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);
}
static void prMiscDiffHdr(unsigned miscDiffFlds)
/* print a header row for miscDiffs table */
{
webPrintLabelCell("mRNA start");
webPrintLabelCell("mRNA end");
if (miscDiffFlds & gbMiscDiffGene)
webPrintLabelCell("Gene");
if (miscDiffFlds & gbMiscDiffReplace)
webPrintLabelCell("Replace");
if (miscDiffFlds & gbMiscDiffNotes)
webPrintLabelCell("Notes");
}
void printIndex(struct section *sectionList)
/* Print index to section. */
{
int maxPerRow = 6, itemPos = 0;
int rowIx = 0;
struct section *section;
hPrintf("<BR>\n");
hPrintf("<BR>\n");
webPrintLinkTableStart();
webPrintLabelCell("Page Index");
itemPos += 1;
for (section=sectionList; section != NULL; section = section->next)
{
if (++itemPos > maxPerRow)
{
hPrintf("</TR><TR>");
itemPos = 1;
++rowIx;
}
webPrintLinkCellStart();
hPrintf("<A HREF=\"#%s\" class=\"toc\">%s</A>",
section->name, section->shortLabel);
webPrintLinkCellEnd();
}
webFinishPartialLinkTable(rowIx, itemPos, maxPerRow);
webPrintLinkTableEnd();
}
static void prOrfeomeCloneLinks(struct sqlConnection *conn, char *acc, struct cloneInfo *ci)
/* print table of clone links */
{
webPrintLinkTableStart();
webPrintLabelCell("Links");
webPrintLinkTableNewRow();
if (ci->gi > 0)
prOrderLink("ORFeome", ci);
#if 0
// link to ORFeome database
// FIXME: this doesn't appear to work, need to ask Christa
// http://www.orfeomecollaboration.org/bin/cloneStatus.pl
#endif
if (ci->imageId > 0)
prImageLink(ci);
prGenbankLink(ci);
if (ci->refSeqAccv != NULL)
prRefSeqLinks(ci);
if (sqlTableExists(conn, "ccdsGene"))
prCcdsLinks(conn, ci);
if (sqlTableExists(conn, "knownGene"))
prUcscGenesLinks(conn, ci);
webPrintLinkTableEnd();
}
static void printHomPairRow(struct bed *parA, struct bed *parB)
/* print a homologous pair */
{
if (!sameString(parA->name, parB->name))
errAbort("invalid PAR homologous pair: %s and %s", parA->name, parB->name);
webPrintLabelCell(parA->name);
printParLink(parA);
printParLink(parB);
}
static void prRefSeqSims(struct cloneInfo *ci)
/* print similarity information for RefSeqs */
{
webNewSection("RefSeq CDS isoform similarity of %s clone %s",
cdnaInfoDbName(ci), ci->acc);
webPrintLinkTableStart();
webPrintLabelCell("RefSeq");
webPrintLabelCell("Position");
webPrintLabelCell("Similarity");
struct geneSim *gs;
for (gs = ci->refSeqs->genes; gs != NULL; gs = gs->next)
prRefSeqSim(ci, gs);
webPrintLinkTableEnd();
printf("This table compares the similarity of the BLAT genomic alignments of "
"the CDS of this %s clone with alignment of RefSeq mRNA CDSs. This is a metric "
"of the similarity of the exon structure of the mRNAs, rather than a measure of their "
"nucleotide sequence similarity.", cdnaInfoDbName(ci));
}
void correlatePage(struct sqlConnection *conn)
/* Put up correlation page. */
{
cartWebStart(cart, database, "Correlations of all pairs of graphs");
hPrintf("<FORM ACTION=\"../cgi-bin/hgGenome\" METHOD=GET>\n");
cartSaveSession(cart);
struct slRef *ggRefList = ggAllVisible(conn);
struct slRef *aRef, *bRef;
hPrintf("<TABLE><TR><TD>");
webPrintLinkTableStart();
webPrintLabelCell("Graph A");
webPrintLabelCell("Graph B");
webPrintLabelCell("R");
webPrintLabelCell("R-Squared");
for (aRef = ggRefList; aRef != NULL; aRef = aRef->next)
{
for (bRef = aRef->next; bRef != NULL; bRef = bRef->next)
{
hPrintf("</TR><TR>");
correlateGraphs(aRef->val, bRef->val);
}
}
webPrintLinkTableEnd();
hPrintf("</TD><TD>");
hPrintf("<CENTER>");
cgiMakeButton("submit", "return to graphs");
hPrintf("</CENTER>");
hPrintf("</TD></TR></TABLE>");
hPrintf("<P>R, also known as Pearson's correlation coefficient, is a measure ");
hPrintf("of the extent that two graphs move together. The value of R ranges ");
hPrintf("between -1 and 1. A positive R indicates that the graphs tend to ");
