\n", idInUrl, "NCBI MapView"); } else { char *label = idInUrl; if (isNotEmpty(itemLabel) && !sameString(itemName, itemLabel)) label = itemLabel; printf("%s
\n", label); } freeMem(eItem); freeDyString(&uUrl); freeDyString(&eUrl); } } } void printCustomUrl(struct trackDb *tdb, char *itemName, boolean encode) /* Wrapper to call printCustomUrlWithLabel using the url setting in trackDb */ { char urlSetting[10]; safef(urlSetting, sizeof(urlSetting), "url"); printCustomUrlWithLabel(tdb, itemName, itemName, urlSetting, encode); } void printOtherCustomUrl(struct trackDb *tdb, char *itemName, char* urlSetting, boolean encode) /* Wrapper to call printCustomUrlWithLabel to use another url setting other than url in trackDb e.g. url2, this allows the use of multiple urls for a track to be set in trackDb. */ { printCustomUrlWithLabel(tdb, itemName, itemName, urlSetting, encode); } void beginCollapsibleSection(char *track, char *section, char *sectionTitle, boolean isOpenDefault) /* Make the hidden input, collapse/expand button and
| \n",
collapseGroupVar, collapseGroupVar, isOpen ? "0" : "1");
printf("\n",
cgiScriptName(), cartSidUrlString(cart), collapseGroupVar, (isOpen ? "1" : "0"), section);
char *buttonImage = (isOpen ? "../images/remove_sm.gif" : "../images/add_sm.gif");
printf(" | \n",
section, track,
section, buttonImage, (isOpen ? "-" : "+"), (isOpen ? "Collapse": "Expand"));
printf("%s |
| ", isOpen ? "" : "style='display: none' ", section, 1); } void endCollapsibleSection() /* End the collapsible | |
| ");
printf("Suh Trees \n"); printf("  ",item); printf(" |  ",item); printf(" |
|---|---|
| ");
printf("NJ Trees \n"); printf("  ",item); printf(" |  ",item); printf(" |
| ");
/*
printf("Gap UPGMA Trees \n"); printf("  ",item); printf(" |  ",item); printf(" |
Multiple Alignment Block %d of %d
", count, numBlocks); mafPrettyOut(stdout, mafAli, 70, FALSE, count++); if (mafAli->next != NULL) { struct mafAli *next = mafAli->next; struct mafComp *comp1 = mafAli->components; struct mafComp *comp2 = next->components; printf("
Gaps:\n"); for(; comp1 ; comp1 = comp1->next, comp2 = comp2->next) { int diff; char dbOnly[4096]; diff = comp2->start - (comp1->start + comp1->size); safef(dbOnly, sizeof(dbOnly), "%s", comp1->src); chopPrefix(dbOnly); printf("%-20s %d\n",hOrganism(dbOnly), diff); } printf("
"); } } } } void genericBedClick(struct sqlConnection *conn, struct trackDb *tdb, char *item, int start, int bedSize) /* Handle click in generic BED track. */ { char table[64]; boolean hasBin; struct bed *bed; char query[512]; struct sqlResult *sr; char **row; boolean firstTime = TRUE; char *escapedName = sqlEscapeString(item); hFindSplitTable(database, seqName, tdb->table, table, &hasBin); if (bedSize <= 3) sprintf(query, "select * from %s where chrom = '%s' and chromStart = %d", table, seqName, start); else { struct hTableInfo *hti = hFindTableInfoWithConn(conn, seqName, tdb->table); if (hti && *hti->nameField && differentString("name", hti->nameField)) sprintf(query, "select * from %s where %s = '%s' and chrom = '%s' and chromStart = %d", table, hti->nameField, escapedName, seqName, start); else sprintf(query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", table, escapedName, seqName, start); } sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { if (firstTime) firstTime = FALSE; else htmlHorizontalLine(); bed = bedLoadN(row+hasBin, bedSize); bedPrintPos(bed, bedSize, tdb); // check for seq1 and seq2 in columns 7+8 (eg, pairedTagAlign) char *setting = trackDbSetting(tdb, BASE_COLOR_USE_SEQUENCE); if (bedSize == 6 && setting && sameString(setting, "seq1Seq2")) printf("
Sequence 1: %s
Sequence 2: %s
\n",row[hasBin+6], row[hasBin+7]); printCompareGenomeLinks(tdb,bed->name); } sqlFreeResult(&sr); getBedTopScorers(conn, tdb, table, item, start, bedSize); } #define INTRON 10 #define CODINGA 11 #define CODINGB 12 #define UTR5 13 #define UTR3 14 #define STARTCODON 15 #define STOPCODON 16 #define SPLICESITE 17 #define NONCONSPLICE 18 #define INFRAMESTOP 19 #define INTERGENIC 20 #define REGULATORY 21 #define LABEL 22 #define RED 0xFF0000 #define GREEN 0x00FF00 #define LTGREEN 0x33FF33 #define BLUE 0x0000FF #define MEDBLUE 0x6699FF #define PURPLE 0x9900cc #define BLACK 0x000000 #define CYAN 0x00FFFF #define ORANGE 0xDD6600 #define BROWN 0x663300 #define YELLOW 0xFFFF00 #define MAGENTA 0xFF00FF #define GRAY 0xcccccc #define LTGRAY 0x999999 #define WHITE 0xFFFFFF int setAttributeColor(int class) { switch (class) { case STARTCODON: return GREEN; case STOPCODON: return RED; case CODINGA: return MEDBLUE; case CODINGB: return PURPLE; case UTR5: case UTR3: return ORANGE; case INTRON: return LTGRAY; case SPLICESITE: case NONCONSPLICE: return BLACK; case INFRAMESTOP: return MAGENTA; case REGULATORY: return YELLOW; case INTERGENIC: return GRAY; case LABEL: default: return BLACK; } } void startColorStr(struct dyString *dy, int color, int track) { currentColor[track] = color; if (prevColor[track] != currentColor[track]) dyStringPrintf(dy,"",color); } void stopColorStr(struct dyString *dy, int track) { prevColor[track] = currentColor[track]; } void addTag(struct dyString *dy, struct dyString *tag) { dyStringPrintf(dy,"",tag->string); } void setClassStr(struct dyString *dy, int class, int track) { if (class == STARTCODON) dyStringAppend(dy,""); startColorStr(dy,setAttributeColor(class),track); } void resetClassStr(struct dyString *dy, int track) { stopColorStr(dy,track); } boolean isBlue(char *s) /* check for to see if this is colored blue (coding region)*/ { /* check for blue */ if (strstr(s,"6699FF") == NULL) return FALSE; else return TRUE; } int numberOfGaps(char *q,int size) /* count number of gaps in a string array */ { int i; int count = 0; for (i = 0 ; i
",qPtr, nextStart+1,nextEnd,nextEndIndex+1, tPtr,prevEnd, tPtr-nextStart-70, tPtr-(prevEnd+70)); else printf(" %d nextExon=%d-%d xon %d t %d prevEnd %d diffs %d %d
",qPtr, nextStart+1,nextEnd,nextEndIndex, tPtr, prevEnd, tPtr-nextStart-70, tPtr-(prevEnd+70)); #endif /* write out alignment, unless we are deep inside an intron */ if (tClass != INTRON || (tClass == INTRON && tPtr < nextStart-LINESIZE && tPtr< (prevEnd + posStrand ? LINESIZE : -LINESIZE))) { intronTruncated = 0; fputs(dyTprot->string,f); fputs(dyT->string,f); for (i=0; i
"); intronTruncated = TRUE; } } /* look for end of line */ if (oneSize > lineSize) oneSize = lineSize; sizeLeft -= oneSize; q += oneSize; t += oneSize; freeDyString(&dyT); freeDyString(&dyQ); freeDyString(&dyQprot); freeDyString(&dyTprot); } } } struct axt *getAxtListForGene(struct genePred *gp, char *nib, char *fromDb, char *toDb, struct lineFile *lf) /* get all axts for a gene */ { struct axt *axt, *axtGap; struct axt *axtList = NULL; int prevEnd = gp->txStart; int prevStart = gp->txEnd; int tmp; while ((axt = axtRead(lf)) != NULL) { if (sameString(gp->chrom , axt->tName) && ( (((axt->tStart <= gp->cdsStart) && (axt->tEnd >= gp->cdsStart)) || ((axt->tStart <= gp->cdsEnd) && (axt->tEnd >= gp->cdsEnd))) || (axt->tStart < gp->cdsEnd && axt->tEnd > gp->cdsStart) ) ) { if (gp->strand[0] == '-') { reverseComplement(axt->qSym, axt->symCount); reverseComplement(axt->tSym, axt->symCount); tmp = hChromSize(fromDb, axt->qName) - axt->qStart; axt->qStart = hChromSize(fromDb, axt->qName) - axt->qEnd; axt->qEnd = tmp; if (prevEnd < (axt->tStart)-1) { axtGap = createAxtGap(nib,gp->chrom,prevEnd,(axt->tStart),gp->strand[0]); reverseComplement(axtGap->qSym, axtGap->symCount); reverseComplement(axtGap->tSym, axtGap->symCount); slAddHead(&axtList, axtGap); } } else if (prevEnd < (axt->tStart)) { axtGap = createAxtGap(nib,gp->chrom,prevEnd,(axt->tStart),gp->strand[0]); slAddHead(&axtList, axtGap); } slAddHead(&axtList, axt); prevEnd = axt->tEnd; prevStart = axt->tStart; } if (sameString(gp->chrom, axt->tName) && (axt->tStart > gp->txEnd)) { if ((prevEnd < axt->tStart) && prevEnd < min(gp->txEnd, axt->tStart)) { axtGap = createAxtGap(nib,gp->chrom,prevEnd,min(axt->tStart,gp->txEnd),gp->strand[0]); if (gp->strand[0] == '-') { reverseComplement(axtGap->qSym, axtGap->symCount); reverseComplement(axtGap->tSym, axtGap->symCount); } slAddHead(&axtList, axtGap); } else if (axtList == NULL) { axtGap = createAxtGap(nib,gp->chrom,prevEnd,gp->txEnd,gp->strand[0]); if (gp->strand[0] == '-') { reverseComplement(axtGap->qSym, axtGap->symCount); reverseComplement(axtGap->tSym, axtGap->symCount); } slAddHead(&axtList, axtGap); } break; } } if (gp->strand[0] == '+') slReverse(&axtList); return axtList ; } struct axt *getAxtListForRange(struct genePred *gp, char *nib, char *fromDb, char *toDb, char *alignment, char *qChrom, int qStart, int qEnd) /* get all axts for a chain */ { struct lineFile *lf ; struct axt *axt, *axtGap; struct axt *axtList = NULL; int prevEnd = gp->txStart; int prevStart = gp->txEnd; int tmp; lf = lineFileOpen(getAxtFileName(gp->chrom, toDb, alignment, fromDb), TRUE); printf("file %s\n",lf->fileName); while ((axt = axtRead(lf)) != NULL) { /* if (sameString(gp->chrom , axt->tName)) * printf("axt %s qstart %d axt tStart %d\n",axt->qName, axt->qStart,axt->tStart); */ if (sameString(gp->chrom , axt->tName) && (sameString(qChrom, axt->qName) && positiveRangeIntersection(qStart, qEnd, axt->qStart, axt->qEnd) )&& positiveRangeIntersection(gp->txStart, gp->txEnd, axt->tStart, axt->tEnd) /* ( (((axt->tStart <= gp->cdsStart) && (axt->tEnd >= gp->cdsStart)) || ((axt->tStart <= gp->cdsEnd) && (axt->tEnd >= gp->cdsEnd))) || (axt->tStart < gp->cdsEnd && axt->tEnd > gp->cdsStart) ) */ ) { if (gp->strand[0] == '-') { reverseComplement(axt->qSym, axt->symCount); reverseComplement(axt->tSym, axt->symCount); tmp = hChromSize(fromDb, axt->qName) - axt->qStart; axt->qStart = hChromSize(fromDb, axt->qName) - axt->qEnd; axt->qEnd = tmp; if (prevEnd < (axt->tStart)-1) { axtGap = createAxtGap(nib,gp->chrom,prevEnd,(axt->tStart)-1,gp->strand[0]); reverseComplement(axtGap->qSym, axtGap->symCount); reverseComplement(axtGap->tSym, axtGap->symCount); slAddHead(&axtList, axtGap); } } else if (prevEnd < (axt->tStart)-1) { axtGap = createAxtGap(nib,gp->chrom,prevEnd,(axt->tStart)-1,gp->strand[0]); slAddHead(&axtList, axtGap); } slAddHead(&axtList, axt); prevEnd = axt->tEnd; prevStart = axt->tStart; } if (sameString(gp->chrom, axt->tName) && (axt->tStart > gp->txEnd+20000)) { if (axt->tStart > prevEnd) { axtGap = createAxtGap(nib,gp->chrom,prevEnd+1,(axt->tStart)-1,gp->strand[0]); if (gp->strand[0] == '-') { reverseComplement(axtGap->qSym, axtGap->symCount); reverseComplement(axtGap->tSym, axtGap->symCount); } slAddHead(&axtList, axtGap); } break; } } if (gp->strand[0] == '+') slReverse(&axtList); return axtList ; } void printCdsStatus(enum cdsStatus cdsStatus) /* print a description of a genePred cds status */ { switch (cdsStatus) { case cdsNone: /* "none" - No CDS (non-coding) */ printf("none (non-coding)
\n"); break; case cdsUnknown: /* "unk" - CDS is unknown (coding, but not known) */ printf("unknown (coding, but not known)
\n"); break; case cdsIncomplete: /* "incmpl" - CDS is not complete at this end */ printf("not complete
\n"); break; case cdsComplete: /* "cmpl" - CDS is complete at this end */ printf("complete
