void doParDetails(struct trackDb *tdb, char *name)
/* show details of a PAR item. */
{
// load entire PAR table (t's tiny) and partition
struct bed *pars = loadParTable(tdb);
if (slCount(pars) & 1)
errAbort("par items not paired in %s", tdb->table);
struct bed *clickedPar = getClickedPar(name, &pars);
struct bed *homPar = getHomologousPar(clickedPar, &pars);
slSort(&pars, parCmp);
cartWebStart(cart, database, "Pseudoautosomal regions");
webPrintLinkTableStart();
// header
webPrintLabelCell("");
webPrintLabelCell("Selected PAR");
webPrintLabelCell("Homologous PAR");
// selected
webPrintLinkTableNewRow();
printHomPairRow(clickedPar, homPar);
if (pars != NULL)
printOtherPars(clickedPar, pars);
webPrintLinkTableEnd();
printTrackHtml(tdb);
webEnd();
bedFreeList(&pars);
bedFree(&clickedPar);
bedFree(&homPar);
}
void doTriangle(struct trackDb *tdb, char *item, char *motifTable)
/* Display detailed info on a regulatory triangle item. */
{
int start = cartInt(cart, "o");
struct dnaSeq *seq = NULL;
struct dnaMotif *motif = loadDnaMotif(item, motifTable);
char *table = tdb->table;
int rowOffset = hOffsetPastBin(database, seqName, table);
char query[256];
struct sqlResult *sr;
char **row;
struct bed *hit = NULL;
struct sqlConnection *conn = hAllocConn(database);
cartWebStart(cart, database, "Regulatory Motif Info");
genericBedClick(conn, tdb, item, start, 6);
sqlSafef(query, sizeof query,
"select * from %s where name = '%s' and chrom = '%s' and chromStart = %d",
table, item, seqName, start);
sr = sqlGetResult(conn, query);
row = sqlNextRow(sr);
if (row != NULL)
hit = bedLoadN(row + rowOffset, 6);
sqlFreeResult(&sr);
if (hit != NULL)
{
seq = hDnaFromSeq(database, hit->chrom, hit->chromStart, hit->chromEnd, dnaLower);
if (hit->strand[0] == '-')
reverseComplement(seq->dna, seq->size);
}
motifHitSection(seq, motif);
printTrackHtml(tdb);
}
void doVcfDetailsCore(struct trackDb *tdb, char *fileOrUrl, boolean isTabix)
/* Show item details using fileOrUrl. */
{
genericHeader(tdb, NULL);
int start = cartInt(cart, "o");
int end = cartInt(cart, "t");
int vcfMaxErr = -1;
struct vcfFile *vcff = NULL;
/* protect against temporary network or parsing error */
struct errCatch *errCatch = errCatchNew();
if (errCatchStart(errCatch))
{
if (isTabix)
vcff = vcfTabixFileMayOpen(fileOrUrl, seqName, start, end, vcfMaxErr, -1);
else
vcff = vcfFileMayOpen(fileOrUrl, seqName, start, end, vcfMaxErr, -1, TRUE);
}
errCatchEnd(errCatch);
if (errCatch->gotError)
{
if (isNotEmpty(errCatch->message->string))
warn("%s", errCatch->message->string);
}
errCatchFree(&errCatch);
if (vcff != NULL)
{
struct vcfRecord *rec;
for (rec = vcff->records; rec != NULL; rec = rec->next)
if (rec->chromStart == start && rec->chromEnd == end) // in pgSnp mode, don't get name
vcfRecordDetails(tdb, rec);
}
else
printf("Sorry, unable to open %s<BR>\n", fileOrUrl);
printTrackHtml(tdb);
}
void doCcdsGene(struct trackDb *tdb, char *ccdsId)
/* Process click on a CCDS gene. */
{
struct sqlConnection *conn = hAllocConn(database);
struct ccdsInfo *rsCcds = ccdsInfoSelectByCcds(conn, ccdsId, ccdsInfoNcbi);
struct ccdsInfo *vegaCcds = ccdsInfoSelectByCcds(conn, ccdsId, ccdsInfoVega);
struct ccdsInfo *ensCcds = ccdsInfoSelectByCcds(conn, ccdsId, ccdsInfoEnsembl);
if (rsCcds == NULL)
errAbort("database inconsistency: no NCBI ccdsInfo entries found for %s", ccdsId);
