3c07e0899280b85976b6fcff458970e8166c4248 baertsch Sun May 29 19:19:12 2011 -0700 use version number in retro click score calc diff --git src/hg/hgc/retroClick.c src/hg/hgc/retroClick.c index 527fabc..07a9c56 100644 --- src/hg/hgc/retroClick.c +++ src/hg/hgc/retroClick.c @@ -1,826 +1,833 @@ /* retroClick - retroGene click handling */ /* * Tables associated with retroGenes: * retroXxxInfo - features of retroGene * retroXxxAli - mapped PSLs aligments * retroXxxAliGene - mapped alignmetns with CDS and frame annotation * * Xxx is: * - Mrna - GenBank mRNAs and refSeq */ #include "common.h" #include "hgc.h" #include "retroClick.h" #include "ucscRetroInfo.h" #include "ucscRetroOrtho.h" #include "genbank.h" #include "hui.h" /* combine blocks separated by gaps less than this number */ #define MAXBLOCKGAP 50 /* space to allocate for a id */ #define ID_BUFSZ 64 struct mappingInfo /* various pieces of information about mapping from table name and * retroXxxInfo table */ { char tblPre[64]; /* table prefix */ char geneSet[6]; /* source gene set abbrv used in table name */ struct ucscRetroInfo *pg; /* general info for retro gene */ boolean indirect; /* an indirect mapping */ char gbAcc[ID_BUFSZ]; /* src accession */ short gbVer; /* version from gbId */ char seqId[ID_BUFSZ]; /* id used to look up sequence, different than * srcAcc if multiple levels of mappings have * been done */ char suffix[ID_BUFSZ]; char *sym; /* src gene symbol and desc */ char *desc; short gbCurVer; /* version from genbank table */ }; static void parseSrcId(struct mappingInfo *mi) /* parse srcId parts and save in mi */ { char idBuf[ID_BUFSZ]; char *id, *colon = NULL, *dot = NULL, *under = NULL, *dash = NULL; /* direct mappings (cDNA is aligned to source organism) have ids in the form: * NM_012345.1-1.1 Indirect mappings, where mapped predictions are used to * form a gene set that is mapped again, have ids in the form * db:NM_012345.1_1.1, where db is the source organism, and '_1' is added so * that db:NM_012345.1_1 uniquely identifies the source. */ safef(idBuf, sizeof(idBuf), "%s", mi->pg->name); id = idBuf; /* find various parts */ colon = strchr(id, ':'); dot = strchr(id, '.'); if (dot != NULL) { under = strchr(dot, '_'); dash = strchr(dot, '-'); } if ((dot == NULL) || (dash == NULL)) errAbort("can't parse accession from srcId: %s", mi->pg->name); mi->indirect = (colon != NULL); /* id used to get sequence is before `-'. For direct, it excludes * genbank version */ *dash = '\0'; if (!mi->indirect) *dot = '\0'; safef(mi->seqId, sizeof(mi->seqId), "%s", id); /* now pull out genbank accession for obtaining description */ id = (colon != NULL) ? colon+1 : id; *dot = '\0'; safef(mi->gbAcc, sizeof(mi->gbAcc), "%s", id); if (under != NULL) *under = '\0'; //mi->gbVer = sqlSigned(dot+1); } static void getGenbankInfo(struct sqlConnection *conn, struct mappingInfo *mi) /* get source gene info and version from gbCdnaInfo and save in mi */ { char query[512], **row; struct sqlResult *sr; char *defDb = database; /* if id has been modified for multi-level ancestor mappings: * NM_012345.1-1.1 -> db:NM_012345a.1.1 * then hack it back to the original accession. However, don't get version, * since the sequence is different. */ safef(query, sizeof(query), "select gbCdnaInfo.version, geneName.name, description.name " "from %s.gbCdnaInfo, %s.geneName, %s.description " "where gbCdnaInfo.acc=\"%s\" and gbCdnaInfo.geneName=geneName.id and gbCdnaInfo.description = description.id", defDb, defDb, defDb, mi->gbAcc); sr = sqlGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { mi->gbCurVer = sqlSigned(row[0]); mi->sym = cloneString(row[1]); mi->desc = cloneString(row[2]); } sqlFreeResult(&sr); } static struct mappingInfo *mappingInfoNew(struct sqlConnection *conn, char *tbl, char *mappedId) /* load mapping info for a mapped gene */ { struct mappingInfo *mi; int preLen; char *suffix = containsStringNoCase(tbl,"Info"); int suffixLen = 4; AllocVar(mi); if (startsWith("retroAnc", tbl)) strcpy(mi->tblPre, "retroAnc"); else if (startsWith("retroOld", tbl)) strcpy(mi->tblPre, "retroOld"); else if (startsWith("retro", tbl)) strcpy(mi->tblPre, "retro"); else { strcpy(mi->tblPre, "ucsc"); suffix = containsStringNoCase(tbl,"Ali"); suffixLen = 3; } if (suffix != NULL) { suffix +=suffixLen; safef(mi->suffix,ID_BUFSZ,"%s",suffix); } preLen = strlen(mi->tblPre); if (startsWith("retroAugust", tbl)) strcpy(mi->geneSet, "August"); else if (startsWith("retro", tbl)) strcpy(mi->geneSet, "Mrna"); else strcpy(mi->geneSet, "Retro"); if (suffix != NULL && strlen(suffix) > 0) mi->pg = sqlQueryObjs(conn, (sqlLoadFunc)ucscRetroInfoLoad, sqlQueryMust|sqlQuerySingle, "select * from %s%sInfo%s where name='%s'", mi->tblPre, mi->geneSet, suffix, mappedId); else { mi->pg = sqlQueryObjs(conn, (sqlLoadFunc)ucscRetroInfoLoad, sqlQueryMust|sqlQuerySingle, "select * from %s%sInfo where name='%s'", mi->tblPre, mi->geneSet, mappedId); } parseSrcId(mi); getGenbankInfo(conn, mi); return mi; } static void mappingInfoFree(struct mappingInfo **mip) /* free mappingInfo object */ { struct mappingInfo *mi = *mip; if (mi != NULL) { ucscRetroInfoFree(&mi->pg); freeMem(mi->sym); freeMem(mi->desc); } } static void displaySrcGene(struct sqlConnection *conn, struct mappingInfo *mi) /* display information about the source gene that was mapped */ { char srcGeneUrl[1024]; /* description will be NULL if deleted */ if (!startsWith("retroAugust",mi->geneSet)) getGenbankInfo(conn, mi); /* construct URL to browser */ safef(srcGeneUrl, sizeof(srcGeneUrl), "../cgi-bin/hgTracks?db=%s&position=%s:%d-%d", database, mi->pg->gChrom, mi->pg->gStart, mi->pg->gEnd); printf("\n"); printf("\n"); printf("\n"); printf("\n"); printf("
Source gene
%s", srcGeneUrl, mi->pg->name); if (mi->desc == NULL) printf(" gene no longer in source database"); else printf("%s%s", mi->sym, mi->desc); printf("
\n"); } static void displayRetroDetails(struct sqlConnection *conn, struct mappingInfo *mi) /* display information from a retroXXXInfo table */ { struct ucscRetroInfo *pg = mi->pg; char query[256]; char orthoTable[128]; if (mi->suffix != NULL && strlen(mi->suffix) > 0) safef(orthoTable, sizeof(orthoTable), "%s%sOrtho%s", mi->tblPre, mi->geneSet, mi->suffix); else safef(orthoTable, sizeof(orthoTable), "%s%sOrtho", mi->tblPre, mi->geneSet); printf("\n"); printf("\n"); printf("\n"); printf("\n"); if (hTableExists(database, orthoTable)) { struct sqlResult *sr; char **row; safef(query, sizeof(query), "select * from %s where name = '%s' ", orthoTable, pg->name); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { struct ucscRetroOrtho *puro = ucscRetroOrthoLoad(row); printf("\n", puro->overlap); } sqlFreeResult(&sr); } else printf("", orthoTable); printf("
Orthology (net) BreakCoverage %%
%s ", puro->db); printf("%d
table %s not found