\n"); break; } } void showGenePos(char *name, struct trackDb *tdb) /* Show gene prediction position and other info. */ { char *rootTable = tdb->table; char query[512]; struct sqlConnection *conn = hAllocConn(database); struct genePred *gpList = NULL, *gp = NULL; boolean hasBin; char table[64]; struct sqlResult *sr = NULL; char **row = NULL; char *classTable = trackDbSetting(tdb, GENEPRED_CLASS_TBL); hFindSplitTable(database, seqName, rootTable, table, &hasBin); safef(query, sizeof(query), "name = \"%s\"", name); gpList = genePredReaderLoadQuery(conn, table, query); for (gp = gpList; gp != NULL; gp = gp->next) { printPos(gp->chrom, gp->txStart, gp->txEnd, gp->strand, FALSE, NULL); if(sameString(tdb->type,"genePred") && startsWith("ENCODE Gencode",tdb->longLabel) && startsWith("ENST",name)) { char *ensemblIdUrl = trackDbSetting(tdb, "ensemblIdUrl"); printf("Ensembl Transcript Id: "); if (ensemblIdUrl != NULL) printf("%s
", ensemblIdUrl,name,name); else printf("%s
",name); } if (gp->name2 != NULL && strlen(trimSpaces(gp->name2))> 0) { /* in Ensembl gene info downloaded from ftp site, sometimes the name2 field is populated with "noXref" because there is no alternate name. Replace this with "none" */ printf("Gene Symbol:"); if (sameString(gp->name2, "noXref")) printf(" none
\n"); else printf(" %s
\n",gp->name2); } if ((gp->exonFrames != NULL) && (!genbankIsRefSeqNonCodingMRnaAcc(gp->name))) { printf("CDS Start: "); printCdsStatus((gp->strand[0] == '+') ? gp->cdsStartStat : gp->cdsEndStat); printf("CDS End: "); printCdsStatus((gp->strand[0] == '+') ? gp->cdsEndStat : gp->cdsStartStat); } /* if a gene class table exists, get gene class and print */ if (classTable != NULL) { if (hTableExists(database, classTable)) { safef(query, sizeof(query), "select class from %s where name = \"%s\"", classTable, name); sr = sqlGetResult(conn, query); /* print class */ if ((row = sqlNextRow(sr)) != NULL) printf("Prediction Class: %s
\n", row[0]); sqlFreeResult(&sr); if (sqlFieldIndex(conn, classTable, "level") > 0 ) { safef(query, sizeof(query), "select level from %s where name = \"%s\"", classTable, name); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) printf("Level: %s
\n", row[0]); sqlFreeResult(&sr); } if (sqlFieldIndex(conn, classTable, "transcriptType") > 0 ) { safef(query, sizeof(query), "select transcriptType from %s where name = \"%s\"", classTable, name); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) printf("Transcript type: %s
\n", row[0]); sqlFreeResult(&sr); } if (sqlFieldIndex(conn, classTable, "geneDesc") > 0 ) { safef(query, sizeof(query), "select geneDesc from %s where name = \"%s\"", classTable, name); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) if (differentString("NULL",row[0])) printf("Gene Description : %s
\n", row[0]); sqlFreeResult(&sr); } if (sqlFieldIndex(conn, classTable, "type") > 0 ) { safef(query, sizeof(query), "select type from %s where name = \"%s\"", classTable, name); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) if (differentString("NULL",row[0])) printf("Gene Type : %s
\n", row[0]); } } } if (gp->next != NULL) printf("
"); } genePredFreeList(&gpList); sqlFreeResult(&sr); hFreeConn(&conn); } void showGenePosMouse(char *name, struct trackDb *tdb, struct sqlConnection *connMm) /* Show gene prediction position and other info. */ { char query[512]; char *rootTable = tdb->table; struct sqlResult *sr; char **row; struct genePred *gp = NULL; boolean hasBin; int posCount = 0; char table[64] ; hFindSplitTable(database, seqName, rootTable, table, &hasBin); sprintf(query, "select * from %s where name = '%s'", table, name); sr = sqlGetResult(connMm, query); while ((row = sqlNextRow(sr)) != NULL) { if (posCount > 0) printf("
\n"); ++posCount; gp = genePredLoad(row + hasBin); printPos(gp->chrom, gp->txStart, gp->txEnd, gp->strand, FALSE, NULL); genePredFree(&gp); } sqlFreeResult(&sr); } void linkToPal(char *track, char *chrom, int start, int end, char *geneName) /* Make anchor tag to open pal window */ { printf("", geneName, hgPalName(), track, geneName, chrom, start, end); printf("CDS FASTA alignment from multiple alignment"); } void addPalLink(struct sqlConnection *conn, char *track, char *chrom, int start, int end, char *geneName) { struct slName *list = hTrackTablesOfType(conn, "wigMaf%%"); if (list != NULL) { puts("
\n", buffer, ya->yaleId); } sqlFreeResult(&sr); hFreeConn(&conn); } } printf("
Links to sequence:
\n"); printf("- \n");
if ((pepTable != NULL) && hGenBankHaveSeq(database, pepName, pepTable))
{
puts("
- \n"); hgcAnchorSomewhere(pepClick, pepName, pepTable, seqName); printf("Predicted Protein
Links to sequence:
\n"); printf("- \n");
puts("
- \n"); hgcAnchorSomewhere(genomicClick, geneName, geneTable, seqName); printf("Genomic Sequence from assembly\n"); puts(" \n"); printf("
Links to sequence:
\n"); printf("- \n");
if (pepTable != NULL && hTableExists(database, pepTable))
{
hgcAnchorSomewhereDb(pepClick, pepName, pepTable, seqName, mousedb);
printf("
- Translated Protein \n"); } hgcAnchorSomewhereDb(mrnaClick, geneName, geneTrack, seqName, mousedb); printf("
- %s\n", mrnaDescription); hgcAnchorSomewhereDb(genomicClick, geneName, geneTrack, seqName, mousedb); printf("
- Genomic Sequence DNA sequence from assembly\n"); printf("
\n", x->oldId); printf("New ID: %s
\n", naForEmpty(x->newId)); printf("Old/New Mapping: %s
\n", x->status); if (x->note[0] != 0) printf("Notes: %s
\n", x->note); printf("
\n"); } sqlFreeResult(&sr); } geneShowCommon(item, tdb, pepTable); } void pslDumpHtml(struct psl *pslList) /* print out psl header and data */ { struct psl* psl; printf("
\n");
printf("#match\tmisMatches\trepMatches\tnCount\tqNumInsert\tqBaseInsert\ttNumInsert\tBaseInsert\tstrand\tqName\tqSize\tqStart\tqEnd\ttName\ttSize\ttStart\ttEnd\tblockCount\tblockSizes\tqStarts\ttStarts\n");
for (psl = pslList; psl != NULL; psl = psl->next)
{
pslTabOut(psl, stdout);
}
printf("\n");
}
void genericPslClick(struct sqlConnection *conn, struct trackDb *tdb,
char *item, int start, char *subType)
/* Handle click in generic psl track. */
{
struct psl* pslList = getAlignments(conn, tdb->table, item);
/* check if there is an alignment available for this sequence. This checks
* both genbank sequences and other sequences in the seq table. If so,
* set it up so they can click through to the alignment. */
if (hGenBankHaveSeq(database, item, NULL))
{
printf("%s/Genomic Alignments
", item); if (sameString("protein", subType)) printAlignments(pslList, start, "htcProteinAli", tdb->table, item); else printAlignments(pslList, start, "htcCdnaAli", tdb->table, item); } else { /* just dump the psls */ pslDumpHtml(pslList); } pslFreeList(&pslList); } static char *getParentTableName(struct trackDb *tdb) /* Get the track table or composite track parent table if applicable. */ { tdb = trackDbTopLevelSelfOrParent(tdb); return tdb->table; } static char *getParentTrackName(struct trackDb *tdb) /* Get the track name or composite track parent name if applicable. */ { tdb = trackDbTopLevelSelfOrParent(tdb); return tdb->track; } void printTBSchemaLink(struct trackDb *tdb) /* Make link to TB schema -- unless this is an on-the-fly (tableless) track. */ { if (hTableOrSplitExists(database, tdb->table)) { char *trackTable = getParentTableName(tdb); printf("\n", database, tdb->grp, trackTable, tdb->table, seqName, winStart+1, winEnd); } } void printTrackUiLink(struct trackDb *tdb) /* Make link to hgTrackUi. */ { char *trackName = getParentTrackName(tdb); struct trackDb *parentTdb = tdb; if (!sameString(trackName, tdb->track)) parentTdb = hTrackDbForTrack(database, trackName); printf("\n", trackName, cartSidUrlString(cart), parentTdb->shortLabel); } void printDataVersion(struct trackDb *tdb) /* If this annotation has a dataVersion trackDb setting, print it */ { metadataForTable(database,tdb,NULL); const char *version = metadataFindValue(tdb,"dataVersion"); if(version != NULL) printf("Data version: %s\n", version); else { version = trackDbSetting(tdb,"dataVersion"); if (version != NULL) printf("Data version: %s
\n", version); } } void printDataRestrictionDate(struct trackDb *tdb) /* If this annotation has a dateUnrestricted trackDb setting, print it */ { char *restrictionDate = encodeRestrictionDateDisplay(database,tdb); if (restrictionDate != NULL) { printf("Restricted until: %s
\n", restrictionDate); freeMem(restrictionDate); } } void printOrigAssembly(struct trackDb *tdb) /* If this annotation has been lifted, print the original * freeze, as indicated by the "origAssembly" trackDb setting */ { trackDbOrigAssembly(tdb); trackDbPrintOrigAssembly(tdb, database); } static char *getHtmlFromSelfOrParent(struct trackDb *tdb) /* Get html from self or from parent if not in self. */ { for (;tdb != NULL; tdb = tdb->parent) { if (tdb->html != NULL && tdb->html[0] != 0) return tdb->html; } return NULL; } void printTrackHtml(struct trackDb *tdb) /* If there's some html associated with track print it out. Also print * last update time for data table and make a link * to the TB table schema page for this table. */ { char *tableName; if (!isCustomTrack(tdb->track)) { extraUiLinks(database,tdb,trackHash); printTrackUiLink(tdb); printDataVersion(tdb); printOrigAssembly(tdb); if ((tableName = hTableForTrack(database, tdb->table)) != NULL) { struct sqlConnection *conn = hAllocConnTrack(database, tdb); char *date = firstWordInLine(sqlTableUpdate(conn, tableName)); if (date != NULL) printf("Data last updated: %s
\n", date); hFreeConn(&conn); } printDataRestrictionDate(tdb); } char *html = getHtmlFromSelfOrParent(tdb); if (html != NULL && html[0] != 0) { htmlHorizontalLine(); // Add pennantIcon printPennantIconNote(tdb); puts(html); } hPrintf("
\n"); } void qChainRangePlusStrand(struct chain *chain, int *retQs, int *retQe) /* Return range of bases covered by chain on q side on the plus * strand. */ { if (chain == NULL) errAbort("Can't find range in null query chain."); if (chain->qStrand == '-') { *retQs = chain->qSize - chain->qEnd+1; *retQe = chain->qSize - chain->qStart; } else { *retQs = chain->qStart+1; *retQe = chain->qEnd; } } struct chain *chainDbLoad(struct sqlConnection *conn, char *db, char *track, char *chrom, int id) /* Load chain. */ { char table[64]; char query[256]; struct sqlResult *sr; char **row; int rowOffset; struct chain *chain; if (!hFindSplitTable(db, seqName, track, table, &rowOffset)) errAbort("No %s track in database %s for %s", track, db, seqName); snprintf(query, sizeof(query), "select * from %s where id = %d", table, id); sr = sqlGetResult(conn, query); row = sqlNextRow(sr); if (row == NULL) errAbort("Can't find %d in %s", id, table); chain = chainHeadLoad(row + rowOffset); sqlFreeResult(&sr); chainDbAddBlocks(chain, track, conn); return chain; } void linkToOtherBrowserExtra(char *otherDb, char *chrom, int start, int end, char *extra) /* Make anchor tag to open another browser window. */ { printf("", hgTracksName(), otherDb, extra, chrom, start+1, end); } void linkToOtherBrowserSearch(char *otherDb, char *tag) /* Make anchor tag to open another browser window. */ { printf("", hgTracksName(), otherDb, tag); } void linkToOtherBrowser(char *otherDb, char *chrom, int start, int end) /* Make anchor tag to open another browser window. */ { printf("", hgTracksName(), otherDb, chrom, start+1, end); } void linkToOtherBrowserTitle(char *otherDb, char *chrom, int start, int end, char *title) /* Make anchor tag to open another browser window. */ { printf("", title, hgTracksName(), otherDb, chrom, start+1, end); } void chainToOtherBrowser(struct chain *chain, char *otherDb, char *otherOrg) /* Put up link that lets us use chain to browser on * corresponding window of other species. */ { struct chain *subChain = NULL, *toFree = NULL; int qs,qe; chainSubsetOnT(chain, winStart, winEnd, &subChain, &toFree); if (subChain != NULL && otherOrg != NULL) { qChainRangePlusStrand(subChain, &qs, &qe); linkToOtherBrowser(otherDb, subChain->qName, qs-1, qe); printf("Open %s browser at position corresponding to the part of chain that is in this window.
