void doMap(char *mapName)
/* Interpret click on map. */
{
FILE *f = mustOpen(mapName, "rb");
int x, y, width, height;
char *mapBac, *mouseBac;
char *repeatMask;
int mouseX, mouseY;
bits16 mt, contig;
int trim;
int qStart, qSize, tStart, tSize;
boolean ok;
/* Figure out where clicked from map file. */
mapReadHead(f, &width, &height, &mapBac, &trim, &repeatMask);
mouseX = cgiInt("clickMe.x");
mouseY = cgiInt("clickMe.y");
ok = mapScanForHit(f, mouseX, mouseY,
&mt, &x, &y, &width, &height,
&mouseBac, &contig, &qStart, &qSize, &tStart, &tSize);
if (!ok)
mt = mtNone;
fclose(f);
if (mt == mtNone)
{
bacTrack(mapBac, trim, repeatMask);
}
else if (mt == mtBlock)
{
showDetailedMatch(mouseBac, contig, qStart, qSize, tStart, tSize, repeatMask);
}
}
void doFuzzyFind()
/* Do fuzzy-finder alignment. */
{
char *bacAcc = cgiString("bacAcc");
char *repeatMask = cgiString("repeatMask");
int contig = cgiInt("contig");
int qStart = cgiInt("qStart");
int qSize = cgiInt("qSize");
int tStart = cgiInt("tStart");
int tSize = cgiInt("tSize");
showDetailedMatch(bacAcc, contig, qStart, qSize, tStart, tSize, repeatMask);
}
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]);
}
int main(int argc, char *argv[])
/* Process command line. */
{
struct hash *liftHash = NULL;
cgiSpoof(&argc, argv);
if (argc != 6)
usage();
if (cgiVarExists("spacing"))
chromInsertsSetDefaultGapSize(cgiInt("spacing"));
if (cgiVarExists("lift"))
liftHash = readLift(cgiString("lift"));
ctgToChromFa(argv[1], argv[2], argv[3], argv[4], argv[5], liftHash);
return 0;
}
void doMiddle()
/* Write HTML file to stdout. */
{
char *mapName;
if ((mapName = cgiOptionalString("map")) != NULL)
{
printf("<TT>\n");
doMap(mapName);
}
else if (cgiVarExists("contig"))
{
doFuzzyFind();
}
else
{
char *bacAcc = cgiString("bacAcc");
char *repeatMask = cgiString("repeatMask");
int trim = cgiInt("trim");
if (trim < 0)
trim = 0;
bacTrack(bacAcc, trim, repeatMask);
}
}
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");
}
int main(int argc, char *argv[])
{
long enteredMainTime = clock1000();
struct dyString *output = newDyString(10000);
setUdcCacheDir();
cgiSpoof(&argc, argv);
pushWarnHandler(htmlVaBadRequestAbort);
pushAbortHandler(htmlVaBadRequestAbort);
char *database = cgiString("db");
char *cmd = cgiString("cmd");
char *jsonp = cgiOptionalString("jsonp");
if (!hDbExists(database))
errAbort("Invalid database '%s'", database);
if (!strcmp(cmd, "defaultPos"))
{
dyStringPrintf(output, "{\"pos\": \"%s\"}", hDefaultPos(database));
}
else if (!strcmp(cmd, "metaDb"))
{
// Return list of values for given metaDb var
// e.g. http://genome.ucsc.edu/hgApi?db=hg18&cmd=metaDb&var=cell
struct sqlConnection *conn = hAllocConn(database);
boolean metaDbExists = sqlTableExists(conn, "metaDb");
if (metaDbExists)
{
char *var = cgiOptionalString("var");
if (!var)
errAbort("Missing var parameter");
boolean fileSearch = (cgiOptionalInt("fileSearch",0) == 1);
struct slPair *pairs = mdbValLabelSearch(conn, var, MDB_VAL_STD_TRUNCATION, FALSE,
!fileSearch, fileSearch);
struct slPair *pair;
dyStringPrintf(output, "[\n");
for (pair = pairs; pair != NULL; pair = pair->next)
{
if (pair != pairs)
dyStringPrintf(output, ",\n");
dyStringPrintf(output, "['%s','%s']", javaScriptLiteralEncode(mdbPairLabel(pair)),
javaScriptLiteralEncode(mdbPairVal(pair)));
}
dyStringPrintf(output, "\n]\n");
}
else
errAbort("Assembly does not support metaDb");
}
// TODO: move to lib since hgTracks and hgApi share
#define METADATA_VALUE_PREFIX "hgt_mdbVal"
else if (startsWith(METADATA_VALUE_PREFIX, cmd))
{
// Returns metaDb value control: drop down or free text, with or without help link.