if ((vegaCcds == NULL) && (ensCcds == NULL))
errAbort("database inconsistency: no Hinxton ccdsInfo entries found for %s", ccdsId);
ccdsInfoMRnaSort(&rsCcds);
ccdsInfoMRnaSort(&vegaCcds);
ccdsInfoMRnaSort(&ensCcds);
cartWebStart(cart, database, "CCDS Gene");
printf("<H2>Consensus CDS Gene %s</H2>\n", ccdsId);
writeBasicInfoHtml(conn, ccdsId, rsCcds, vegaCcds, ensCcds);
writeLinksHtml(conn, ccdsId, rsCcds, vegaCcds, ensCcds);
writePublicNotesHtml(conn, ccdsId);
writeRefSeqSummaryHtml(conn, ccdsId, rsCcds);
htmlHorizontalLine();
printTrackHtml(tdb);
ccdsInfoFreeList(&rsCcds);
ccdsInfoFreeList(&vegaCcds);
ccdsInfoFreeList(&ensCcds);
hFreeConn(&conn);
}
void doHgdpGeo(struct trackDb *tdb, char *item)
/* Show details page for HGDP SNP with population allele frequencies
* plotted on a world map. */
{
struct sqlConnection *conn = hAllocConn(database);
char query[512];
struct sqlResult *sr;
char **row;
int start = cartInt(cart, "o");
genericHeader(tdb, item);
int hasBin=1;
sqlSafef(query, sizeof(query),
"select * from %s where name = '%s' and chrom = '%s' and chromStart = %d",
tdb->table, item, seqName, start);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) == NULL)
errAbort("doHgdpGeo: no match in %s for %s at %s:%d", tdb->table, item, seqName, start);
struct hgdpGeo *geo = hgdpGeoLoad(row+hasBin);
sqlFreeResult(&sr);
printCustomUrl(tdb, item, TRUE);
bedPrintPos((struct bed *)geo, 4, tdb);
printf("<B>Ancestral Allele:</B> %c<BR>\n", geo->ancestralAllele);
printf("<B>Derived Allele:</B> %c<BR>\n", geo->derivedAllele);
printOtherSnpMappings(tdb->table, item, start, conn, hasBin);
printf("<BR>\n");
printf("<TABLE><TR><TD>\n");
hgdpGeoFreqTable(geo);
printf("</TD><TD valign=top>\n");
hgdpGeoImg(geo);
printf("</TD></TR></TABLE>\n");
printTrackHtml(tdb);
hFreeConn(&conn);
}
void doH1n1Gene(struct trackDb *tdb, char *item)
/* Show details page for H1N1 Genes and Regions annotations track. */
{
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr;
char query[256];
char **row;
char *chrom, *chromStart, *chromEnd;
char *gene=NULL;
genericHeader(tdb, item);
gene = item;
printf("<B>Gene: </B> %s\n<BR>", gene);
sqlSafef(query, sizeof query, "select chrom, chromStart, chromEnd from h1n1Gene where name='%s';", gene);
sr = sqlMustGetResult(conn, query);
row = sqlNextRow(sr);
if (row != NULL)
{
chrom = row[0];
chromStart = row[1];
chromEnd = row[2];
printPosOnChrom(chrom, atoi(chromStart), atoi(chromEnd), NULL, FALSE, item);
}
sqlFreeResult(&sr);
hFreeConn(&conn);
htmlHorizontalLine();
printf("<H3>Protein Structure Analysis and Prediction</H3>");
printf("<B>3D Structure Prediction of consensus sequence (with variations of all selected sequences highlighted):");
printf("<BR>PDB file:</B> ");
char pdbUrl[PATH_LEN];
safef(pdbUrl, sizeof(pdbUrl), "%s/%s/decoys/%s.try1-opt3.pdb.gz", getH1n1StructUrl(), item, item);
// Modeller stuff
char modelPdbUrl[PATH_LEN];
if (getH1n1Model(gene, modelPdbUrl))
{
char *selectFile = cartOptionalString(cart, gisaidAaSeqList);
struct tempName imageFile, chimeraScript, chimerax;
mkH1n1StructData(gene, selectFile, NULL, &imageFile, &chimeraScript);
mkChimerax(gene, modelPdbUrl, chimeraScript.forCgi, &chimerax);
printf("<A HREF=\"%s\" TARGET=_blank>%s</A>, view with <A HREF=\"%s\">Chimera</A><BR>\n",
modelPdbUrl, gene, chimerax.forHtml);
printf("<TABLE>\n");
printf("<TR>\n");