\n", otherOrg); } chainFree(&toFree); } void genericChainClick(struct sqlConnection *conn, struct trackDb *tdb, char *item, int start, char *otherDb) /* Handle click in chain track, at least the basics. */ { char *thisOrg = hOrganism(database); char *otherOrg = NULL; struct chain *chain = NULL, *subChain = NULL, *toFree = NULL; int chainWinSize; double subSetScore = 0.0; int qs, qe; boolean nullSubset = FALSE; if (! sameWord(otherDb, "seq")) { otherOrg = hOrganism(otherDb); } if (otherOrg == NULL) { /* use first word of chain label (count on org name as first word) */ otherOrg = firstWordInLine(cloneString(tdb->shortLabel)); } chain = chainLoadIdRange(database, tdb->table, seqName, winStart, winEnd, atoi(item)); chainSubsetOnT(chain, winStart, winEnd, &subChain, &toFree); if (subChain == NULL) nullSubset = TRUE; else if (hDbIsActive(otherDb) && subChain != chain) { char *linearGap = trackDbSettingOrDefault(tdb, "chainLinearGap", "loose"); struct gapCalc *gapCalc = gapCalcFromFile(linearGap); struct axtScoreScheme *scoreScheme = axtScoreSchemeDefault(); int qStart = subChain->qStart; int qEnd = subChain->qEnd ; struct dnaSeq *tSeq = hDnaFromSeq(database, subChain->tName, subChain->tStart, subChain->tEnd, dnaLower); struct dnaSeq *qSeq = NULL; char *matrix = trackDbSetting(tdb, "matrix"); if (matrix != NULL) { char *words[64]; int size = chopByWhite(matrix, words, 64) ; if (size == 2 && atoi(words[0]) == 16) { scoreScheme = axtScoreSchemeFromBlastzMatrix(words[1], 400, 30); } else { if (size != 2) errAbort("error parsing matrix entry in trackDb, expecting 2 word got %d ", size); else errAbort("error parsing matrix entry in trackDb, size 16 matrix, got %d ", atoi(words[0])); } } if (subChain->qStrand == '-') reverseIntRange(&qStart, &qEnd, subChain->qSize); qSeq = hChromSeq(otherDb, subChain->qName, qStart, qEnd); if (subChain->qStrand == '-') reverseComplement(qSeq->dna, qSeq->size); subChain->score = chainCalcScoreSubChain(subChain, scoreScheme, gapCalc, qSeq, tSeq); subSetScore = subChain->score; } chainFree(&toFree); printf("%s position: %s:%d-%d" " size: %d
\n", thisOrg, hgTracksName(), cartSidUrlString(cart), database, chain->tName, chain->tStart+1, chain->tEnd, chain->tName, chain->tStart+1, chain->tEnd, chain->tEnd-chain->tStart); printf("Strand: %c
\n", chain->qStrand); qChainRangePlusStrand(chain, &qs, &qe); if (sameWord(otherDb, "seq")) { printf("%s position: %s:%d-%d size: %d
\n", otherOrg, chain->qName, qs, qe, chain->qEnd - chain->qStart); } else { /* prints link to other db browser only if db exists and is active */ /* else just print position with no link for the other db */ printf("%s position: ", otherOrg); if (hDbIsActive(otherDb)) printf(" ", hgTracksName(), otherDb, chain->qName, qs, qe); printf("%s:%d-%d", chain->qName, qs, qe); if (hDbIsActive(otherDb)) printf(""); printf(" size: %d
\n", chain->qEnd - chain->qStart); } printf("Chain ID: %s
\n", item); printf("Score: %1.0f\n", chain->score); if (nullSubset) printf("Score within browser window: N/A (no aligned bases)
\n"); else if (hDbIsActive(otherDb) && subChain != chain) printf(" Approximate Score within browser window: %1.0f
\n", subSetScore); else printf("
\n"); printf("
Fields above refer to entire chain or gap, not just the part inside the window.
\n"); boolean normScoreAvailable = chainDbNormScoreAvailable(tdb); if (normScoreAvailable) { boolean hasBin; char tableName[HDB_MAX_TABLE_STRING]; hFindSplitTable(database, chain->tName, tdb->table, tableName, &hasBin); char query[256]; struct sqlResult *sr; char **row; safef(query, ArraySize(query), "select normScore from %s where id = '%s'", tableName, item); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) printf("Normalized Score: %1.0f (bases matched: %d)
\n", atof(row[0]), (int) (chain->score/atof(row[0]))); sqlFreeResult(&sr); } printf("
\n"); chainWinSize = min(winEnd-winStart, chain->tEnd - chain->tStart); /* Show alignment if the database exists and */ /* if there is a chromInfo table for that database and the sequence */ /* file exists. This means that alignments can be shown on the archive */ /* server (or in other cases) if there is a database with a chromInfo table, */ /* the sequences are available and there is an entry added to dbDb for */ /* the otherDb. */ if (sqlDatabaseExists(otherDb) && chromSeqFileExists(otherDb, chain->qName)) { if (chainWinSize < 1000000) { hgcAnchorSomewhere("htcChainAli", item, tdb->track, chain->tName); printf("View details of parts of chain within browser " "window.
\n"); } else { printf("Zoom so that browser window covers 1,000,000 bases or less " "and return here to see alignment details.
\n"); } if (!sameWord(otherDb, "seq") && (hDbIsActive(otherDb))) { chainToOtherBrowser(chain, otherDb, otherOrg); } } /* if (!sameWord(otherDb, "seq") && (hDbIsActive(otherDb))) { chainToOtherBrowser(chain, otherDb, otherOrg); } */ chainFree(&chain); } char *trackTypeInfo(char *track) /* Return type info on track. You can freeMem result when done. */ { struct slName *trackDbs = hTrackDbList(), *oneTrackDb; struct sqlConnection *conn = hAllocConn(database); char buf[512]; char query[256]; for (oneTrackDb = trackDbs; oneTrackDb != NULL; oneTrackDb = oneTrackDb->next) { if (sqlTableExists(conn, oneTrackDb->name)) { safef(query, sizeof(query), "select type from %s where tableName = '%s'", oneTrackDb->name, track); if (sqlQuickQuery(conn, query, buf, sizeof(buf)) != NULL) break; } } if (oneTrackDb == NULL) errAbort("%s isn't in the trackDb from the hg.conf", track); slNameFreeList(&trackDbs); hFreeConn(&conn); return cloneString(buf); } void findNib(char *db, char *chrom, char nibFile[512]) /* Find nib file corresponding to chromosome in given database. */ { struct sqlConnection *conn = sqlConnect(db); char query[256]; snprintf(query, sizeof(query), "select fileName from chromInfo where chrom = '%s'", chrom); if (sqlQuickQuery(conn, query, nibFile, 512) == NULL) errAbort("Sequence %s isn't in database %s", chrom, db); sqlDisconnect(&conn); } struct dnaSeq *loadGenomePart(char *db, char *chrom, int start, int end) /* Load genomic dna from given database and position. */ { char nibFile[512]; findNib(db, chrom, nibFile); return hFetchSeq(nibFile, chrom, start, end); } void printLabeledNumber(char *org, char *label, long long number) /* Print label: in bold face, and number with commas. */ { char *space = " "; if (org == NULL) org = space = ""; printf("%s%s%s: ", org, space, label); printLongWithCommas(stdout, number); printf("
\n"); } void printLabeledPercent(char *org, char *label, long p, long q) /* Print label: in bold, then p, and then 100 * p/q */ { char *space = " "; if (org == NULL) org = space = ""; printf("%s%s%s: ", org, space, label); printLongWithCommas(stdout, p); if (q != 0) printf(" (%3.1f%%)", 100.0 * p / q); printf("
\n"); } void genericNetClick(struct sqlConnection *conn, struct trackDb *tdb, char *item, int start, char *otherDb, char *chainTrack) /* Generic click handler for net tracks. */ { char table[64]; int rowOffset; char query[256]; struct sqlResult *sr; char **row; struct netAlign *net; char *org = hOrganism(database); char *otherOrg = hOrganism(otherDb); char *otherOrgBrowser = otherOrg; int tSize, qSize; int netWinSize; struct chain *chain; if (otherOrg == NULL) { /* use first word in short track label */ otherOrg = firstWordInLine(cloneString(tdb->shortLabel)); } hFindSplitTable(database, seqName, tdb->table, table, &rowOffset); snprintf(query, sizeof(query), "select * from %s where tName = '%s' and tStart <= %d and tEnd > %d " "and level = %s", table, seqName, start, start, item); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) == NULL) errAbort("Couldn't find %s:%d in %s", seqName, start, table); net = netAlignLoad(row+rowOffset); sqlFreeResult(&sr); tSize = net->tEnd - net->tStart; qSize = net->qEnd - net->qStart; if (net->chainId != 0) { netWinSize = min(winEnd-winStart, net->tEnd - net->tStart); printf("
\n"); /* Show alignment if the database exists and */ /* if there is a chromInfo table for that database and the sequence */ /* file exists. This means that alignments can be shown on the archive */ /* server (or in other cases) if there is a database with a chromInfo */ /* table, the sequences are available and there is an entry added to */ /* dbDb for the otherDb. */ if (chromSeqFileExists(otherDb, net->qName)) { if (netWinSize < 1000000) { int ns = max(winStart, net->tStart); int ne = min(winEnd, net->tEnd); if (ns < ne) { char id[20]; snprintf(id, sizeof(id), "%d", net->chainId); hgcAnchorWindow("htcChainAli", id, ns, ne, chainTrack, seqName); printf("View alignment details of parts of net within browser window.
\n"); } else { printf("Odd, net not in window
\n"); } } else { printf("To see alignment details zoom so that the browser window covers 1,000,000 bases or less.