// e.g. http://genome.ucsc.edu/hgApi?db=hg18&cmd=hgt_mdbVal3&var=cell
// TODO: Move guts to lib, so that hgTracks::searchTracks.c and hgApi.c can share
struct sqlConnection *conn = hAllocConn(database);
boolean metaDbExists = sqlTableExists(conn, "metaDb");
if (metaDbExists)
{
char *var = cgiOptionalString("var");
if (!var)
errAbort("Missing var parameter");
int ix = atoi(cmd+strlen(METADATA_VALUE_PREFIX)); // 1 based index
if (ix == 0) //
errAbort("Unsupported 'cmd' parameter");
enum cvSearchable searchBy = cvSearchMethod(var);
char name[128];
safef(name,sizeof name,"%s%i",METADATA_VALUE_PREFIX,ix);
if (searchBy == cvSearchBySingleSelect || searchBy == cvSearchByMultiSelect)
{
boolean fileSearch = (cgiOptionalInt("fileSearch",0) == 1);
struct slPair *pairs = mdbValLabelSearch(conn, var, MDB_VAL_STD_TRUNCATION, FALSE,
!fileSearch, fileSearch);
if (slCount(pairs) > 0)
{
char *dropDownHtml =
cgiMakeSelectDropList((searchBy == cvSearchByMultiSelect),
name, pairs, NULL, ANYLABEL, "mdbVal",
"style='min-width: 200px; font-size: .9em;' "
"onchange='findTracksMdbValChanged(this);'");
if (dropDownHtml)
{
dyStringAppend(output,dropDownHtml);
freeMem(dropDownHtml);
}
slPairFreeList(&pairs);
}
}
else if (searchBy == cvSearchByFreeText)
{
dyStringPrintf(output,"<input type='text' name='%s' value='' class='mdbVal freeText' "
"onchange='findTracksMdbValChanged(this);' style='max-width:310px; "
"width:310px; font-size:.9em;'>", name);
}
else if (searchBy == cvSearchByWildList)
{
dyStringPrintf(output,"<input type='text' name='%s' value='' class='mdbVal wildList' "
"title='enter comma separated list of values' "
"onchange='findTracksMdbValChanged(this);' style='max-width:310px; "
"width:310px; font-size:.9em;'>", name);
}
else if (searchBy == cvSearchByDateRange || searchBy == cvSearchByIntegerRange)
{
// TO BE IMPLEMENTED
}
else
errAbort("Metadata variable not searchable");
dyStringPrintf(output,"<span id='helpLink%i'> </span>",ix);
}
else
errAbort("Assembly does not support metaDb");
}
else if (!strcmp(cmd, "tableMetadata"))
{ // returns an html table with metadata for a given track
char *trackName = cgiOptionalString("track");
boolean showLonglabel = (NULL != cgiOptionalString("showLonglabel"));
boolean showShortLabel = (NULL != cgiOptionalString("showShortLabel"));
if (trackName != NULL)
{
// hTrackDbForTrackAndAncestors avoids overhead of getting whole track list!
struct trackDb *tdb = hTrackDbForTrackAndAncestors(database, trackName);
if (tdb != NULL)
{
char * html = metadataAsHtmlTable(database,tdb,showLonglabel,showShortLabel);
if (html)
{
dyStringAppend(output,html);
freeMem(html);
}
else
dyStringPrintf(output,"No metadata found for track %s.",trackName);
}
else
dyStringPrintf(output,"Track %s not found",trackName);
}
else
dyStringAppend(output,"No track variable found");
}
else if (sameString(cmd, "codonToPos") || sameString(cmd, "exonToPos"))
{
char query[256];
struct sqlResult *sr;
char **row;
struct genePred *gp;
char *name = cgiString("name");
char *table = cgiString("table");
int num = cgiInt("num");
struct sqlConnection *conn = hAllocConn(database);
sqlSafef(query, sizeof(query), "select name, chrom, strand, txStart, txEnd, cdsStart, cdsEnd, exonCount, exonStarts, exonEnds from %s where name = '%s'", table, name);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
{
gp = genePredLoad(row);
boolean found;
int start, end;
if (sameString(cmd, "codonToPos"))
found = codonToPos(gp, num, &start, &end);
else
found = exonToPos(gp, num, &start, &end);
if (found)
dyStringPrintf(output, "{\"pos\": \"%s:%d-%d\"}", gp->chrom, start + 1, end);
else
dyStringPrintf(output, "{\"error\": \"%d is an invalid %s for this gene\"}", num, sameString(cmd, "codonToPos") ? "codon" : "exon");
}
else
dyStringPrintf(output, "{\"error\": \"Couldn't find item: %s\"}", name);
sqlFreeResult(&sr);
hFreeConn(&conn);
}
else
{
warn("unknown cmd: %s",cmd);
errAbort("Unsupported 'cmd' parameter");
}
apiOut(dyStringContents(output), jsonp);
cgiExitTime("hgApi", enteredMainTime);
return 0;
}