printf("<TD ALIGN=\"center\"><img src=\"%s\"></TD>", imageFile.forHtml);
printf("</TR>\n");
printf("</TABLE>\n");
}
htmlHorizontalLine();
printTrackHtml(tdb);
sqlFreeResult(&sr);
hFreeConn(&conn);
}
void doPeakClusters(struct trackDb *tdb, char *item)
/* Display detailed info about a cluster of DNase peaks from other tracks. */
{
int start = cartInt(cart, "o");
char *table = tdb->table;
int rowOffset = hOffsetPastBin(database, seqName, table);
char query[256];
struct sqlResult *sr;
char **row;
struct bed *cluster = NULL;
struct sqlConnection *conn = hAllocConn(database);
cartWebStart(cart, database, "%s item details", tdb->shortLabel);
sqlSafef(query, sizeof(query),
"select * from %s where name = '%s' and chrom = '%s' and chromStart = %d",
table, item, seqName, start);
sr = sqlGetResult(conn, query);
row = sqlNextRow(sr);
if (row != NULL)
cluster = bedLoadN(row+rowOffset, 5);
sqlFreeResult(&sr);
if (cluster != NULL)
{
/* Get list of subgroups to display */
char *inputTableFieldDisplay = trackDbSetting(tdb, "inputTableFieldDisplay");
if (inputTableFieldDisplay != NULL)
{
struct slName *fieldList = stringToSlNames(inputTableFieldDisplay);
char *inputTrackTable = trackDbRequiredSetting(tdb, "inputTrackTable");
/* Print out some information about the cluster overall. */
printf("<B>Items in Cluster:</B> %s of %d<BR>\n", cluster->name,
sqlRowCount(conn, sqlCheckIdentifier(inputTrackTable)));
printf("<B>Cluster Score (out of 1000):</B> %d<BR>\n", cluster->score);
printPos(cluster->chrom, cluster->chromStart, cluster->chromEnd, NULL, TRUE, NULL);
/* In a new section put up list of hits. */
webNewSection("List of Items in Cluster");
webPrintLinkTableStart();
printClusterTableHeader(fieldList, FALSE, FALSE, TRUE);
printPeakClusterInfo(tdb, cart, conn, inputTrackTable, fieldList, cluster);
}
else
errAbort("Missing required trackDb setting %s for track %s",
"inputTableFieldDisplay", tdb->track);
webPrintLinkTableEnd();
}
printf("<A HREF=\"%s&g=htcListItemsAssayed&table=%s\" TARGET_blank>", hgcPathAndSettings(),
tdb->track);
printf("List all items assayed");
printf("</A><BR>\n");
webNewSection("Track Description");
printTrackHtml(tdb);
hFreeConn(&conn);
}
void doTransRegCode(struct trackDb *tdb, char *item, char *motifTable)
/* Display detailed info on a transcriptional regulatory code item. */
{
struct dnaMotif *motif = loadDnaMotif(item, motifTable);
int start = cartInt(cart, "o");
struct dnaSeq *seq = NULL;
char *table = tdb->table;
int rowOffset = hOffsetPastBin(database, seqName, table);
char query[256];
struct sqlResult *sr;
char **row;
struct sqlConnection *conn = hAllocConn(database);
struct transRegCode *trc = NULL;
cartWebStart(cart, database, "Regulatory Code Info");
sqlSafef(query, sizeof query,
"select * from %s where name = '%s' and chrom = '%s' and chromStart = %d",
table, item, seqName, start);
sr = sqlGetResult(conn, query);
row = sqlNextRow(sr);
if (row != NULL)
trc = transRegCodeLoad(row+rowOffset);
sqlFreeResult(&sr);
if (trc != NULL)
{
char strand[2];
seq = hDnaFromSeq(database, trc->chrom, trc->chromStart, trc->chromEnd, dnaLower);
if (seq->size != motif->columnCount)
{
printf("WARNING: seq->size = %d, motif->colCount=%d<BR>\n",
seq->size, motif->columnCount);
strand[0] = '?';
seq = NULL;
}
else
{
strand[0] = dnaMotifBestStrand(motif, seq->dna);
if (strand[0] == '-')