\n"); } } chain = chainDbLoad(conn, database, chainTrack, seqName, net->chainId); if (chain != NULL) { /* print link to browser for otherDb only if otherDb is active */ if (hDbIsActive(otherDb)) chainToOtherBrowser(chain, otherDb, otherOrgBrowser); chainFree(&chain); } htmlHorizontalLine(); } printf("Type: %s
\n", net->type); printf("Level: %d
\n", (net->level+1)/2); printf("%s position: %s:%d-%d
\n", org, net->tName, net->tStart+1, net->tEnd); printf("%s position: %s:%d-%d
\n", otherOrg, net->qName, net->qStart+1, net->qEnd); printf("Strand: %c
\n", net->strand[0]); printLabeledNumber(NULL, "Score", net->score); if (net->chainId) { printf("Chain ID: %u
\n", net->chainId); printLabeledNumber(NULL, "Bases aligning", net->ali); if (net->qOver >= 0) printLabeledNumber(otherOrg, "parent overlap", net->qOver); if (net->qFar >= 0) printLabeledNumber(otherOrg, "parent distance", net->qFar); if (net->qDup >= 0) printLabeledNumber(otherOrg, "bases duplicated", net->qDup); } if (net->tN >= 0) printLabeledPercent(org, "N's", net->tN, tSize); if (net->qN >= 0) printLabeledPercent(otherOrg, "N's", net->qN, qSize); if (net->tTrf >= 0) printLabeledPercent(org, "tandem repeat (trf) bases", net->tTrf, tSize); if (net->qTrf >= 0) printLabeledPercent(otherOrg, "tandem repeat (trf) bases", net->qTrf, qSize); if (net->tR >= 0) printLabeledPercent(org, "RepeatMasker bases", net->tR, tSize); if (net->qR >= 0) printLabeledPercent(otherOrg, "RepeatMasker bases", net->qR, qSize); if (net->tOldR >= 0) printLabeledPercent(org, "old repeat bases", net->tOldR, tSize); if (net->qOldR >= 0) printLabeledPercent(otherOrg, "old repeat bases", net->qOldR, qSize); if (net->tNewR >= 0) printLabeledPercent(org, "new repeat bases", net->tOldR, tSize); if (net->qNewR >= 0) printLabeledPercent(otherOrg, "new repeat bases", net->qOldR, qSize); if (net->tEnd >= 0) printLabeledNumber(org, "size", net->tEnd - net->tStart); if (net->qEnd >= 0) printLabeledNumber(otherOrg, "size", net->qEnd - net->qStart); printf("
Fields above refer to entire chain or gap, not just the part inside the window.
\n"); netAlignFree(&net); } void tfbsConsSites(struct trackDb *tdb, char *item) /* detail page for tfbsConsSites track */ { boolean printedPlus = FALSE; boolean printedMinus = FALSE; char *dupe, *words[16]; int wordCount; int start = cartInt(cart, "o"); struct sqlConnection *conn = hAllocConn(database); char table[64]; boolean hasBin; char query[512]; struct sqlResult *sr; char **row; struct tfbsConsSites *tfbsConsSites; struct tfbsConsSites *tfbsConsSitesList = NULL; struct tfbsConsFactors *tfbsConsFactor; struct tfbsConsFactors *tfbsConsFactorList = NULL; boolean firstTime = TRUE; char *mappedId = NULL; char protMapTable[256]; char *factorDb; dupe = cloneString(tdb->type); genericHeader(tdb, item); wordCount = chopLine(dupe, words); hFindSplitTable(database, seqName, tdb->table, table, &hasBin); sprintf(query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", table, item, seqName, start); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { tfbsConsSites = tfbsConsSitesLoad(row+hasBin); slAddHead(&tfbsConsSitesList, tfbsConsSites); } sqlFreeResult(&sr); slReverse(&tfbsConsSitesList); hFindSplitTable(database, seqName, "tfbsConsFactors", table, &hasBin); sprintf(query, "select * from %s where name = '%s' ", table, item); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { tfbsConsFactor = tfbsConsFactorsLoad(row+hasBin); slAddHead(&tfbsConsFactorList, tfbsConsFactor); } sqlFreeResult(&sr); slReverse(&tfbsConsFactorList); if (tfbsConsFactorList) mappedId = cloneString(tfbsConsFactorList->ac); printf("Transcription Factor Binding Site information:
"); for(tfbsConsSites=tfbsConsSitesList ; tfbsConsSites != NULL ; tfbsConsSites = tfbsConsSites->next) { /* print each strand only once */ if ((printedMinus && (tfbsConsSites->strand[0] == '-')) || (printedPlus && (tfbsConsSites->strand[0] == '+'))) continue; if (!firstTime) htmlHorizontalLine(); else firstTime = FALSE; printf("Item: %s
\n", tfbsConsSites->name); if (mappedId != NULL) printCustomUrl(tdb, mappedId, FALSE); printf("Score: %d
\n", tfbsConsSites->score ); printf("zScore: %.2f
\n", tfbsConsSites->zScore ); printf("Strand: %s
\n", tfbsConsSites->strand); printPos(tfbsConsSites->chrom, tfbsConsSites->chromStart, tfbsConsSites->chromEnd, NULL, TRUE, tfbsConsSites->name); printedPlus = printedPlus || (tfbsConsSites->strand[0] == '+'); printedMinus = printedMinus || (tfbsConsSites->strand[0] == '-'); } if (tfbsConsFactorList) { htmlHorizontalLine(); printf("Transcription Factors known to bind to this site:
"); for(tfbsConsFactor =tfbsConsFactorList ; tfbsConsFactor != NULL ; tfbsConsFactor = tfbsConsFactor ->next) { if (!sameString(tfbsConsFactor->species, "N")) { printf("
Factor: %s
\n", tfbsConsFactor->factor); printf("Species: %s
\n", tfbsConsFactor->species); printf("SwissProt ID: %s
\n", sameString(tfbsConsFactor->id, "N")? "unknown": tfbsConsFactor->id); factorDb = hDefaultDbForGenome(tfbsConsFactor->species); safef(protMapTable, sizeof(protMapTable), "%s.kgProtMap", factorDb); /* Only display link if entry exists in protein browser */ if (hTableExists(database, protMapTable)) { sprintf(query, "select * from %s where qName = '%s'", protMapTable, tfbsConsFactor->id ); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { printf("Proteome Browser Entry
", tfbsConsFactor->id,factorDb); sqlFreeResult(&sr); } } } } } printTrackHtml(tdb); freez(&dupe); hFreeConn(&conn); } void tfbsCons(struct trackDb *tdb, char *item) /* detail page for tfbsCons track */ { boolean printFactors = FALSE; boolean printedPlus = FALSE; boolean printedMinus = FALSE; char *dupe, *words[16]; int wordCount; int start = cartInt(cart, "o"); struct sqlConnection *conn = hAllocConn(database); char table[64]; boolean hasBin; char query[512]; struct sqlResult *sr; char **row; struct tfbsCons *tfbs; struct tfbsCons *tfbsConsList = NULL; struct tfbsConsMap tfbsConsMap; boolean firstTime = TRUE; char *mappedId = NULL; dupe = cloneString(tdb->type); genericHeader(tdb, item); wordCount = chopLine(dupe, words); hFindSplitTable(database, seqName, tdb->table, table, &hasBin); sprintf(query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", table, item, seqName, start); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { tfbs = tfbsConsLoad(row+hasBin); slAddHead(&tfbsConsList, tfbs); } sqlFreeResult(&sr); slReverse(&tfbsConsList); if (hTableExists(database, "tfbsConsMap")) { sprintf(query, "select * from tfbsConsMap where id = '%s'", tfbsConsList->name); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { tfbsConsMapStaticLoad(row, &tfbsConsMap); mappedId = cloneString(tfbsConsMap.ac); } } sqlFreeResult(&sr); printf("Transcription Factor Binding Site information:
"); for(tfbs=tfbsConsList ; tfbs != NULL ; tfbs = tfbs->next) { if (!sameString(tfbs->species, "N")) printFactors = TRUE; /* print each strand only once */ if ((printedMinus && (tfbs->strand[0] == '-')) || (printedPlus && (tfbs->strand[0] == '+'))) continue; if (!firstTime) htmlHorizontalLine(); else firstTime = FALSE; printf("Item: %s
\n", tfbs->name); if (mappedId != NULL) printCustomUrl(tdb, mappedId, FALSE); printf("Score: %d
\n", tfbs->score ); printf("Strand: %s
\n", tfbs->strand); printPos(tfbsConsList->chrom, tfbs->chromStart, tfbs->chromEnd, NULL, TRUE, tfbs->name); printedPlus = printedPlus || (tfbs->strand[0] == '+'); printedMinus = printedMinus || (tfbs->strand[0] == '-'); } if (printFactors) { char protMapTable[256]; char *factorDb; htmlHorizontalLine(); printf("Transcription Factors known to bind to this site:
"); for(tfbs=tfbsConsList ; tfbs != NULL ; tfbs = tfbs->next) { /* print only the positive strand when factors are on both strands */ if ((tfbs->strand[0] == '-') && printedPlus) continue; if (!sameString(tfbs->species, "N")) { printf("
Factor: %s
\n", tfbs->factor); printf("Species: %s
\n", tfbs->species); printf("SwissProt ID: %s
\n", sameString(tfbs->id, "N")? "unknown": tfbs->id); factorDb = hDefaultDbForGenome(tfbs->species); safef(protMapTable, sizeof(protMapTable), "%s.kgProtMap", factorDb); /* Only display link if entry exists in protein browser */ if (hTableExists(database, protMapTable)) { sprintf(query, "select * from %s where qName = '%s';", protMapTable, tfbs->id ); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { printf("Proteome Browser
", tfbs->id); sqlFreeResult(&sr); } } } } } printTrackHtml(tdb); freez(&dupe); hFreeConn(&conn); } void firstEF(struct trackDb *tdb, char *item) { char *dupe, *words[16]; int wordCount; int start = cartInt(cart, "o"); struct sqlConnection *conn = hAllocConn(database); char table[64]; boolean hasBin; struct bed *bed; char query[512]; struct sqlResult *sr; char **row; boolean firstTime = TRUE; /* itemForUrl = item; */ dupe = cloneString(tdb->type); genericHeader(tdb, item); wordCount = chopLine(dupe, words); printCustomUrl(tdb, item, FALSE); /* printCustomUrl(tdb, itemForUrl, item == itemForUrl); */ hFindSplitTable(database, seqName, tdb->table, table, &hasBin); sprintf(query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", table, item, seqName, start); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { if (firstTime) firstTime = FALSE; else htmlHorizontalLine(); bed = bedLoadN(row+hasBin, 6); printf("Item: %s
\n", bed->name); printf("Probability: %g
\n", bed->score / 1000.0); printf("Strand: %s
\n", bed->strand); printPos(bed->chrom, bed->chromStart, bed->chromEnd, NULL, TRUE, bed->name); } printTrackHtml(tdb); freez(&dupe); hFreeConn(&conn); } void doBed5FloatScore(struct trackDb *tdb, char *item) /* Handle click in BED 5+ track: BED 5 with 0-1000 score (for useScore * shading in hgTracks) plus real score for display in details page. */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr = NULL; char table[64]; boolean hasBin; struct bed5FloatScore *b5; struct dyString *query = newDyString(512); char **row; boolean firstTime = TRUE; int start = cartInt(cart, "o"); int bedSize = 5; hFindSplitTable(database, seqName, tdb->table, table, &hasBin); dyStringPrintf(query, "select * from %s where chrom = '%s' and ", table, seqName); hAddBinToQuery(winStart, winEnd, query); dyStringPrintf(query, "name = '%s' and chromStart = %d", item, start); sr = sqlGetResult(conn, query->string); while ((row = sqlNextRow(sr)) != NULL) { if (firstTime) firstTime = FALSE; else htmlHorizontalLine(); b5 = bed5FloatScoreLoad(row+hasBin); bedPrintPos((struct bed *)b5, 4, tdb); printf("Score: %f