\n"); } static struct psl *loadPslRangeT(char *table, char *qName, char *tName, int tStart, int tEnd) /* Load a list of psls given qName tName tStart tEnd */ { struct sqlResult *sr = NULL; char **row; struct psl *psl = NULL, *pslList = NULL; boolean hasBin; char splitTable[64]; char query[256]; struct sqlConnection *conn = hAllocConn(database); hFindSplitTable(database, seqName, table, splitTable, &hasBin); safef(query, sizeof(query), "select * from %s where qName = '%s' and tName = '%s' and tEnd > %d and tStart < %d", splitTable, qName, tName, tStart, tEnd); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { psl = pslLoad(row+hasBin); slAddHead(&pslList, psl); } sqlFreeResult(&sr); slReverse(&pslList); hFreeConn(&conn); return pslList; } /* get overlap with psl and set the number of overlapping blocks to numBlocks */ int getOverlap(struct psl *psl, int start, int end, int *numBlocks) { int total = 0; int i; int blocks = 0; for (i = 0 ; i < psl->blockCount ; i++) { int qs = psl->qStarts[i]; int qe = psl->qStarts[i] + psl->blockSizes[i]; int overlap = 0; float coverage = 0; if (psl->strand[0] == '-') reverseIntRange(&qs, &qe, psl->qSize); overlap = positiveRangeIntersection(start, end, qs, qe); coverage = (float)overlap/(float)(qe-qe); total += overlap; if (overlap > 25 || coverage > 0.4) blocks++; } *numBlocks = blocks; return total; } void printBlocks (struct psl *psl, int maxBlockGap, struct psl *nestedPsl) { int i, qsStart = 0; int exonsCovered = 0; int totalBases = 0; int totalExons = 0; int intronsPresent = 0; int intronsPresentBases = 0; int intronsSpliced = 0; for (i = 0 ; i < psl->blockCount ; i++) { int qs = psl->qStarts[i]; int qe = psl->qStarts[i] + psl->blockSizes[i]; int te = psl->tStarts[i] + psl->blockSizes[i]; int tdiff = 0; int qdiff = 0; int cumTdiff = 0; int oqs, oqe; int tsNext = 999999; int qsNext = 0; float coverage = 0; int bases = 0; int oldte = te; int gapRatio = 0; if (i < psl->blockCount -1) { tsNext = psl->tStarts[i+1]; qsNext = psl->qStarts[i+1]; tdiff = tsNext - te; qdiff = qsNext - qe; } else tdiff = 9999999; cumTdiff = tdiff; qsStart = qs; /* combine blocks that are close together */ while (tdiff < maxBlockGap && i< (psl->blockCount)-1) { i++; te = psl->tStarts[i] + psl->blockSizes[i]; qe = psl->qStarts[i] + psl->blockSizes[i]; if (i < psl->blockCount -1) { tsNext = psl->tStarts[i+1]; qsNext = psl->qStarts[i+1]; tdiff = tsNext - te; qdiff = qsNext - qe; } else tdiff = 9999999; cumTdiff += tdiff; oldte = te; } oqs = qs; oqe = qe; if (psl->strand[0] == '-') reverseIntRange(&oqs, &oqe, psl->qSize); gapRatio = qdiff*100/tdiff; printf("%d-%d:%d",oqs,oqe,gapRatio); if (gapRatio < 30 && tdiff > 30 && i < (psl->blockCount)-1) { int bases = (tdiff-qdiff > 0) ? tdiff - qdiff : 0; intronsPresent++; intronsPresentBases += bases; } if (nestedPsl != NULL) { int numBlocks = 0; bases = getOverlap(nestedPsl, oqs, oqe, &numBlocks); coverage = (float)bases/(float)(oqe-oqs); totalBases += bases; totalExons++; if (coverage > 0.20) exonsCovered++; printf("/%d", numBlocks-1); intronsSpliced += numBlocks-1; } printf(", "); } } struct psl *pslFromGenePred(struct genePred *gp, int targetSize) /* Create a psl record from a genePred record. */ { struct psl *psl = NULL; int i; AllocVar(psl); psl->tName = cloneString(gp->chrom); psl->qName = cloneString(gp->name); psl->tStart = gp->txStart; psl->tEnd = gp->txEnd; psl->strand[0] = gp->strand[0]; AllocArray(psl->blockSizes, gp->exonCount); AllocArray(psl->tStarts, gp->exonCount); AllocArray(psl->qStarts, gp->exonCount); for(i=0; iexonCount; i++) { psl->blockSizes[i] = gp->exonEnds[i] - gp->exonStarts[i]; psl->qStarts[i] = psl->qSize; psl->qSize += psl->blockSizes[i]; psl->tStarts[i] = gp->exonStarts[i]; } psl->match = psl->qSize; psl->misMatch = 0; psl->repMatch = 0; psl->nCount = 0; psl->qNumInsert = gp->exonCount; psl->tNumInsert = 0; psl->tBaseInsert = 0; psl->qStart = 0; psl->qEnd = psl->qSize; psl->tSize = targetSize; psl->tStart = gp->txStart; psl->tEnd = gp->txEnd; psl->blockCount = gp->exonCount; return psl; } struct psl *getParentAligns(struct sqlConnection *conn, struct mappingInfo *mi, char **table) { struct ucscRetroInfo *pg = mi->pg; struct psl *pslList = NULL; char query[512]; if (startsWith("August",mi->geneSet)) { if (hTableExists(database, "augustusXAli")) { *table = cloneString( "augustusXAli"); pslList = loadPslRangeT(*table, mi->seqId, pg->gChrom, pg->gStart, pg->gEnd); } else if (hTableExists(database, "augustusX")) { struct sqlResult *sr; char **row; int targetSize = 0; *table = cloneString( "augustusX"); safef(query, sizeof(query), "select * from augustusX where chrom = '%s' and txEnd > %d and txStart < %d and name like '%s%%'", pg->gChrom, pg->gStart, pg->gEnd , mi->seqId ); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { struct genePred *gp = genePredLoad(row+1); safef(query, sizeof(query), "select size from chromInfo where chrom = '%s' " , gp->chrom); sqlFreeResult(&sr); targetSize = sqlNeedQuickNum(conn, query) ; pslList = pslFromGenePred(gp, targetSize); } } } else if (hTableExists(database, "all_mrna")) { char parent[255]; char *dotPtr ; *table = cloneString( "all_mrna"); safef(parent, sizeof(parent), "%s",pg->name); /* strip off version and unique suffix when looking for parent gene*/ dotPtr = rStringIn(".",parent) ; if (dotPtr != NULL) *dotPtr = '\0'; pslList = loadPslRangeT(*table, mi->gbAcc, pg->gChrom, pg->gStart, pg->gEnd); if (pslList == NULL) { *table = cloneString( "refSeqAli"); pslList = loadPslRangeT(*table, mi->gbAcc, pg->gChrom, pg->gStart, pg->gEnd); } } else printf("no all_mrna table found
\n"); return pslList; } static void displayParentAligns(struct mappingInfo *mi, struct psl *pslList, char *table) { struct ucscRetroInfo *pg = mi->pg; if (pslList != NULL && *table ) { printf("

Parent Locus/Parent mRNA Alignments

"); printAlignments(pslList, pslList->tStart, "htcCdnaAli", table, \ mi->gbAcc); } else printf("missing alignment %s chr %s:%d-%d from table %s
\n", mi->gbAcc, pg->gChrom, pg->gStart, pg->gEnd, table); } /* return count of coding exons */ int genePredcountCdsExons(struct genePred *gp) { int i; int count = 0; for (i=0; i<(gp->exonCount); i++) { if ( (gp->cdsStart <= gp->exonEnds[i]) && (gp->cdsEnd >= gp->exonStarts[i]) ) count++; } return count; } 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); + safef(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); + safef(scoreSql, sizeof(scoreSql), "select max(score) from %s%sInfo%s", mi->tblPre, mi->geneSet, mi->suffix); + } printf("\n"); printf("\n"); printf("\n"); printf("\n"); printf("\n"); if (sameString(pg->type, "singleExon")) printf("\n",pg->type); else printf("\n",pg->type); printf("\n", pg->score, - sqlQuickNum(conn, "select max(score) from ucscRetroInfo") ); + sqlQuickNum(conn, scoreSql) ); printf("\n", pg->coverage, pg->matches); printf("\n", pg->conservedSpliceSites); printf("\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("\n"); } if (pslList != NULL) { printf("\n"); pslFreeList(&pslList); } #endif printf("\n",pg->posConf); #ifdef score printf("\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->oldIntronCount, wt[10]*pg->oldIntronCount); printf("\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->oldIntronCount); if (pg->kaku > 0 && pg->kaku < 1000000) printf("\n", pg->kaku); #endif #ifdef xxx safef(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("\n"); if ( differentString("none",pg->overName) && sqlFieldIndex(conn, "refGene", "exonFrames") != -1) { safef(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("\n", pg->overName, sqlQuickString(conn, query)); } name = cloneString(pg->name); chopSuffix(name); safef(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("\n", name, sqlQuickString(conn, query)); } printf("
Retrogene stats
FeatureValue
Type of Parent%s
Expression of Retrocopy%s
Score %d (range from 0 - %d)
Alignment Coverage of parent gene (Bases matching Parent) %d %%  (%d bp)
Introns Procesed Out %d out of %d (%d exons covered)\n", pg->processedIntrons, (pg->parentSpliceCount/2), pg->exonCover); printf("
Possible Introns (or gaps) in Retro%d + %d\n", pg->intronCount, pg->oldIntronCount); printf("
Conserved Splice Sites%d
Parent Splice Sites%d
Blocks in retro:gap%%/intronsSpliced \n"); printBlocks(psl, MAXBLOCKGAP, pslList); printf("
Exons in parent:gap%% \n"); printBlocks(pslList, MAXBLOCKGAP, NULL); printf("
Length of PolyA Tail%d As out of %d bp
PolyA Tail %% A's(position)%5.1f %%\n",pg->polyA,pg->polyAlen, (float)pg->polyA*100/(float)pg->polyAlen); if (pg->polyAstart < 0) printf(" (%d bp before end of retrocopy)
\n",-(pg->polyAstart)); else printf(" (%d bp past end of retrocopy)
\n",pg->polyAstart); printf("
mRNA expression evidence"); if (!sameString(pg->overName, "none")) printf("%s (overlap:  %d bp)\n", pg->overName, pg->maxOverlap); else printf("No overlapping"); printf("
bestorf score (>50 is good)%4.0f
score function1: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
score function%4.1f+ %4.1f+ %4.1f+ %4.1f+ %4.1f - %4.1f - %4.1f+ %4.1f - %4.1f - %4.1f
KA/KU mutation rate in non-syn sites vs utr with repect to parent gene%4.2f
Frame of retro %s (start)%s
Frames of mapped parent %s (start)%s
\n"); } static void printRetroAlignments(struct psl *pslList, int startFirst, char *hgcCommand, char *aliTable, char *itemIn) /* Print list of mRNA alignments. */ { if (pslList == NULL || aliTable == NULL) return; printAlignmentsSimple(pslList, startFirst, hgcCommand, aliTable, itemIn); #ifdef UNUSED /* Does nothing in face in the end except trim the psls that nobody looks at. */ struct psl *psl = pslList; for (psl = pslList; psl != NULL; psl = psl->next) { if ( pslTrimToTargetRange(psl, winStart, winEnd) != NULL && !startsWith("xeno", aliTable) && !(startsWith("user", aliTable) && pslIsProtein(psl)) && psl->tStart == startFirst ) { char otherString[512]; safef(otherString, sizeof(otherString), "%d&aliTable=%s", psl->tStart, aliTable); } } #endif /* DOES_NOTHING */ } 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("

Retro Locus/Parent mRNA Alignments

"); printRetroAlignments(psl, start, "hgcRetroCdnaAli", alignTbl, mi->pg->name); pslFreeList(&psl); } 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("Description: Retrogenes are processed mRNAs that are inserted back into the genome. Most are pseudogenes, and some are functional genes or anti-sense transcripts that may impede mRNA translation.