reverseComplement(seq->dna, seq->size);
}
strand[1] = 0;
printf("<B>Name:</B> ");
sacCerHgGeneLinkName(conn, trc->name);
printf("<BR>\n");
printf("<B>ChIP-chip Evidence:</B> %s<BR>\n", trc->chipEvidence);
printf("<B>Species conserved in:</B> %d of 2<BR>\n", trc->consSpecies);
if (seq != NULL)
printf("<B>Bit Score of Motif Hit:</B> %4.2f<BR>\n",
dnaMotifBitScore(motif, seq->dna));
printf("<B>Item score:</B> %d<BR>\n", trc->score);
printPosOnChrom(trc->chrom, trc->chromStart, trc->chromEnd, strand, TRUE, trc->name);
}
motifHitSection(seq, motif);
printTrackHtml(tdb);
}
void doFlyreg(struct trackDb *tdb, char *item)
/* flyreg.org: Drosophila DNase I Footprint db. */
{
struct dyString *query = newDyString(256);
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr = NULL;
char **row;
int start = cartInt(cart, "o");
int end = cartInt(cart, "t");
char fullTable[HDB_MAX_TABLE_STRING];
boolean hasBin = FALSE;
char *motifTable = "flyregMotif";
struct dnaMotif *motif = NULL;
boolean isVersion2 = sameString(tdb->table, "flyreg2");
genericHeader(tdb, item);
if (!hFindSplitTable(database, seqName, tdb->table, fullTable, sizeof fullTable, &hasBin))
errAbort("track %s not found", tdb->table);
sqlDyStringPrintf(query, "select * from %s where chrom = '%s' and ",
fullTable, seqName);
hAddBinToQuery(start, end, query);
sqlDyStringPrintf(query, "chromStart = %d and name = '%s'", start, item);
sr = sqlGetResult(conn, query->string);
if ((row = sqlNextRow(sr)) != NULL)
{
struct flyreg2 fr;
if (isVersion2)
flyreg2StaticLoad(row+hasBin, &fr);
else
flyregStaticLoad(row+hasBin, (struct flyreg *)(&fr));
printf("<B>Factor:</B> %s<BR>\n", fr.name);
printf("<B>Target:</B> %s<BR>\n", fr.target);
if (isVersion2)
printf("<B>Footprint ID:</B> %06d<BR>\n", fr.fpid);
printf("<B>PubMed ID:</B> <A HREF=\"");
printEntrezPubMedUidUrl(stdout, fr.pmid);
printf("\" TARGET=_BLANK>%d</A><BR>\n", fr.pmid);
bedPrintPos((struct bed *)(&fr), 3, tdb);
if (hTableExists(database, motifTable))
{
motif = loadDnaMotif(item, motifTable);
if (motif != NULL)
motifHitSection(NULL, motif);
}
}
else
errAbort("query returned no results: \"%s\"", query->string);
dyStringFree(&query);
sqlFreeResult(&sr);
hFreeConn(&conn);
if (motif != NULL)
webNewSection("%s",tdb->longLabel);
printTrackHtml(tdb);
}
void retroClickHandler(struct trackDb *tdb, char *mappedId)
/* Handle click on a transMap tracks */
{
struct sqlConnection *conn = hAllocConn(database);
struct mappingInfo *mi = mappingInfoNew(conn, tdb->table, mappedId);
struct psl *pslList = NULL;
char *table;
genericHeader(tdb, mappedId);
printf("<TABLE border=0>\n");
printf("<TR CLASS=\"transMapLayout\">\n");
printf("<TD COLSPAN=3>\n");
displaySrcGene(conn, mi);
printf("</TR>\n");
printf("<TR CLASS=\"transMapLayout\">\n");
printf("<TD>\n");
displayMappingInfo(conn, mi);
printf("<TD>\n");
#if 0
struct geneCheck *gc = displayGeneCheck(conn, &mti, mappedId);
printf("<TD>\n");
displayProtSim(conn, &mti, mappedId);
#endif
printf("</TR>\n");
#if 0
if (!sameString(gc->stat, "ok"))
{
printf("<TR CLASS=\"transMapLayout\">\n");
printf("<TD COLSPAN=3>\n");
displayGeneCheckDetails(conn, &mti, gc);
printf("</TR>\n");
}
#endif
printf("</TABLE>\n");
displayRetroDetails(conn, mi);
displayAligns(conn, mi);
pslList = getParentAligns(conn, mi, &table);
displayParentAligns(mi, pslList, table);
pslFreeList(&pslList);
printTrackHtml(tdb);