\n", b5->floatScore); if (sameString(tdb->type, "bed5FloatScoreWithFdr")) { if (row[7] != NULL) printf("False Discovery Rate (FDR): %s%%
\n", row[7]); } } getBedTopScorers(conn, tdb, table, item, start, bedSize); sqlFreeResult(&sr); hFreeConn(&conn); /* printTrackHtml is done in genericClickHandlerPlus. */ } void doBed6FloatScore(struct trackDb *tdb, char *item) /* Handle click in BED 4+ track that's like BED 6 but with floating pt score */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr = NULL; char table[64]; boolean hasBin; struct bed6FloatScore *b6; struct dyString *query = newDyString(512); char **row; boolean firstTime = TRUE; int start = cartInt(cart, "o"); genericHeader(tdb, item); hFindSplitTable(database, seqName, tdb->table, table, &hasBin); dyStringPrintf(query, "select * from %s where chrom = '%s' and ", table, seqName); hAddBinToQuery(winStart, winEnd, query); dyStringPrintf(query, "name = '%s' and chromStart = %d", item, start); sr = sqlGetResult(conn, query->string); while ((row = sqlNextRow(sr)) != NULL) { if (firstTime) firstTime = FALSE; else htmlHorizontalLine(); b6 = bed6FloatScoreLoad(row+hasBin); bedPrintPos((struct bed *)b6, 4, tdb); printf("Score: %f
\n", b6->score); printf("Strand: %s
\n", b6->strand); } sqlFreeResult(&sr); hFreeConn(&conn); /* printTrackHtml is done in genericClickHandlerPlus. */ } void doColoredExon(struct trackDb *tdb, char *item) /* Print information for coloredExon type tracks. */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char query[256]; char **row; genericHeader(tdb, item); safef(query, sizeof(query), "select chrom,chromStart,chromEnd,name,score,strand from %s where name='%s'", tdb->table, item); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { struct bed *itemBed = bedLoad6(row); bedPrintPos(itemBed, 6, tdb); bedFree(&itemBed); } else { hPrintf("Could not find info for %s
\n", item); } sqlFreeResult(&sr); printTrackHtml(tdb); hFreeConn(&conn); } void doImageItemBed(struct trackDb *tdb, char *item) /* Print bed plus an image */ { } void doChromGraph(struct trackDb *tdb) /* Print information for coloredExon type tracks. */ { genericHeader(tdb, NULL); printTrackHtml(tdb); } static void genericContainerClick(struct sqlConnection *conn, char *containerType, struct trackDb *tdb, char *item, char *itemForUrl) /* Print page for container of some sort. */ { if (sameString(containerType, "multiWig")) { errAbort("It's suprising that multiWig container gets to hgc. It should go to hgTrackUi."); } else { errAbort("Unrecognized container type %s for %s", containerType, tdb->track); } } void genericClickHandlerPlus( struct trackDb *tdb, char *item, char *itemForUrl, char *plus) /* Put up generic track info, with additional text appended after item. */ { char *dupe, *type, *words[16], *headerItem; int wordCount; int start = cartInt(cart, "o"); struct sqlConnection *conn = hAllocConnTrack(database, tdb); char *imagePath = trackDbSetting(tdb, ITEM_IMAGE_PATH); char *container = trackDbSetting(tdb, "container"); if (itemForUrl == NULL) itemForUrl = item; dupe = cloneString(tdb->type); wordCount = chopLine(dupe, words); headerItem = cloneString(item); /* Suppress printing item name in page header, as it is not informative for these types of * tracks... */ if (container == NULL && wordCount > 0) { type = words[0]; if (sameString(type, "maf") || sameString(type, "wigMaf") || sameString(type, "netAlign") || sameString(type, "encodePeak")) headerItem = NULL; else if ((sameString(type, "narrowPeak") || sameString(type, "broadPeak") || sameString(type, "gappedPeak")) && headerItem && sameString(headerItem, ".")) headerItem = NULL; } /* Print header. */ genericHeader(tdb, headerItem); printCustomUrl(tdb, itemForUrl, item == itemForUrl); if (plus != NULL) { fputs(plus, stdout); } if (container != NULL) { genericContainerClick(conn, container, tdb, item, itemForUrl); } else if (wordCount > 0) { type = words[0]; if (sameString(type, "bed")) { int num = 0; if (wordCount > 1) num = atoi(words[1]); if (num < 3) num = 3; genericBedClick(conn, tdb, item, start, num); } else if (sameString(type, "bigBed")) { int num = 0; if (wordCount > 1) num = atoi(words[1]); if (num < 3) num = 3; genericBigBedClick(conn, tdb, item, start, num); } else if (sameString(type, "sample")) { int num = 9; genericSampleClick(conn, tdb, item, start, num); } else if (sameString(type, "genePred")) { char *pepTable = NULL, *mrnaTable = NULL; if ((wordCount > 1) && !sameString(words[1], ".")) pepTable = words[1]; if ((wordCount > 2) && !sameString(words[2], ".")) mrnaTable = words[2]; genericGenePredClick(conn, tdb, item, start, pepTable, mrnaTable); } else if (sameString(type, "psl")) { char *subType = "."; if (wordCount > 1) subType = words[1]; genericPslClick(conn, tdb, item, start, subType); } else if (sameString(type, "netAlign")) { if (wordCount < 3) errAbort("Missing field in netAlign track type field"); genericNetClick(conn, tdb, item, start, words[1], words[2]); } else if (sameString(type, "chain")) { if (wordCount < 2) errAbort("Missing field in chain track type field"); genericChainClick(conn, tdb, item, start, words[1]); } else if (sameString(type, "maf")) { genericMafClick(conn, tdb, item, start); } else if (sameString(type, "wigMaf")) { genericMafClick(conn, tdb, item, start); } else if (startsWith("wigMafProt", type)) { genericMafClick(conn, tdb, item, start); } else if (sameString(type, "axt")) { genericAxtClick(conn, tdb, item, start, words[1]); } else if (sameString(type, "expRatio")) { doExpRatio(tdb, item, NULL); } else if (sameString(type, "coloredExon")) { doColoredExon(tdb, item); } else if (sameString(type, "encodePeak") || sameString(type, "narrowPeak") || sameString(type, "broadPeak") || sameString(type, "gappedPeak")) { doEncodePeak(tdb, NULL); } else if (sameString(type, "encodeFiveC")) { doEncodeFiveC(conn, tdb); } else if (sameString(type, "chromGraph")) { doChromGraph(tdb); } else if (sameString(type, "wig")) { genericWiggleClick(conn, tdb, item, start); } else if (sameString(type, "bigWig")) { genericBigWigClick(conn, tdb, item, start); } else if (sameString(type, "factorSource")) { doFactorSource(conn, tdb, item, start); } else if (sameString(type, "bed5FloatScore") || sameString(type, "bed5FloatScoreWithFdr")) { doBed5FloatScore(tdb, item); } else if (sameString(type, "bed6FloatScore")) { doBed6FloatScore(tdb, item); } else if (sameString(type, "altGraphX")) { doAltGraphXDetails(tdb,item); } //add bedDetail here else if (startsWith("bedDetail", type)) { doBedDetail(tdb, NULL, item); } #ifdef USE_BAM else if (sameString(type, "bam")) doBamDetails(tdb, item); #endif // USE_BAM } if (imagePath) { char *bigImagePath = trackDbSettingClosestToHome(tdb, ITEM_BIG_IMAGE_PATH); char *bothWords[2]; int shouldBeTwo = chopLine(imagePath, bothWords); if (shouldBeTwo != 2) errAbort("itemImagePath setting for %s track incorrect. Needs to be \"itemImagePath
\n", bothWords[0], item, bothWords[1]); shouldBeTwo = chopLine(bigImagePath, bothWords); if (shouldBeTwo != 2) errAbort("bigItemImagePath setting for %s track incorrect. Needs to be \"itemImagePath
\n", bothWords[0], item, bothWords[1]); } printTrackHtml(tdb); freez(&dupe); hFreeConn(&conn); } void genericClickHandler(struct trackDb *tdb, char *item, char *itemForUrl) /* Put up generic track info */ { #ifdef OLD /* Called now by cartWebStart... */ jsIncludeFile("jquery.js", NULL); jsIncludeFile("utils.js",NULL); #endif /* OLD */ genericClickHandlerPlus(tdb, item, itemForUrl, NULL); } void savePosInTextBox(char *chrom, int start, int end) /* Save basic position/database info in text box and hidden var. Positions becomes chrom:start-end*/ { char position[128]; char *newPos; snprintf(position, 128, "%s:%d-%d", chrom, start, end); newPos = addCommasToPos(database, position); cgiMakeTextVar("getDnaPos", newPos, strlen(newPos) + 2); cgiContinueHiddenVar("db"); } char *hgTablesUrl(boolean usePos, char *track) /* Make up URL for table browser. */ { struct dyString *url = dyStringNew(0); dyStringAppend(url, "../cgi-bin/hgTables?"); dyStringAppend(url, cartSidUrlString(cart)); dyStringPrintf(url, "&db=%s", database); if (usePos) { dyStringPrintf(url, "&position=%s:%d-%d", seqName, winStart+1, winEnd); dyStringAppend(url, "&hgta_regionType=range"); } if (track != NULL) { struct trackDb *tdb = hashFindVal(trackHash, track); if (tdb != NULL) { char *grp = tdb->grp; if (grp != NULL && grp[0] != 0) { dyStringPrintf(url, "&hgta_group=%s", grp); dyStringPrintf(url, "&hgta_track=%s", track); dyStringPrintf(url, "&hgta_table=%s", track); } } } return dyStringCannibalize(&url); } char *traceUrl(char *traceId) /* Make up URL for trace archive. */ { struct dyString *url = dyStringNew(0); dyStringAppend(url, "http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?"); dyStringPrintf(url, "cmd=retrieve&size=1&val=%s&", traceId); dyStringAppend(url, "file=trace&dopt=trace"); return dyStringCannibalize(&url); } void doGetDna1() /* Do first get DNA dialog. */ { struct hTableInfo *hti = NULL; char *tbl = cgiUsualString("table", ""); if (dbIsFound) { char rootName[256]; char parsedChrom[32]; hParseTableName(database, tbl, rootName, parsedChrom); hti = hFindTableInfo(database, seqName, rootName); } char *thisOrg = hOrganism(database); cartWebStart(cart, database, "Get DNA in Window (%s/%s)", database, thisOrg); printf("
Get DNA for
\n"); printf(""); if (dbIsFound) puts("Note: The \"Mask repeats\" option applies only to \"get DNA\", not to \"extended case/color options\".
