Exemple #1
0
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);
}
Exemple #2
0
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");
}
Exemple #3
0
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();
}
Exemple #4
0
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();
}
Exemple #5
0
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);
}
Exemple #6
0
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));
}
Exemple #7
0
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();
}
Exemple #8
0
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("&nbsp;");
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");
}
Exemple #10
0
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", "&nbsp;", 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", "&nbsp;", 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, "&nbsp;", 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();
}
Exemple #13
0
static void prCellLabelVal(char *label, char *val)
/* print label and value as adjacent cells  */
{
webPrintLabelCell(label);
webPrintLinkCell(val);
}
Exemple #14
0
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);
}