#if 0
geneCheckFree(&gc);
#endif
mappingInfoFree(&mi);
hFreeConn(&conn);
}
void doH1n1Seq(struct trackDb *tdb, char *item)
/* Show extra info for H1N1 Seq Annotations track. */
{
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr;
char query[256];
char **row;
char *geneSymbol=NULL;
genericHeader(tdb, item);
sqlSafef(query, sizeof query, "select seqId, geneSymbol, strain, islId from h1n1SeqXref where seqId = '%s'", item);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
{
char *seqId, *strain, *islId;
seqId = row[0];
geneSymbol = row[1];
strain = row[2];
islId = row[3];
printf("<B>Sequence ID: %s</B> <BR>", seqId);
printf("<B>Gene: %s</B> <BR>", geneSymbol);
printf("<B>Strain: %s</B> <BR>", strain);
printf("<B>Isolate: </B> ");
printf("<A HREF=\"../cgi-bin/gisaidSample?hgs_sample=%s&submit=Go\">%s</A>",
islId, islId);
}
htmlHorizontalLine();
//showSAM_h1n1(item);
showProtH1n1(item, geneSymbol);
htmlHorizontalLine();
printTrackHtml(tdb);
sqlFreeResult(&sr);
hFreeConn(&conn);
}
void showSchemaBigBed(char *table, struct trackDb *tdb)
/* Show schema on bigBed. */
{
/* Figure out bigBed file name and open it. Get contents for first chromosome as an example. */
struct sqlConnection *conn = NULL;
if (!trackHubDatabase(database))
conn = hAllocConn(database);
char *fileName = bigBedFileName(table, conn);
struct bbiFile *bbi = bigBedFileOpen(fileName);
struct bbiChromInfo *chromList = bbiChromList(bbi);
struct lm *lm = lmInit(0);
struct bigBedInterval *ivList = getNElements(bbi, chromList, lm, 10);
/* Get description of columns, making it up from BED records if need be. */
struct asObject *as = bigBedAsOrDefault(bbi);
hPrintf("<B>Database:</B> %s", database);
hPrintf(" <B>Primary Table:</B> %s<br>", table);
hPrintf("<B>Big Bed File:</B> %s", fileName);
if (bbi->version >= 2)
{
hPrintf("<BR><B>Item Count:</B> ");
printLongWithCommas(stdout, bigBedItemCount(bbi));
}
hPrintf("<BR>\n");
hPrintf("<B>Format description:</B> %s<BR>", as->comment);
/* Put up table that describes fields. */
hTableStart();
hPrintf("<TR><TH>field</TH>");
if (ivList != NULL)
hPrintf("<TH>example</TH>");
hPrintf("<TH>description</TH> ");
puts("</TR>\n");
struct asColumn *col;
int colCount = 0;
char *row[bbi->fieldCount];
char startBuf[16], endBuf[16];
if (ivList != NULL)
{
char *dupeRest = lmCloneString(lm, ivList->rest); /* Manage rest-stomping side-effect */
bigBedIntervalToRow(ivList, chromList->name, startBuf, endBuf, row, bbi->fieldCount);
ivList->rest = dupeRest;
}
for (col = as->columnList; col != NULL; col = col->next)
{
hPrintf("<TR><TD><TT>%s</TT></TD>", col->name);
if (ivList != NULL)
hPrintf("<TD>%s</TD>", row[colCount]);
hPrintf("<TD>%s</TD></TR>", col->comment);
++colCount;
}
/* If more fields than descriptions put up minimally helpful info (at least has example). */
for ( ; colCount < bbi->fieldCount; ++colCount)
{
hPrintf("<TR><TD><TT>column%d</TT></TD>", colCount+1);
if (ivList != NULL)
hPrintf("<TD>%s</TD>", row[colCount]);
hPrintf("<TD>n/a</TD></TR>\n");
}
hTableEnd();
if (ivList != NULL)
{
/* Put up another section with sample rows. */
webNewSection("Sample Rows");
hTableStart();
/* Print field names as column headers for example */
hPrintf("<TR>");
int colIx = 0;
for (col = as->columnList; col != NULL; col = col->next)
{
hPrintf("<TH>%s</TH>", col->name);
++colIx;
}
for (; colIx < colCount; ++colIx)