"); } boolean dnaIgnoreTrack(char *track) /* Return TRUE if this is one of the tracks too boring * to put DNA on. */ { return (sameString("cytoBand", track) || sameString("gcPercent", track) || sameString("gold", track) || sameString("gap", track) || startsWith("mouseSyn", track)); } struct customTrack *getCtList() /* initialize theCtList if necessary and return it */ { if (theCtList == NULL) theCtList = customTracksParseCart(database, cart, NULL, NULL); return(theCtList); } struct trackDb *tdbForCustomTracks() /* Load custom tracks (if any) and translate to list of trackDbs */ { struct customTrack *ctList = getCtList(); struct customTrack *ct; struct trackDb *tdbList = NULL, *tdb; for (ct=ctList; ct != NULL; ct=ct->next) { AllocVar(tdb); tdb->track = ct->tdb->track; tdb->table = ct->tdb->table; tdb->shortLabel = ct->tdb->shortLabel; tdb->type = ct->tdb->type; tdb->longLabel = ct->tdb->longLabel; tdb->visibility = ct->tdb->visibility; tdb->priority = ct->tdb->priority; tdb->colorR = ct->tdb->colorR; tdb->colorG = ct->tdb->colorG; tdb->colorB = ct->tdb->colorB; tdb->altColorR = ct->tdb->altColorR; tdb->altColorG = ct->tdb->altColorG; tdb->altColorB = ct->tdb->altColorB; tdb->useScore = ct->tdb->useScore; tdb->private = ct->tdb->private; tdb->url = ct->tdb->url; tdb->grp = ct->tdb->grp; tdb->canPack = ct->tdb->canPack; trackDbPolish(tdb); slAddHead(&tdbList, tdb); } slReverse(&tdbList); return(tdbList); } struct customTrack *lookupCt(char *name) /* Return custom track for name, or NULL. */ { struct customTrack *ct; for (ct=getCtList(); ct != NULL; ct=ct->next) if (sameString(name, ct->tdb->track)) return(ct); return(NULL); } void parseSs(char *ss, char **retPslName, char **retFaName, char **retQName) /* Parse space separated 'ss' item. */ { static char buf[512*2]; int wordCount; char *words[4]; strcpy(buf, ss); wordCount = chopLine(buf, words); if (wordCount < 1) errAbort("Empty user cart variable ss."); *retPslName = words[0]; if (retFaName != NULL) { if (wordCount < 2) errAbort("Expecting psl filename and fa filename in cart variable ss, but only got one word: %s", ss); *retFaName = words[1]; } if (retQName != NULL) { if (wordCount < 3) errAbort("Expecting psl filename, fa filename and query name in cart variable ss, but got this: %s", ss); *retQName = words[2]; } } boolean ssFilesExist(char *ss) /* Return TRUE if both files in ss exist. -- Copied from hgTracks! */ { char *faFileName, *pslFileName; parseSs(ss, &pslFileName, &faFileName, NULL); return fileExists(pslFileName) && fileExists(faFileName); } struct trackDb *tdbForUserPsl() /* Load up user's BLAT results into trackDb. */ { char *ss = cartOptionalString(cart, "ss"); if ((ss != NULL) && !ssFilesExist(ss)) { ss = NULL; cartRemove(cart, "ss"); } if (ss == NULL) return(NULL); else { struct trackDb *tdb; AllocVar(tdb); tdb->track = cloneString(USER_PSL_TRACK_NAME); tdb->table = cloneString(USER_PSL_TRACK_NAME); tdb->shortLabel = cloneString(USER_PSL_TRACK_LABEL); tdb->type = cloneString("psl"); tdb->longLabel = cloneString(USER_PSL_TRACK_LONGLABEL); tdb->visibility = tvFull; tdb->priority = 11.0; trackDbPolish(tdb); return(tdb); } } void doGetDnaExtended1() /* Do extended case/color get DNA options. */ { struct trackDb *tdbList = hTrackDb(database), *tdb; struct trackDb *ctdbList = tdbForCustomTracks(); struct trackDb *utdbList = tdbForUserPsl(); boolean isRc = cartUsualBoolean(cart, "hgc.dna.rc", FALSE); boolean revComp = cartUsualBoolean(cart, "hgSeq.revComp", FALSE); boolean maskRep = cartUsualBoolean(cart, "hgSeq.maskRepeats", FALSE); int padding5 = cartUsualInt(cart, "hgSeq.padding5", 0); int padding3 = cartUsualInt(cart, "hgSeq.padding3", 0); char *casing = cartUsualString(cart, "hgSeq.casing", ""); char *repMasking = cartUsualString(cart, "hgSeq.repMasking", ""); boolean caseUpper= FALSE; char *pos = NULL; ctdbList = slCat(ctdbList, tdbList); tdbList = slCat(utdbList, ctdbList); cartWebStart(cart, database, "Extended DNA Case/Color"); if (NULL != (pos = stripCommas(cartOptionalString(cart, "getDnaPos")))) hgParseChromRange(database, pos, &seqName, &winStart, &winEnd); if (winEnd - winStart > 1000000) { printf("Please zoom in to 1 million bases or less to color the DNA"); return; } printf("
Extended DNA Case/Color Options
\n"); puts( "Use this page to highlight features in genomic DNA text. " "DNA covered by a particular track can be highlighted by " "case, underline, bold, italic, or color. See below for " "details about color, and for examples. Tracks in " ""hide" display mode are not shown in the grid below."); if (cgiBooleanDefined("hgSeq.revComp")) { isRc = revComp; /* don't set revComp in cart -- it shouldn't be a default. */ } if (cgiBooleanDefined("hgSeq.maskRepeats")) cartSetBoolean(cart, "hgSeq.maskRepeats", maskRep); if (*repMasking != 0) cartSetString(cart, "hgSeq.repMasking", repMasking); if (maskRep) { struct trackDb *rtdb; char *visString = cartOptionalString(cart, "rmsk"); for (rtdb = tdbList; rtdb != NULL; rtdb=rtdb->next) { if (startsWith(rtdb->table, "rmsk")) break; } printf("
Note: repeat masking style from previous page will not apply to this page.\n"); if ((rtdb != NULL) && ((visString == NULL) || !sameString(visString, "hide"))) printf("Use the case/color options for the RepeatMasker track below.
\n"); else printf("Unhide the RepeatMasker track in the genome browser, then return to this page and use the case/color options for the RepeatMasker track below.
\n"); } cartSetInt(cart, "padding5", padding5); cartSetInt(cart, "padding3", padding3); if (sameString(casing, "upper")) caseUpper = TRUE; if (*casing != 0) cartSetString(cart, "hgSeq.casing", casing); printf("
\n"); if (hIsGsidServer()) { printf("Coloring Information and Examples
\n"); puts("The color values range from 0 (darkest) to 255 (lightest) and are additive.\n"); puts("The examples below show a few ways to highlight individual tracks, " "and their interplay. It's good to keep it simple at first. It's easy " "to make pretty but completely cryptic displays with this feature."); puts( "- "
"
- To put Genes in upper case red text, check the " "appropriate box in the Toggle Case column and set the color to pure " "red, RGB (255,0,0). Upon submitting, any Gene within the " "designated chromosomal interval will now appear in red capital letters.\n" "
- To see the overlap between Genes and InterPro Domains try " "setting the Genes/Regions to red (255,0,0) and InterPro to green (0,255,0). " "Places where the Genes and InterPro Domains overlap will be painted yellow " "(255,255,0).\n" "
- To get a level-of-coverage effect for tracks like Genes with " "multiple overlapping items, initially select a darker color such as deep " "green, RGB (0,64,0). Nucleotides covered by a single Gene will appear dark " "green, while regions covered with more Genes get progressively brighter — " "saturating at 4 Genes." "
- Another track can be used to mask unwanted features. Setting the " "InterPro track to RGB (255,255,255) will white-out Genes within InterPro " "domains. " "
Further Details and Ideas
"); puts("Copying and pasting the web page output to a text editor such as Word " "will retain upper case but lose colors and other formatting. That's still " "useful because other web tools such as " "NCBI Blast " "can be set to ignore lower case. To fully capture formatting such as color " "and underlining, view the output as \"source\" in your web browser, or download " "it, or copy the output page into an html editor.
"); puts("The default line width of 60 characters is standard, but if you have " "a reasonable sized monitor it's useful to set this higher - to 125 characters " "or more. You can see more DNA at once this way, and fewer line breaks help " "in finding DNA strings using the web browser search function.
"); } else { printf("Coloring Information and Examples
\n"); puts("The color values range from 0 (darkest) to 255 (lightest) and are additive.\n"); puts("The examples below show a few ways to highlight individual tracks, " "and their interplay. It's good to keep it simple at first. It's easy " "to make pretty but completely cryptic displays with this feature."); puts( "- "
"
- To put exons from RefSeq Genes in upper case red text, check the " "appropriate box in the Toggle Case column and set the color to pure " "red, RGB (255,0,0). Upon submitting, any RefSeq Gene within the " "designated chromosomal interval will now appear in red capital letters.\n" "
- To see the overlap between RefSeq Genes and Genscan predictions try " "setting the RefSeq Genes to red (255,0,0) and Genscan to green (0,255,0). " "Places where the RefSeq Genes and Genscan overlap will be painted yellow " "(255,255,0).\n" "
- To get a level-of-coverage effect for tracks like Spliced Ests with " "multiple overlapping items, initially select a darker color such as deep " "green, RGB (0,64,0). Nucleotides covered by a single EST will appear dark " "green, while regions covered with more ESTs get progressively brighter — " "saturating at 4 ESTs." "
- Another track can be used to mask unwanted features. Setting the " "RepeatMasker track to RGB (255,255,255) will white-out Genscan predictions " "of LINEs but not mainstream host genes; masking with RefSeq Genes will show " "what is new in the gene prediction sector." "
Further Details and Ideas
"); puts("Copying and pasting the web page output to a text editor such as Word " "will retain upper case but lose colors and other formatting. That's still " "useful because other web tools such as " "NCBI Blast " "can be set to ignore lower case. To fully capture formatting such as color " "and underlining, view the output as \"source\" in your web browser, or download " "it, or copy the output page into an html editor.
"); puts("The default line width of 60 characters is standard, but if you have " "a reasonable sized monitor it's useful to set this higher - to 125 characters " "or more. You can see more DNA at once this way, and fewer line breaks help " "in finding DNA strings using the web browser search function.
"); puts("Be careful about requesting complex formatting for a very large " "chromosomal region. After all the html tags are added to the output page, " "the file size may exceed size limits that your browser, clipboard, and " "other software can safely display. The tool will format 10Mbp and more though.
"); } trackDbFreeList(&tdbList); } void doGetBlastPep(char *readName, char *table) /* get predicted protein */ { int qStart; struct psl *psl; int start, end; struct sqlResult *sr; struct sqlConnection *conn = hAllocConn(database); struct dnaSeq *tSeq; char query[256], **row; char fullTable[64]; boolean hasBin; char *buffer, *str; int i, j; char *ptr; start = cartInt(cart, "o"); hFindSplitTable(database, seqName, table, fullTable, &hasBin); sprintf(query, "select * from %s where qName = '%s' and tName = '%s' and tStart=%d", fullTable, readName, seqName, start); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) == NULL) errAbort("Couldn't find alignment for %s at %d", readName, start); psl = pslLoad(row+hasBin); sqlFreeResult(&sr); hFreeConn(&conn); printf("");
end = psl->tEnd;
if (psl->strand[1] == '+')
end = psl->tStarts[psl->blockCount - 1] + psl->blockSizes[psl->blockCount - 1] *3;
if ((ptr = strchr(readName, '.')) != NULL)
*ptr++ = 0;
printf(">%s-%s\n", readName,database);
tSeq = hDnaFromSeq(database, psl->tName, start, end, dnaLower);
if (psl->strand[1] == '-')
{
start = psl->tSize - end;
reverseComplement(tSeq->dna, tSeq->size);
}
str = buffer = needMem(psl->qSize + 1);
qStart = 0;
