSize > 0))
{
addFeature(&count, starts, sizes, exonFlags, cdsFlags,
bedItem->chromEnd, downstreamSize, FALSE, FALSE, chromSize);
}
else if (isRc && promoter && (promoterSize > 0))
{
addFeature(&count, starts, sizes, exonFlags, cdsFlags,
bedItem->chromEnd, promoterSize, FALSE, FALSE, chromSize);
}
snprintf(itemName, sizeof(itemName), "%s_%s", hti->rootName, bedItem->name);
hgSeqRegionsAdjDb(db, bedItem->chrom, chromSize, bedItem->strand[0], itemName,
concatRegions, concatAdjacent,
count, starts, sizes, exonFlags, cdsFlags);
totalCount += count;
freeMem(starts);
freeMem(sizes);
freeMem(exonFlags);
freeMem(cdsFlags);
}
return totalCount;
}
void doRegressionPlot(struct dyString *script, char *skipPset,
char *incTable, char *skipTable, char *geneTable)
/* Put up a regression plot. */
{
struct dMatrix *skip = NULL, *inc = NULL, *gene = NULL;
char query[256];
int i = 0;
struct tempName regPlot;
double thresh = .75;
if(cgiBoolean("allPoints"))
thresh = -1;
if(cgiBoolean("pdf"))
makeTempName(®Plot, "sp", ".pdf");
else
makeTempName(®Plot, "sp", ".png");
touchBlank(regPlot.forCgi);
sqlSafef(query, sizeof(query), "select * from %s where name like '%%%s%%';",
incTable, skipPset);
inc = dataFromTable(incTable, query);
sqlSafef(query, sizeof(query), "select * from %s where name like '%%%s%%';",
skipTable, skipPset);
skip = dataFromTable(skipTable, query);
sqlSafef(query, sizeof(query), "select * from %s where name like '%%%s%%';",
geneTable, skipPset);
gene = dataFromTable(geneTable, query);
initRegPlotOutput(script, regPlot.forCgi);
dyStringPrintf(script, "incDat = c(");
for(i = 0; i< inc->colCount; i++)
dyStringPrintf(script, "%.4f,", inc->matrix[0][i]);
dyStringPrintf(script, ");\n");
dyStringPrintf(script, "skipDat = c(");
for(i = 0; i< skip->colCount; i++)
dyStringPrintf(script, "%.4f,", skip->matrix[0][i]);
dyStringPrintf(script, ");\n");
dyStringPrintf(script, "geneDat = c(");
for(i = 0; i< gene->colCount; i++)
dyStringPrintf(script, "%.4f,", gene->matrix[0][i]);
dyStringPrintf(script, ");\n");
dyStringPrintf(script, "expressed = geneDat > %.4f;\n", thresh);
dyStringPrintf(script, abbv);
if(cgiBoolean("muscle"))
{
dyStringPrintf(script, isMuscle);
dyStringPrintf(script, plotRegression, altEvent->geneName, "Muscle", "Muscle");
}
else
{
dyStringPrintf(script, isBrain);
dyStringPrintf(script, plotRegression, altEvent->geneName, "Brain", "Brain");
}
closePlotOutput(script);
makePlotLink("Include vs. Skip", regPlot.forCgi);
dyStringPrintf(html, "<table width=600><tr><td>\n");
dyStringPrintf(html, "Tissues for which the gene expression was too low to be considered are in lighter colors.<br><br>\n");
dyStringPrintf(html, "%s\n", key);
dyStringPrintf(html, "</td></tr></table><br>\n");
//dyStringPrintf(html, "<img src='%s'><br>\n", regPlot.forCgi);
}