hPrintf("<TH>column%d</TH>", colIx+1);
hPrintf("</TR>\n");
/* Print sample lines. */
struct bigBedInterval *iv;
for (iv=ivList; iv != NULL; iv = iv->next)
{
bigBedIntervalToRow(iv, chromList->name, startBuf, endBuf, row, bbi->fieldCount);
hPrintf("<TR>");
for (colIx=0; colIx<colCount; ++colIx)
{
writeHtmlCell(row[colIx]);
}
hPrintf("</TR>\n");
}
hTableEnd();
}
printTrackHtml(tdb);
/* Clean up and go home. */
lmCleanup(&lm);
bbiFileClose(&bbi);
freeMem(fileName);
hFreeConn(&conn);
}
void showSchemaBam(char *table, struct trackDb *tdb)
/* Show schema on bam. */
{
struct sqlConnection *conn = NULL;
if (!trackHubDatabase(database))
conn = hAllocConn(database);
char *fileName = bamFileName(table, conn, NULL);
struct asObject *as = bamAsObj();
hPrintf("<B>Database:</B> %s", database);
hPrintf(" <B>Primary Table:</B> %s<br>", table);
hPrintf("<B>BAM File:</B> %s", fileName);
hPrintf("<BR>\n");
hPrintf("<B>Format description:</B> %s<BR>", as->comment);
hPrintf("See the <A HREF=\"%s\" target=_blank>SAM Format Specification</A> for more details<BR>\n",
"http://samtools.sourceforge.net/SAM1.pdf");
/* Put up table that describes fields. */
hTableStart();
hPrintf("<TR><TH>field</TH>");
hPrintf("<TH>description</TH> ");
puts("</TR>\n");
struct asColumn *col;
int colCount = 0;
for (col = as->columnList; col != NULL; col = col->next)
{
hPrintf("<TR><TD><TT>%s</TT></TD>", col->name);
hPrintf("<TD>%s</TD></TR>", col->comment);
++colCount;
}
hTableEnd();
/* Put up another section with sample rows. */
webNewSection("Sample Rows");
hTableStart();
/* Print field names as column headers for example */
hPrintf("<TR>");
int colIx = 0;
for (col = as->columnList; col != NULL; col = col->next)
{
hPrintf("<TH>%s</TH>", col->name);
++colIx;
}
hPrintf("</TR>\n");
/* Fetch sample rows. */
samfile_t *fh = bamOpen(fileName, NULL);
struct lm *lm = lmInit(0);
struct samAlignment *sam, *samList = bamReadNextSamAlignments(fh, 10, lm);
/* Print sample lines. */
char *row[SAMALIGNMENT_NUM_COLS];
char numBuf[BAM_NUM_BUF_SIZE];
for (sam=samList; sam != NULL; sam = sam->next)
{
samAlignmentToRow(sam, numBuf, row);
hPrintf("<TR>");
for (colIx=0; colIx<colCount; ++colIx)
{
hPrintf("<TD>");
xmlEscapeStringToFile(row[colIx], stdout);
hPrintf("</TD>");
}
hPrintf("</TR>\n");
}
hTableEnd();
printTrackHtml(tdb);
/* Clean up and go home. */
bamClose(&fh);
lmCleanup(&lm);
freeMem(fileName);
hFreeConn(&conn);
}
void showSchemaVcf(char *table, struct trackDb *tdb, boolean isTabix)
/* Show schema on vcf. */
{
struct sqlConnection *conn = hAllocConn(database);
char *fileName = vcfFileName(tdb, conn, table, hDefaultChrom(database));
struct asObject *as = vcfAsObj();
hPrintf("<B>Database:</B> %s", database);
hPrintf(" <B>Primary Table:</B> %s<br>", table);
hPrintf("<B>VCF File:</B> %s", fileName);
hPrintf("<BR>\n");
hPrintf("<B>Format description:</B> %s<BR>", as->comment);
hPrintf("See the <A HREF=\"%s\" target=_blank>Variant Call Format specification</A> for more details<BR>\n",
"http://www.1000genomes.org/wiki/analysis/vcf4.0");
/* Put up table that describes fields. */
hTableStart();
hPrintf("<TR><TH>field</TH>");
hPrintf("<TH>description</TH> ");
puts("</TR>\n");
struct asColumn *col;
int colCount = 0;
for (col = as->columnList; col != NULL; col = col->next)
{
hPrintf("<TR><TD><TT>%s</TT></TD>", col->name);
hPrintf("<TD>%s</TD></TR>", col->comment);