for (i=0; iblockCount; ++i)
{
int ts = psl->tStarts[i] - start;
int sz = psl->blockSizes[i];
for (;qStart < psl->qStarts[i]; qStart++)
*str++ = 'X';
for (j=0; jdna[codonStart];
if ((*str = lookupCodon(codon)) == 0)
*str = '*';
str++;
qStart++;
}
}
*str = 0;
printLines(stdout, buffer, 50);
printf(" ");
}
void doGetDna2()
/* Do second DNA dialog (or just fetch DNA) */
{
char *tbl = cgiUsualString("table", "");
char *action = cgiUsualString("submit", "");
int itemCount;
char *pos = NULL;
char *chrom = NULL;
int start = 0;
int end = 0;
if (sameString(action, EXTENDED_DNA_BUTTON))
{
doGetDnaExtended1();
return;
}
pushWarnHandler(htmlVaWarn);
hgBotDelay();
puts("");
if (tbl[0] == 0)
{
itemCount = 1;
if ( NULL != (pos = stripCommas(cartOptionalString(cart, "getDnaPos"))) &&
hgParseChromRange((dbIsFound ? database : NULL), pos, &chrom, &start, &end))
{
hgSeqRange(database, chrom, start, end, '?', "dna");
}
else
{
hgSeqRange(database, seqName, cartInt(cart, "l"), cartInt(cart, "r"),
'?', "dna");
}
}
else
{
struct hTableInfo *hti = NULL;
char rootName[256];
char parsedChrom[32];
/* use the values from the dnaPos dialog box */
if (!( NULL != (pos = stripCommas(cartOptionalString(cart, "getDnaPos"))) &&
hgParseChromRange(database, pos, &chrom, &start, &end)))
{
/* if can't get DnaPos from dialog box, use "o" and "t" */
start = cartInt(cart, "o");
end = cartInt(cart, "t");
}
/* Table might be a custom track if it's not in the database,
* or bigBed if it is in the database but has only one column called 'fileName';
* in which case, just get DNA as if no table were given. */
hParseTableName(database, tbl, rootName, parsedChrom);
hti = hFindTableInfo(database, seqName, rootName);
if (hti == NULL || hti->startField[0] == 0)
{
itemCount = 1;
hgSeqRange(database, seqName, start, end, '?', tbl);
}
else
{
char *where = NULL;
char *item = cgiUsualString("i", "");
char buf[256];
if ((hti->nameField[0] != 0) && (item[0] != 0))
{
char *quotedItem = makeQuotedString(item, '\'');
safef(buf, sizeof(buf), "%s = %s", hti->nameField, quotedItem);
where = buf;
freeMem(quotedItem);
}
itemCount = hgSeqItemsInRange(database, tbl, seqName, start, end, where);
}
}
if (itemCount == 0)
printf("\n# No results returned from query.\n\n");
puts("");
}
struct hTableInfo *ctToHti(struct customTrack *ct)
/* Create an hTableInfo from a customTrack. */
{
struct hTableInfo *hti;
AllocVar(hti);
hti->rootName = cloneString(ct->tdb->table);
hti->isPos = TRUE;
hti->isSplit = FALSE;
hti->hasBin = FALSE;
hti->type = cloneString(ct->tdb->type);
int fieldCount = 3;
if (sameWord(ct->dbTrackType, "bedDetail"))
fieldCount = ct->fieldCount - 2;
else if (sameWord(ct->dbTrackType, "pgSnp"))
fieldCount = 4;
else
fieldCount = ct->fieldCount;
if (fieldCount >= 3)
{
strncpy(hti->chromField, "chrom", 32);
strncpy(hti->startField, "chromStart", 32);
strncpy(hti->endField, "chromEnd", 32);
}
if (fieldCount >= 4)
{
strncpy(hti->nameField, "name", 32);
}
if (fieldCount >= 5)
{
strncpy(hti->scoreField, "score", 32);
}
if (fieldCount >= 6)
{
strncpy(hti->strandField, "strand", 32);
}
if (fieldCount >= 8)
{
strncpy(hti->cdsStartField, "thickStart", 32);
strncpy(hti->cdsEndField, "thickEnd", 32);
hti->hasCDS = TRUE;
}
if (fieldCount >= 12)
{
strncpy(hti->countField, "blockCount", 32);
strncpy(hti->startsField, "chromStarts", 32);
strncpy(hti->endsSizesField, "blockSizes", 32);
hti->hasBlocks = TRUE;
}
return(hti);
}
struct hTableInfo *htiForUserPsl()
/* Create an hTableInfo for user's BLAT results. */
{
struct hTableInfo *hti;
AllocVar(hti);
hti->rootName = cloneString(USER_PSL_TRACK_NAME);
hti->isPos = TRUE;
hti->isSplit = FALSE;
hti->hasBin = FALSE;
hti->type = cloneString("psl");
strncpy(hti->chromField, "tName", 32);
strncpy(hti->startField, "tStart", 32);
strncpy(hti->endField, "tEnd", 32);
strncpy(hti->nameField, "qName", 32);
/* psl can be scored... but strictly speaking, does not have a score field! */
strncpy(hti->strandField, "strand", 32);
hti->hasCDS = FALSE;
strncpy(hti->countField, "blockCount", 32);
strncpy(hti->startsField, "tStarts", 32);
strncpy(hti->endsSizesField, "tSizes", 32);
hti->hasBlocks = TRUE;
return(hti);
}
struct bed *bedFromUserPsl()
/* Load up user's BLAT results into bedList. */
{
struct bed *bedList = NULL;
char *ss = cartOptionalString(cart, "ss");
if ((ss != NULL) && ! ssFilesExist(ss))
{
ss = NULL;
cartRemove(cart, "ss");
}
if (ss == NULL)
return(NULL);
else
{
struct lineFile *f;
struct psl *psl;
enum gfType qt, tt;
char *faFileName, *pslFileName;
int i;
parseSs(ss, &pslFileName, &faFileName, NULL);
pslxFileOpen(pslFileName, &qt, &tt, &f);
while ((psl = pslNext(f)) != NULL)
{
struct bed *bed;
AllocVar(bed);
bed->chrom = cloneString(seqName);
bed->chromStart = psl->tStart;
bed->chromEnd = psl->tEnd;
bed->name = cloneString(psl->qName);
bed->score = pslScore(psl);
if ((psl->strand[0] == '-' && psl->strand[1] == '+') ||
(psl->strand[0] == '+' && psl->strand[1] == '-'))
strncpy(bed->strand, "-", 2);
else
strncpy(bed->strand, "+", 2);
bed->thickStart = bed->chromStart;
bed->thickEnd = bed->chromEnd;
bed->blockCount = psl->blockCount;
bed->chromStarts = needMem(bed->blockCount * sizeof(int));
bed->blockSizes = needMem(bed->blockCount * sizeof(int));
for (i=0; i < bed->blockCount; i++)
{
bed->chromStarts[i] = psl->tStarts[i];
bed->blockSizes[i] = psl->blockSizes[i];
}
if (qt == gftProt)
for (i=0; i < bed->blockCount; i++)
{
/* If query is protein, blockSizes are in aa units; fix 'em. */
bed->blockSizes[i] *= 3;
}
if (psl->strand[1] == '-')
{
/* psl: if target strand is '-', flip the coords.
* (this is the target part of pslRc from src/lib/psl.c) */
for (i=0; i < bed->blockCount; ++i)
{
bed->chromStarts[i] =
psl->tSize - (bed->chromStarts[i] +
bed->blockSizes[i]);
}
reverseInts(bed->chromStarts, bed->blockCount);
reverseInts(bed->blockSizes, bed->blockCount);
assert(bed->chromStart == bed->chromStarts[0]);
}
/* translate absolute starts to relative starts (after handling
* target-strand coord-flipping) */
for (i=0; i < bed->blockCount; i++)
{
bed->chromStarts[i] -= bed->chromStart;
}
slAddHead(&bedList, bed);
pslFree(&psl);
}
lineFileClose(&f);
slReverse(&bedList);
return(bedList);
}
}
void addColorToRange(int r, int g, int b, struct rgbColor *colors, int start, int end)
/* Add rgb values to colors array from start to end. Don't let values
* exceed 255 */
{
struct rgbColor *c;
int rr, gg, bb;
int i;
for (i=start; i");
printf(">%s:%d-%d %s\n", seqName, winStart+1, winEnd,
(isRc ? "(reverse complement)" : ""));
seq = hDnaFromSeq(database, seqName, winStart, winEnd, dnaLower);
if (isRc)
reverseComplement(seq->dna, seq->size);
if (defaultUpper)
touppers(seq->dna);
AllocArray(colors, winSize);
for (tdb = tdbList; tdb != NULL; tdb = tdb->next)
{
char *track = tdb->track;
char *table = tdb->table;
struct featureBits *fbList = NULL, *fb;
struct customTrack *ct = lookupCt(track);
if (sameString(USER_PSL_TRACK_NAME, table) ||
(ct != NULL) ||
(fbUnderstandTrack(database, table) && !dnaIgnoreTrack(table)))
{
char buf[256];
int r,g,b;
/* to save a LOT of time, don't fetch track features unless some
* coloring/formatting has been specified for them. */
boolean hasSettings = FALSE;
safef(buf, sizeof(buf), "%s_u", track);
hasSettings |= cgiBoolean(buf);
safef(buf, sizeof(buf), "%s_b", track);
hasSettings |= cgiBoolean(buf);
safef(buf, sizeof(buf), "%s_i", track);
hasSettings |= cgiBoolean(buf);
safef(buf, sizeof(buf), "%s_case", track);
hasSettings |= cgiBoolean(buf);
safef(buf, sizeof(buf), "%s_red", track);
hasSettings |= (cgiOptionalInt(buf, 0) != 0);
safef(buf, sizeof(buf), "%s_green", track);
hasSettings |= (cgiOptionalInt(buf, 0) != 0);
safef(buf, sizeof(buf), "%s_blue", track);
hasSettings |= (cgiOptionalInt(buf, 0) != 0);
if (! hasSettings)
continue;
if (sameString(USER_PSL_TRACK_NAME, track))
{
struct hTableInfo *hti = htiForUserPsl();
struct bedFilter *bf;
struct bed *bedList, *bedList2;
AllocVar(bf);
bedList = bedFromUserPsl();
bedList2 = bedFilterListInRange(bedList, bf, seqName, winStart,
winEnd);
fbList = fbFromBed(database, track, hti, bedList2, winStart, winEnd,
TRUE, FALSE);
bedFreeList(&bedList);
bedFreeList(&bedList2);
}
else if (ct != NULL)
{
struct hTableInfo *hti = ctToHti(ct);
struct bedFilter *bf;
struct bed *bedList2, *ctBedList = NULL;
AllocVar(bf);
if (ct->dbTrack)
{
struct bed *bed;
int fieldCount = ct->fieldCount;
char query[512];
int rowOffset;
char **row;
struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH);
struct sqlResult *sr = NULL;
safef(query, sizeof(query), "select * from %s", ct->dbTableName);
sr = hRangeQuery(conn, ct->dbTableName, seqName,
winStart, winEnd, NULL, &rowOffset);
while ((row = sqlNextRow(sr)) != NULL)
{
bed = bedLoadN(row+rowOffset, fieldCount);
if (bf == NULL || bedFilterOne(bf, bed))
{
struct bed *copy = cloneBed(bed);
slAddHead(&ctBedList, copy);
}
}
sqlFreeResult(&sr);
hFreeConn(&conn);
}
else
{
ctBedList = ct->bedList;
}
bedList2 = bedFilterListInRange(ctBedList, bf, seqName, winStart,
winEnd);
fbList = fbFromBed(database, track, hti, bedList2, winStart, winEnd,
TRUE, FALSE);
bedFreeList(&bedList2);
if (!ct->bedList)
bedFreeList(&ctBedList);
}
else
fbList = fbGetRange(database, tdb->table, seqName, winStart, winEnd);
/* Flip underline/italic/bold bits. */
getDnaHandleBits(track, "u", uBits, winStart, winEnd, isRc, fbList);
getDnaHandleBits(track, "b", bBits, winStart, winEnd, isRc, fbList);
getDnaHandleBits(track, "i", iBits, winStart, winEnd, isRc, fbList);
/* Toggle case if necessary. */
sprintf(buf, "%s_case", track);
if (cgiBoolean(buf))
{
for (fb = fbList; fb != NULL; fb = fb->next)
{
DNA *dna;
int start = fb->start - winStart;
int end = fb->end - winStart;
int size = fb->end - fb->start;
if (isRc)
reverseIntRange(&start, &end, seq->size);
dna = seq->dna + start;
if (defaultUpper)
toLowerN(dna, size);
else
toUpperN(dna, size);
}
}
/* Add in RGB values if necessary. */
sprintf(buf, "%s_red", track);
r = cartInt(cart, buf);
sprintf(buf, "%s_green", track);
g = cartInt(cart, buf);
sprintf(buf, "%s_blue", track);
b = cartInt(cart, buf);
if (r != 0 || g != 0 || b != 0)
{
for (fb = fbList; fb != NULL; fb = fb->next)
{
int s = fb->start - winStart;
int e = fb->end - winStart;
if (isRc)
reverseIntRange(&s, &e, winEnd - winStart);
addColorToRange(r, g, b, colors, s, e);
}
}
}
}
cfm = cfmNew(0, lineWidth, FALSE, FALSE, stdout, 0);
for (i=0; isize; ++i)
{
struct rgbColor *color = colors+i;
int c = (color->r<<16) + (color->g<<8) + color->b;
cfmOutExt(cfm, seq->dna[i], c,
bitReadOne(uBits, i), bitReadOne(bBits, i), bitReadOne(iBits, i));
}
cfmFree(&cfm);
freeDnaSeq(&seq);
bitFree(&uBits);
bitFree(&iBits);
bitFree(&bBits);
}
void medlineLinkedTermLine(char *title, char *text, char *search, char *keyword)
/* Produce something that shows up on the browser as
* TITLE: value
* with the value hyperlinked to medline using a specified search term. */
{
char *encoded = cgiEncode(search);
char *encodedKeyword = cgiEncode(keyword);
printf("%s: ", title);
if (sameWord(text, "n/a") || sameWord(text, "none"))
printf("n/a
\n");
else
{
printf("%s
\n", text);
}
freeMem(encoded);
}
void medlineLinkedLine(char *title, char *text, char *search)
/* Produce something that shows up on the browser as
* TITLE: value
* with the value hyperlinked to medline. */
{
char *encoded = cgiEncode(search);
printf("%s: ", title);
if (sameWord(text, "n/a"))
printf("n/a
\n");
else
{
printf("%s
\n", text);
}
freeMem(encoded);
}
void medlineProductLinkedLine(char *title, char *text)
/* Produce something that shows up on the browser as
* TITLE: value
* with the value hyperlinked to medline.