hPrintf("move in the same direction, while a negative R indicates that they ");
hPrintf("tend to move in opposite directions.</P>\n");
hPrintf("<P>R-Squared (which is indeed just R*R) measures how much of the ");
hPrintf("variation in one graph can be explained by a linear dependence on ");
hPrintf("the other graph. R-Squared ranges between 0 when the two graphs are ");
hPrintf("independent to 1 when the graphs are completely dependent.</P>");
hPrintf("</FORM>");
cartWebEnd();
}
static void prAligns(struct sqlConnection *conn, struct cloneInfo *ci)
/* print table of alignments */
{
struct psl* pslList = getAlignments(conn, ci->pslTbl, ci->acc);
assert(pslList != NULL);
slSort(&pslList, pslCmpMatch);
// header, print note about order only if we have multiple alignments and didn't
// come from another details page
webNewSection("Alignments");
if ((pslList->next != NULL) && (winStart < winEnd))
printf("<span style='font-size:smaller;'><em>The alignment you clicked on is shown first.</em></span>\n");
webPrintLinkTableStart();
webPrintLabelCell("genomic (browser)");
webPrintLabelCell("span");
webPrintLabelCell(" ");
webPrintLabelCell("mRNA (alignment details)");
webPrintLabelCell("identity");
webPrintLabelCell("aligned");
// print with clicked alignment first
struct psl* psl;
int pass;
for (pass = 1; pass <= 2; pass++)
{
for (psl = pslList; psl != NULL; psl = psl->next)
if ((pass == 1) == (psl->tStart == ci->start))
{
webPrintLinkTableNewRow();
prAlign(conn, ci->pslTbl, psl);
}
}
webPrintLinkTableEnd();
}
static void printClusterTableHeader(struct slName *otherCols,
boolean withAbbreviation, boolean withDescription, boolean withSignal)
/* Print out header fields table of tracks in cluster */
{
webPrintLabelCell("#");
if (withSignal)
webPrintLabelCell("signal");
if (withAbbreviation)
webPrintLabelCell("abr");
struct slName *col;
for (col = otherCols; col != NULL; col = col->next)
webPrintLabelCell(col->name);
if (withDescription)
webPrintLabelCell("description");
webPrintLabelCell("more info");
}
static void prMgcCloneLinks(struct sqlConnection *conn, struct mgcDb *mgcDb, struct cloneInfo *ci)
/* print table of clone links */
{
webPrintLinkTableStart();
webPrintLabelCell("Links");
if (ci->gi > 0)
prOrderLink(mgcDb->name, ci);
// link to MGC database
webPrintLinkTableNewRow();
webPrintLinkCellStart();
printf("<a href=\"");
printMgcUrl(ci->imageId);
printf("\" TARGET=_blank>%s clone database</a>", mgcDb->name);
webPrintLinkCellEnd();
prImageLink(ci);
prGenbankLink(ci);
if (ci->refSeqAccv != NULL)
prRefSeqLinks(ci);
if (sqlTableExists(conn, "ccdsGene"))
prCcdsLinks(conn, ci);
if (sqlTableExists(conn, "knownGene"))
prUcscGenesLinks(conn, ci);
// Brent lab validation database
if (isInMBLabValidDb(ci->acc))
{
webPrintLinkTableNewRow();
webPrintLinkCellStart();
printf("<a href=\"");
printMBLabValidDbUrl(ci->acc);
printf("\" TARGET=_blank>Brent Lab Clone Validation</a>");
webPrintLinkCellEnd();
}
webPrintLinkTableEnd();
}
static void rnaStructurePrint(struct section *section,
struct sqlConnection *conn, char *geneId)
/* Print out rnaStructure table. */
{
static boolean firstTime = TRUE;
static char *names[2] =
{"5' UTR", "3' UTR"};
static char *tables[2] = {"foldUtr5", "foldUtr3"};
int side;
if (firstTime)
{
rnaTrashDirsInit(tables, ArraySize(tables));
firstTime = FALSE;
}
webPrintLinkTableStart();
webPrintLabelCell("Region");
webPrintLabelCell("Fold Energy");
webPrintLabelCell("Bases");
webPrintLabelCell("Energy/Base");
webPrintWideCenteredLabelCell("Display As", 3);
for (side = 0; side < ArraySize(names); ++side)
{
char *table = tables[side];
struct sqlResult *sr;
char query[256], **row;
safef(query, sizeof(query), "select * from %s where name = '%s'",
table, geneId);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
{
struct rnaFold fold;
int bases;
char psName[128];
/* Load fold and save it as postScript. */