++colCount;
}
hTableEnd();
/* Put up another section with sample rows. */
webNewSection("Sample Rows");
hTableStart();
/* Fetch sample rows. */
struct lineFile *lf = isTabix ? lineFileTabixMayOpen(fileName, TRUE) :
lineFileMayOpen(fileName, TRUE);
if (lf == NULL)
noWarnAbort();
char *row[VCF_MAX_SCHEMA_COLS];
int i;
for (i = 0; i < 10; i++)
{
int colCount = lineFileChop(lf, row);
int colIx;
if (i == 0)
{
// Print field names as column headers, using colCount to compute genotype span
hPrintf("<TR>");
for (colIx = 0, col = as->columnList; col != NULL && colIx < colCount;
colIx++, col = col->next)
{
if (sameString("genotypes", col->name) && colCount > colIx+1)
hPrintf("<TH colspan=%d>%s</TH>", colCount - colIx, col->name);
else
hPrintf("<TH>%s</TH>", col->name);
}
hPrintf("</TR>\n");
}
hPrintf("<TR>");
for (colIx=0; colIx < colCount; ++colIx)
{
if (colCount > VCFDATALINE_NUM_COLS && colIx == colCount - 1)
hPrintf("<TD>...</TD>");
else
writeHtmlCell(row[colIx]);
}
hPrintf("</TR>\n");
}
hTableEnd();
printTrackHtml(tdb);
/* Clean up and go home. */
lineFileClose(&lf);
freeMem(fileName);
hFreeConn(&conn);
}
void doTransRegCodeProbe(struct trackDb *tdb, char *item,
char *codeTable, char *motifTable,
char *tfToConditionTable, char *conditionTable)
/* Display detailed info on a ChIP-chip probe from transRegCode experiments. */
{
char query[256];
struct sqlResult *sr;
char **row;
int rowOffset = hOffsetPastBin(database, seqName, tdb->table);
struct sqlConnection *conn = hAllocConn(database);
struct transRegCodeProbe *probe = NULL;
cartWebStart(cart, database, "ChIP-chip Probe Info");
sqlSafef(query, sizeof(query), "select * from %s where name = '%s'",
tdb->table, item);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
probe = transRegCodeProbeLoad(row+rowOffset);
sqlFreeResult(&sr);
if (probe != NULL)
{
struct tfData *tfList = NULL, *tf;
struct hash *tfHash = newHash(0);
struct transRegCode *trc;
int i;
/* Print basic info. */
printf("<B>Name:</B> %s<BR>\n", probe->name);
printPosOnChrom(probe->chrom, probe->chromStart, probe->chromEnd,
NULL, TRUE, probe->name);
/* Make up list of all transcriptionFactors. */
for (i=0; i<probe->tfCount; ++i)
{
/* Parse out factor and condition. */
char *tfName = probe->tfList[i];
char *condition = strchr(tfName, '_');
struct tfCond *cond;
if (condition != NULL)
*condition++ = 0;
else
condition = "n/a";
tf = hashFindVal(tfHash, tfName);
if (tf == NULL)
{
AllocVar(tf);
hashAddSaveName(tfHash, tfName, tf, &tf->name);
slAddHead(&tfList, tf);
}
AllocVar(cond);
cond->name = cloneString(condition);
cond->binding = probe->bindVals[i];
slAddHead(&tf->conditionList, cond);
}
slSort(&tfList, tfDataCmpName);
/* Fold in motif hits in region. */
if (sqlTableExists(conn, codeTable))
{
sr = hRangeQuery(conn, codeTable,
probe->chrom, probe->chromStart, probe->chromEnd,
"chipEvidence != 'none'", &rowOffset);
while ((row = sqlNextRow(sr)) != NULL)
{
trc = transRegCodeLoad(row+rowOffset);
tf = hashFindVal(tfHash, trc->name);
if (tf != NULL)
slAddTail(&tf->trcList, trc);
}
sqlFreeResult(&sr);
}
if (tfList == NULL)
printf("No significant immunoprecipitation.");
else
{
tfBindLevelSection(tfList, conn, motifTable, tfToConditionTable);
}
transRegCodeProbeFree(&probe);
growthConditionSection(conn, conditionTable);
}
printf("\n<HR>\n");
printTrackHtml(tdb);
hFreeConn(&conn);
}