\n"); printf("\n"); printf("\n"); printf("\n"); printf("\n"); printf("\n"); #if 0 if (!sameString(gc->stat, "ok")) { printf("\n"); printf("\n"); } #endif printf("
\n"); displaySrcGene(conn, mi); printf("
\n"); displayMappingInfo(conn, mi); printf("\n"); #if 0 struct geneCheck *gc = displayGeneCheck(conn, &mti, mappedId); printf("\n"); displayProtSim(conn, &mti, mappedId); #endif printf("
\n"); displayGeneCheckDetails(conn, &mti, gc); printf("
\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); } static struct genbankCds getCds(struct sqlConnection *conn, struct mappingInfo *mi) /* Get CDS, return empty genebankCds if not found or can't parse */ { char query[256]; struct sqlResult *sr; struct genbankCds cds; char **row; safef(query, sizeof(query), "select cds.name " "from %s.gbCdnaInfo, %s.cds " "where gbCdnaInfo.acc=\"%s\" and gbCdnaInfo.cds=cds.id", database, database, mi->gbAcc); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if ((row == NULL) || !genbankCdsParse(row[0], &cds)) ZeroVar(&cds); /* can't get or parse cds */ sqlFreeResult(&sr); return cds; } static struct psl *loadAlign(struct sqlConnection *conn, struct mappingInfo *mi, int start) /* load a psl that must exist */ { char rootTable[256], table[256], query[256]; boolean hasBin; struct sqlResult *sr; char **row; struct psl *psl; if (mi->suffix == NULL) safef(rootTable, sizeof(rootTable), "%s%sAli", mi->tblPre, mi->geneSet); else safef(rootTable, sizeof(rootTable), "%s%sAli%s", mi->tblPre, mi->geneSet,mi->suffix); hFindSplitTable(database, seqName, rootTable, table, &hasBin); safef(query, sizeof(query), "select * from %s where qName = '%s' and tStart = %d", table, mi->pg->name, start); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); psl = pslLoad(row+hasBin); sqlFreeResult(&sr); return psl; } void retroShowCdnaAli(char *mappedId) /* Show alignment for accession, mostly ripped off from htcCdnaAli */ { char *track = cartString(cart, "aliTable"); struct trackDb *tdb = hashMustFindVal(trackHash, track); char *table = cartString(cart, "table"); int start = cartInt(cart, "o"); struct sqlConnection *conn = hAllocConn(database); struct sqlConnection *defDbConn = NULL; struct mappingInfo *mi = mappingInfoNew(conn, table, mappedId); struct genbankCds cds = getCds(conn, mi); struct psl *psl; struct dnaSeq *rnaSeq = NULL; char *spec = trackDbRequiredSetting(tdb, BASE_COLOR_USE_SEQUENCE); char *specCopy = cloneString(spec); char *words[3]; int nwords = chopByWhite(specCopy, words, ArraySize(words)); char acc[512]; /* Print start of HTML. */ writeFramesetType(); puts(""); printf("\n%s vs Genomic [%s]\n\n\n", mi->seqId, track); /* Look up alignment and sequence in database. Always get sequence * from defaultDb */ psl = loadAlign(conn, mi, start); if (startsWith("August",mi->geneSet)) safef(acc, sizeof(acc), "aug-%s.T1",mi->seqId); else safef(acc, sizeof(acc), "%s",mi->seqId); // value is: extFile seqTbl extFileTbl if ((nwords != (int)ArraySize(words)) || !sameString(words[0], "extFile")) errAbort("invalid %s track setting: %s ", BASE_COLOR_USE_SEQUENCE, spec); char *seqTable = words[1]; char *extTable = words[2]; rnaSeq = hDnaSeqGet(database, acc, seqTable, extTable); if (rnaSeq == NULL) { char *acc = mi->seqId; rnaSeq = hExtSeq(database, acc); if (rnaSeq == NULL) errAbort("can't get mRNA sequence from %s prefix %s for %s from %s mappedId %s", database, mi->geneSet, acc, track, mappedId); } sqlDisconnect(&defDbConn); showSomeAlignment(psl, rnaSeq, gftDna, 0, rnaSeq->size, NULL, cds.start, cds.end); pslFree(&psl); dnaSeqFree(&rnaSeq); mappingInfoFree(&mi); hFreeConn(&conn); }