rnaFoldStaticLoad(row, &fold);
safef(psName, sizeof(psName), "../trash/%s/%s_%s.ps", table, table, geneId);
if (!fileExists(psName))
{
FILE *f;
f = popen("../cgi-bin/RNAplot", "w");
if (f != NULL)
{
fprintf(f, ">%s\n", psName); /* This tells where to put file. */
fprintf(f, "%s\n%s\n", fold.seq, fold.fold);
pclose(f);
}
}
/* Print row of table, starting with energy terms . */
hPrintf("</TR><TR>");
bases = strlen(fold.seq);
webPrintLinkCell(names[side]);
webPrintLinkCellStart();
hPrintf("%1.2f", fold.energy);
webPrintLinkCellEnd();
webPrintLinkCellStart();
hPrintf("%d", bases);
webPrintLinkCellEnd();
webPrintLinkCellStart();
hPrintf("%1.3f", fold.energy/bases);
webPrintLinkCellEnd();
/* Print link to png image. */
webPrintLinkCellStart();
hPrintf("<A HREF=\"%s?%s&%s=%s&%s=%s&%s=%s\" class=\"toc\" TARGET=_blank>",
geneCgi, cartSidUrlString(cart),
hggMrnaFoldRegion, table,
hggMrnaFoldPs, psName,
hggDoRnaFoldDisplay, "picture");
hPrintf(" Picture ");
hPrintf("</A>");
webPrintLinkCellEnd();
/* Print link to PostScript. */
webPrintLinkCellStart();
hPrintf("<A HREF=\"%s\" class=\"toc\">", psName);
hPrintf(" PostScript ");
hPrintf("</A>");
webPrintLinkCellEnd();
/* Print link to text. */
webPrintLinkCellStart();
hPrintf("<A HREF=\"%s?%s&%s=%s&%s=%s\" class=\"toc\" TARGET=_blank>",
geneCgi, cartSidUrlString(cart),
hggMrnaFoldRegion, table,
hggDoRnaFoldDisplay, "text");
hPrintf(" Text ");
hPrintf("</A>");
webPrintLinkCellEnd();
}
sqlFreeResult(&sr);
}
webPrintLinkTableEnd();
hPrintf("<BR>The RNAfold program from the ");
hPrintf("<A HREF=\"http://www.tbi.univie.ac.at/~ivo/RNA/\" TARGET=_blank>");
hPrintf("Vienna RNA Package</A> is used to perform the ");
hPrintf("secondary structure predictions and folding calculations. ");
hPrintf("The estimated folding energy is in kcal/mol. The more ");
hPrintf("negative the energy, the more secondary structure the RNA ");
hPrintf("is likely to have.");
}
static void otherOrgsPrint(struct section *section, struct sqlConnection *conn,
char *geneId)
/* Print the otherOrgs section. */
{
struct otherOrg *otherOrg, *otherOrgList = section->items;
hPrintf(
"Orthologies between human, mouse, and rat are computed by taking the "
"best BLASTP hit, and filtering out non-syntenic hits. For "
"more distant species reciprocal-best BLASTP hits are used. "
"Note that the absence of an ortholog in the table below may "
"reflect incomplete annotations in the other species rather than "
"a true absence of the orthologous gene.");
webPrintLinkTableStart();
for (otherOrg = otherOrgList; otherOrg != NULL; otherOrg = otherOrg->next)
webPrintLabelCell(otherOrg->shortLabel);
hPrintf("</TR>\n<TR>");
for (otherOrg = otherOrgList; otherOrg != NULL; otherOrg = otherOrg->next)
{
char *pos = otherOrgPosition(otherOrg, conn, geneId);
otherOrgPrintLink(otherOrg, "Genome Browser", "No ortholog", TRUE,
pos, otherOrg->genomeUrl);
freeMem(pos);
}
hPrintf("</TR>\n<TR>");
for (otherOrg = otherOrgList; otherOrg != NULL; otherOrg = otherOrg->next)
{
char *id = otherOrgId(otherOrg, conn, geneId);
otherOrgPrintLink(otherOrg, "Gene Details", " ", TRUE,
id, otherOrg->geneUrl);
freeMem(id);
}
hPrintf("</TR>\n<TR>");
for (otherOrg = otherOrgList; otherOrg != NULL; otherOrg = otherOrg->next)
{
char *id = otherOrgId(otherOrg, conn, geneId);
otherOrgPrintLink(otherOrg, "Gene Sorter", " ", TRUE,
id, otherOrg->sorterUrl);
freeMem(id);
}
hPrintf("</TR>\n<TR>");
for (otherOrg = otherOrgList; otherOrg != NULL; otherOrg = otherOrg->next)
{
char *id = otherOrgId(otherOrg, conn, geneId);
id = otherOrgExternalId(otherOrg, id);
otherOrgPrintLink(otherOrg, otherOrg->otherName, " ", FALSE,
id, otherOrg->otherUrl);
freeMem(id);
}
hPrintf("</TR>\n<TR>");
for (otherOrg = otherOrgList; otherOrg != NULL; otherOrg = otherOrg->next)
{
char *id = otherOrgProteinId(otherOrg, conn, geneId);
