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 displayAligns(struct sqlConnection *conn, struct mappingInfo *mi)
/* display cDNA alignments */
{
int start = cartInt(cart, "o");
char alignTbl[128];
struct psl *psl;
safef(alignTbl, sizeof(alignTbl), "%s%sAli%s", mi->tblPre, mi->geneSet,mi->suffix);
/* this should only ever have one alignment */
psl = getAlignments(conn, alignTbl, mi->pg->name);
printf("<H3>Retro Locus/Parent mRNA Alignments</H3>");
printRetroAlignments(psl, start, "hgcRetroCdnaAli", alignTbl, mi->pg->name);
pslFreeList(&psl);
}
static void displayMappingInfo(struct sqlConnection *conn, struct mappingInfo *mi)
/* display information from a transMap table */
{
struct ucscRetroInfo *pg = mi->pg;
double wt[12]; /* weights on score function*/
char query[512];
char *name;
char alignTbl[128];
char scoreSql[128];
struct psl *psl;
float coverFactor = 0;
float maxOverlap = 0;
if (mi->suffix == NULL)
{
safef(alignTbl, sizeof(alignTbl), "%s%sAli", mi->tblPre, mi->geneSet);
sqlSafef(scoreSql, sizeof(scoreSql), "select max(score) from %s%sInfo", mi->tblPre, mi->geneSet);
}
else
{
safef(alignTbl, sizeof(alignTbl), "%s%sAli%s", mi->tblPre, mi->geneSet, mi->suffix);
sqlSafef(scoreSql, sizeof(scoreSql), "select max(score) from %s%sInfo%s", mi->tblPre, mi->geneSet, mi->suffix);
}
printf("<TABLE class=\"transMap\">\n");
printf("<H3>Retrogene Statistics:</H3>\n");
printf("<THEAD>\n");
printf("<TR><TH>Feature<TH>Value </TR>\n");
printf("</THEAD><TBODY>\n");
if (sameString(pg->type, "singleExon"))
printf("<TR><TH>Type of Parent<TD>%s</tr>\n",pg->type);
else
printf("<TR><TH>Expression of Retrogene<TD>%s</TR>\n",pg->type);
printf("<TR><TH>Score <TD>%d (range from 0 - %d)</TR>\n",
pg->score,
sqlQuickNum(conn, scoreSql) );
printf("<TR><TH>Parent Gene Alignment Coverage (Bases Matching Parent) <TD>%d %% (%d bp) </TR>\n", pg->coverage, pg->matches);
printf("<TR><TH>Introns Processed Out <TD>%d out of %d (%d exons covered)\n", pg->processedIntrons, (pg->parentSpliceCount/2), pg->exonCover);
printf("<TR><TH>Possible Introns or Gaps in Retrogene<TD>%d,%d\n", pg->intronCount, pg->alignGapCount);
printf("<TR><TH>Conserved Splice Sites<TD>%d</TR>\n", pg->conservedSpliceSites);
printf("<TR><TH>Parent Splice Sites<TD>%d</TR>\n", pg->parentSpliceCount);
psl = getAlignments(conn, alignTbl, mi->pg->name);
if (psl != NULL)
{
maxOverlap = (float)pg->maxOverlap/(float)(psl->match+psl->misMatch+psl->repMatch) ;
coverFactor = ((float)(psl->qSize-psl->qEnd)/(float)psl->qSize);
}
else
{
maxOverlap = 0;
}
wt[0] = 0; wt[1] = 0.85; wt[2] = 0.2; wt[3] = 0.3; wt[4] = 0.8;
wt[5] = 1; wt[6] = 1 ; wt[7] = 0.5; wt[8] = 0.5; wt[9] = 1; wt[10] = 1;
#ifdef debug
char table[512];
struct psl *pslList = getParentAligns(conn, mi, &table);
if (psl != NULL)
{
printf("<TR><TH>Blocks in retro:gap%%/intronsSpliced <TD>\n");
printBlocks(psl, MAXBLOCKGAP, pslList);
printf("</td></TR>\n");
}
if (pslList != NULL)
{
printf("<TR><TH>Exons in parent:gap%% <TD>\n");
printBlocks(pslList, MAXBLOCKGAP, NULL);
printf("</td></TR>\n");
pslFreeList(&pslList);
}
#endif
printf("<TR><TH>Length of PolyA Tail<TD>%d As out of %d bp </TR><TR><TH>%% A's from Parent PolyA tail (Position)<TD>%5.1f %%\n",pg->polyA,pg->polyAlen, (float)pg->polyA*100/(float)pg->polyAlen);
if (pg->polyAstart < 0)
printf(" (%d bp before end of retrogene)<br>\n",-(pg->polyAstart));
else
printf(" (%d bp past end of retrogene)<br>\n",pg->polyAstart);
printf("<tr><th>mRNA Expression Evidence<td>");
if (!sameString(pg->overName, "none"))
printf("%s (overlap: %d bp)\n", pg->overName, pg->maxOverlap);
else
printf("No overlapping");
printf("<TR><TH>BESTORF Score (>50 is good)<TD>%4.0f</td></TR>\n",pg->posConf);
#ifdef score
printf("<TR><TH>score function<TD>1:xon %d %4.1f conSS %d 2: ax %4.1f 3: pA %4.1f 4: net + %4.1f max (%d, %d) 5: procIntrons %d %4.1f 6:in.cnt %d -%4.1f 7:overlap - %4.1f 8:cov %d*(qe %d- qsz %d)/%d=%4.1f 9:tRep - %4.1f 10:oldintron %d %4.1f </td></TR>\n",
pg->exonCover,
wt[1]*(log(pg->exonCover+1)/log(2))*200 ,
pg->conservedSpliceSites,
wt[2]*(((log(pg->axtScore>0?pg->axtScore:1)/log(2))*170)-1000),
wt[3]*(log(pg->polyAlen+2)*200) ,
wt[4]*overlapOrtholog*10 , pg->overlapMouse, pg->overlapDog,
pg->processedIntrons,
wt[5]*(((log(pg->processedIntrons > 0 ? pg->processedIntrons : 1))/log(2))*600) ,
pg->intronCount,
wt[6]*pow(pg->intronCount,0.5)*750 ,
wt[7]*(maxOverlap*300),
pg->coverage, pg->qEnd, pg->qSize , pg->qSize,
wt[8]*((pg->coverage/100.0)*(1.0-coverFactor)*300.0),
wt[9]*(pg->tReps*10),
pg->alignGapCount,
wt[10]*pg->alignGapCount);
printf("<TR><TH>score function<TD>%4.1f+ %4.1f+ %4.1f+ %4.1f+ %4.1f - %4.1f - %4.1f+ %4.1f - %4.1f - %4.1f</td></TR>\n",
wt[1]*(log(pg->exonCover+1)/log(2))*200 ,
wt[2]*(((log(pg->axtScore>0?pg->axtScore:1)/log(2))*170)-1000),
wt[3]*(log(pg->polyAlen+2)*200) ,
wt[4]*overlapOrtholog*10 ,
wt[5]*(((log(pg->processedIntrons > 0 ? pg->processedIntrons : 1))/log(2))*600) ,
(float)wt[6]*pow(pg->intronCount,0.5)*750 ,
(float)wt[7]*(maxOverlap*300),
wt[8]*((pg->coverage/100.0)*(1.0-coverFactor)*300.0),
wt[9]*(pg->tReps*10),
wt[10]*pg->alignGapCount);
if (pg->kaku > 0 && pg->kaku < 1000000)
printf("<TR><TH>KA/KU mutation rate in non-syn sites vs utr with repect to parent gene<TD>%4.2f</TR>\n", pg->kaku);
#endif
#ifdef xxx
sqlSafef(query, sizeof(query), "select * from refGene where chrom = '%d' and txEnd > %d and txStart %d and name = '%s'",
pg->chrom, pg->gStart, pg->gEnd , pg->overName );
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
overlappingGene = genePredLoad(row);
if (overlappingGene != NULL)
{
printf ("CDS exons %d ",genePredcountCdsExons(overlappingGene));
}
#endif
printf("</tr>\n");
if ( differentString("none",pg->overName) &&
sqlFieldIndex(conn, "refGene", "exonFrames") != -1)
{
sqlSafef(query, sizeof(query),
"select concat(exonFrames,'(',cdsStart,')') from refGene where name = '%s' and chrom = '%s'" ,
pg->overName, pg->chrom);
if (sqlQuickString(conn, query) != NULL)
printf("<TR><TH>Frame of retro %s (start)<TD>%s</TR>\n",
pg->overName, sqlQuickString(conn, query));
}
name = cloneString(pg->name);
chopSuffix(name);
sqlSafef(query, sizeof(query),
"select concat(exonFrames,'(',cdsStart,')') from rbRetroParent where name like '%s%%' and chrom = '%s'" ,
name, pg->chrom);
if (hTableExists(database, "rbRetroParent"))
{
if ( sqlQuickString(conn, query) != NULL)
printf("<TR><TH>Frames of mapped parent %s (start)<TD>%s</TR>\n",
name, sqlQuickString(conn, query));
}
printf("</TBODY></TABLE>\n");
}