otherOrgPepLink(otherOrg, hggDoOtherProteinSeq, "Protein Sequence", id, conn);
freeMem(id);
}
hPrintf("</TR>\n<TR>");
for (otherOrg = otherOrgList; otherOrg != NULL; otherOrg = otherOrg->next)
{
char *id = otherOrgProteinId(otherOrg, conn, geneId);
otherOrgPepLink(otherOrg, hggDoOtherProteinAli, "Alignment", id, conn);
freeMem(id);
}
webPrintLinkTableEnd();
}
static void prCellLabelVal(char *label, char *val)
/* print label and value as adjacent cells */
{
webPrintLabelCell(label);
webPrintLinkCell(val);
}
void showCdsEvidence(char *geneName, struct trackDb *tdb, char *evTable)
/* Print out stuff from cdsEvidence table. */
{
struct sqlConnection *conn = hAllocConn(database);
double bestScore = 0;
if (sqlTableExists(conn, evTable))
{
webNewSection("CDS Prediction Information");
char query[512];
sqlSafef(query, sizeof(query),
"select count(*) from %s where name='%s'", evTable, geneName);
if (sqlQuickNum(conn, query) > 0)
{
sqlSafef(query, sizeof(query),
"select * from %s where name='%s' order by score desc", evTable, geneName);
struct sqlResult *sr = sqlGetResult(conn, query);
char **row;
webPrintLinkTableStart();
webPrintLabelCell("ORF<BR>size");
webPrintLabelCell("start in<BR>transcript");
webPrintLabelCell("end in<BR>transcript");
webPrintLabelCell("source");
webPrintLabelCell("accession");
webPrintLabelCell("ad-hoc<BR>score");
webPrintLabelCell("start<BR>codon");
webPrintLabelCell("end<BR>codon");
webPrintLabelCell("piece<BR>count");
webPrintLabelCell("piece list");
webPrintLabelCell("frame");
webPrintLinkTableNewRow();
while ((row = sqlNextRow(sr)) != NULL)
{
struct cdsEvidence *ev = cdsEvidenceLoad(row);
webPrintIntCell(ev->end - ev->start);
int i;
webPrintIntCell(ev->start+1);
webPrintIntCell(ev->end);
webPrintLinkCell(ev->source);
webPrintLinkCell(ev->accession);
webPrintLinkCellRightStart();
printf("%3.2f", ev->score);
bestScore = max(ev->score, bestScore);
webPrintLinkCellEnd();
webPrintLinkCell(ev->startComplete ? "yes" : "no");
webPrintLinkCell(ev->endComplete ? "yes" : "no");
webPrintIntCell(ev->cdsCount);
webPrintLinkCellRightStart();
for (i=0; i<ev->cdsCount; ++i)
{
int start = ev->cdsStarts[i];
int end = start + ev->cdsSizes[i];
printf("%d-%d ", start+1, end);
}
webPrintLinkCellEnd();
webPrintLinkCellRightStart();
for (i=0; i<ev->cdsCount; ++i)
{
if (i>0) printf(",");
printf("%d", ev->cdsStarts[i]%3 + 1);
}
webPrintLinkCellEnd();
webPrintLinkTableNewRow();
}
sqlFreeResult(&sr);
webPrintLinkTableEnd();
printf("This table shows CDS predictions for this transcript from a number of "
"sources including alignments against UniProtKB proteins, alignments against Genbank "
"mRNAs with CDS regions annotated by the sequence submitter, and "
"Victor Solovyev's bestorf program. Each prediction is assigned an ad-hoc score "
"score is based on several factors including the quality of "
"any associated alignments, the quality of the source, and the length of the "
"prediction. For RefSeq transcripts with annotated CDSs the ad-hoc score "
"is over a million unless there are severe problems mapping the mRNA to the "
"genome. In other cases the score generally ranges from 0 to 50,000. "
"The highest scoring prediction in this table is used to define the CDS "
"boundaries for this transcript.<P>If no score is 2000 or more, the transcript "
"is considered non-coding. In cases where the CDS is subject to "
"nonsense-mediated decay the CDS is removed. The CDS is also removed "
"from transcripts when evidence points to it being in an artifact of an "
"incompletely processed transcript. Specifically if the CDS is entirely "
"enclosed in the 3' UTR or an intron of a refSeq or other high quality "
"transcript, the CDS is removed.");
}
else
{
printf("no significant CDS prediction found, likely %s is noncoding",
geneName);
}
}
hFreeConn(&conn);
}