* Replaces commas in the product name with spaces, as commas sometimes
* interfere with PubMed search */
{
subChar(text, ',', ' ');
medlineLinkedLine(title, text, text);
}
void appendAuthor(struct dyString *dy, char *gbAuthor, int len)
/* Convert from Kent,W.J. to Kent WJ and append to dy.
* gbAuthor gets eaten in the process.
* Also strip web URLs since Entrez doesn't like those. */
{
char buf[2048];
char *ptr;
if (len >= sizeof(buf))
warn("author %s too long to process", gbAuthor);
else
{
memcpy(buf, gbAuthor, len);
buf[len] = 0;
stripChar(buf, '.');
subChar(buf, ',' , ' ');
if ((ptr = strstr(buf, " http://")) != NULL)
*ptr = 0;
dyStringAppend(dy, buf);
dyStringAppend(dy, " ");
}
}
void gbToEntrezAuthor(char *authors, struct dyString *dy)
/* Convert from Genbank author format:
* Kent,W.J., Haussler,D. and Zahler,A.M.
* to Entrez search format:
* Kent WJ,Haussler D,Zahler AM
*/
{
char *s = authors, *e;
/* Parse first authors, which will be terminated by '.,' */
while ((e = strstr(s, ".,i ")) != NULL)
{
int len = e - s + 1;
appendAuthor(dy, s, len);
s += len+2;
}
if ((e = strstr(s, " and")) != NULL)
{
int len = e - s;
appendAuthor(dy, s, len);
s += len+4;
}
if ((s = skipLeadingSpaces(s)) != NULL && s[0] != 0)
{
int len = strlen(s);
appendAuthor(dy, s, len);
}
}
/* --- !!! Riken code is under development Fan. 4/16/02 */
void printRikenInfo(char *acc, struct sqlConnection *conn )
/* Print Riken annotation info */
{
struct sqlResult *sr;
char **row;
char qry[512];
char *seqid, *accession, *comment;
char *qualifier, *anntext, *datasrc, *srckey, *href, *evidence;
accession = acc;
snprintf(qry, sizeof(qry),
"select seqid from rikenaltid where altid='%s';", accession);
sr = sqlMustGetResult(conn, qry);
row = sqlNextRow(sr);
if (row != NULL)
{
seqid=cloneString(row[0]);
snprintf(qry, sizeof(qry),
"select Qualifier, Anntext, Datasrc, Srckey, Href, Evidence "
"from rikenann where seqid='%s';", seqid);
sqlFreeResult(&sr);
sr = sqlMustGetResult(conn, qry);
row = sqlNextRow(sr);
while (row !=NULL)
{
qualifier = row[0];
anntext = row[1];
datasrc = row[2];
srckey = row[3];
href = row[4];
evidence = row[5];
row = sqlNextRow(sr);
}
snprintf(qry, sizeof(qry),
"select comment from rikenseq where id='%s';", seqid);
sqlFreeResult(&sr);
sr = sqlMustGetResult(conn, qry);
row = sqlNextRow(sr);
if (row != NULL)
{
comment = row[0];
printf("Riken/comment: %s
\n",comment);
}
}
}
void printStanSource(char *acc, char *type)
/* Print out a link (Human/Mouse/Rat only) to Stanford's SOURCE web resource.
Types known are: est,mrna,unigene,locusLink. */
{
if (startsWith("Human", organism) || startsWith("Mouse", organism) ||
startsWith("Rat", organism))
{
char *stanSourceLink = "http://smd.stanford.edu/cgi-bin/source/sourceResult?";
if(sameWord(type, "est"))
{
printf("Stanford SOURCE: %s [Gene Info] ",acc,stanSourceLink,acc);
printf("[Clone Info]
\n",stanSourceLink,acc);
}
else if(sameWord(type,"unigene"))
{
printf("Stanford SOURCE: %s [Gene Info] ",acc,stanSourceLink,acc);
printf("[Clone Info]
\n",stanSourceLink,acc);
}
else if(sameWord(type,"mrna"))
printf("Stanford SOURCE: %s
\n",stanSourceLink,acc,acc);
else if(sameWord(type,"locusLink"))
printf("Stanford SOURCE Locus Link: %s
\n",stanSourceLink,acc,acc);
}
}
void printGeneCards(char *geneName)
/* Print out a link to GeneCards (Human only). */
{
if (startsWith("hg", database) && isNotEmpty(geneName))
{
printf("GeneCards: "
"%s
\n",
geneName, geneName);
}
}
int getImageId(struct sqlConnection *conn, char *acc)
/* get the image id for a clone, or 0 if none */
{
int imageId = 0;
if (sqlTableExists(conn, "imageClone"))
{
struct sqlResult *sr;
char **row;
char query[128];
safef(query, sizeof(query),
"select imageId from imageClone where acc = '%s'", acc);
sr = sqlMustGetResult(conn, query);
row = sqlNextRow(sr);
if (row != NULL)
imageId = sqlUnsigned(row[0]);
sqlFreeResult(&sr);
}
return imageId;
}
void htcDisplayMrna(char *acc)
/* Display mRNA available from genback or seq table.. */
{
struct dnaSeq *seq = hGenBankGetMrna(database, acc, NULL);
if (seq == NULL)
errAbort("mRNA sequence %s not found", acc);
hgcStart("mRNA sequence");
printf("");
faWriteNext(stdout, seq->name, seq->dna, seq->size);
printf("");
dnaSeqFree(&seq);
}
static int getEstTranscriptionDir(struct sqlConnection *conn, struct psl *psl)
/* get the direction of transcription for an EST; return splice support count */
{
char query[256], estOrient[64];
safef(query, sizeof(query),
"select intronOrientation from %s.estOrientInfo where chrom = '%s' and chromStart = %d and name = '%s'",
database, psl->tName, psl->tStart, psl->qName);
if (sqlQuickQuery(conn, query, estOrient, sizeof(estOrient)) != NULL)
return sqlSigned(estOrient) * ((psl->strand[0] == '+') ? 1 : -1);
else
return 0;
}
static struct gbWarn *checkGbWarn(struct sqlConnection *conn, char *acc)
/* check if there is a gbWarn entry for this accession, return NULL if none */
{
struct gbWarn *gbWarn = NULL;
if (hTableExists(database, "gbWarn"))
gbWarn = sqlQueryObjs(conn, (sqlLoadFunc)gbWarnLoad, sqlQuerySingle,
"SELECT * FROM gbWarn WHERE acc = \"%s\"", acc);
return gbWarn;
}
static void printGbWarn(char *acc, struct gbWarn *gbWarn)
/* print descriptive information about an accession in the gbWarn table */
{
char *msg = NULL;
switch (gbWarn->reason) {
case gbWarnInvitroNorm:
msg = "is from the InVitroGen/Genoscope full-length library. Some of the entries "
"associated with this dataset appear to have been aligned to the reference "
"genome and the sequences subsequently modified to match the genome. This "
"process may have resulted in apparent high-quality alignments to pseudogenes.";
break;
case gbWarnAthRage:
msg = "is from the Athersys RAGE library. These sequences were created by inducing expression and may not "
"be an indication of in vivo expression.";
break;
case gbWarnOrestes:
msg = "is from an ORESTES library. This protocol includes a PCR step subject to genomic contamination.";
break;
}
assert(msg != NULL);
char *msg2= "Care should be taken in using alignments of this sequence as evidence of transcription.";
printf("Warning: %s %s %s
\n", acc, msg, msg2);
}
static void printRnaSpecs(struct trackDb *tdb, char *acc, struct psl *psl)
/* Print auxiliarry info on RNA. */
{
struct dyString *dy = newDyString(1024);
struct sqlConnection *conn = hAllocConn(database);
struct sqlConnection *conn2= hAllocConn(database);
struct sqlResult *sr;
char **row;
char rgdEstId[512];
char query[256];
char *type,*direction,*source,*orgFullName,*library,*clone,*sex,*tissue,
*development,*cell,*cds,*description, *author,*geneName,
*date,*productName;
int seqSize,fileSize;
long fileOffset;
char *ext_file;
boolean hasVersion = hHasField(database, "gbCdnaInfo", "version");
boolean haveGbSeq = sqlTableExists(conn, "gbSeq");
char *seqTbl = haveGbSeq ? "gbSeq" : "seq";
char *version = NULL;
struct trackDb *tdbRgdEst;
char *chrom = cartString(cart, "c");
int start = cartInt(cart, "o");
int end = cartUsualInt(cart, "t",0);
struct gbWarn *gbWarn = checkGbWarn(conn, acc);
/* This sort of query and having to keep things in sync between
* the first clause of the select, the from clause, the where
* clause, and the results in the row ... is really tedious.
* One of my main motivations for going to a more object
* based rather than pure relational approach in general,
* and writing 'autoSql' to help support this. However
* the pure relational approach wins for pure search speed,
* and these RNA fields are searched. So it looks like
* the code below stays. Be really careful when you modify
* it.
*
* Uses the gbSeq table if available, otherwise use seq for older databases.
*/
dyStringAppend(dy,
"select gbCdnaInfo.type,gbCdnaInfo.direction,"
"source.name,organism.name,library.name,mrnaClone.name,"
"sex.name,tissue.name,development.name,cell.name,cds.name,"
"description.name,author.name,geneName.name,productName.name,");
if (haveGbSeq)
dyStringAppend(dy,
"gbSeq.size,gbCdnaInfo.moddate,gbSeq.gbExtFile,gbSeq.file_offset,gbSeq.file_size ");
else
dyStringAppend(dy,
"seq.size,seq.gb_date,seq.extFile,seq.file_offset,seq.file_size ");
/* If the gbCdnaInfo table has a "version" column then will show it */
if (hasVersion)
{
dyStringAppend(dy,
", gbCdnaInfo.version ");
}
dyStringPrintf(dy,
" from gbCdnaInfo,%s,source,organism,library,mrnaClone,sex,tissue,"
"development,cell,cds,description,author,geneName,productName "
" where gbCdnaInfo.acc = '%s' and gbCdnaInfo.id = %s.id ",
seqTbl, acc, seqTbl);
dyStringAppend(dy,
"and gbCdnaInfo.source = source.id and gbCdnaInfo.organism = organism.id "
"and gbCdnaInfo.library = library.id and gbCdnaInfo.mrnaClone = mrnaClone.id "
"and gbCdnaInfo.sex = sex.id and gbCdnaInfo.tissue = tissue.id "
"and gbCdnaInfo.development = development.id and gbCdnaInfo.cell = cell.id "
"and gbCdnaInfo.cds = cds.id and gbCdnaInfo.description = description.id "
"and gbCdnaInfo.author = author.id and gbCdnaInfo.geneName = geneName.id "
"and gbCdnaInfo.productName = productName.id");
sr = sqlMustGetResult(conn, dy->string);
row = sqlNextRow(sr);
if (row != NULL)
{
type=row[0];direction=row[1];source=row[2];orgFullName=row[3];library=row[4];clone=row[5];
sex=row[6];tissue=row[7];development=row[8];cell=row[9];cds=row[10];description=row[11];
author=row[12];geneName=row[13];productName=row[14];
seqSize = sqlUnsigned(row[15]);
date = row[16];
ext_file = row[17];
fileOffset=sqlUnsigned(row[18]);
fileSize=sqlUnsigned(row[19]);
boolean isEst = sameWord(type, "est");
if (hasVersion)
{
version = row[20];
}
/* Now we have all the info out of the database and into nicely named
* local variables. There's still a few hoops to jump through to
* format this prettily on the web with hyperlinks to NCBI. */
printf("Information on %s %s
\n", acc);
printf("Description: %s
\n", description);
if (gbWarn != NULL)
printGbWarn(acc, gbWarn);
medlineLinkedLine("Gene", geneName, geneName);
medlineProductLinkedLine("Product", productName);
dyStringClear(dy);
gbToEntrezAuthor(author, dy);
medlineLinkedLine("Author", author, dy->string);
printf("Organism: ");
printf("",
cgiEncode(orgFullName));
printf("%s
\n", orgFullName);
printf("Tissue: %s
\n", tissue);
printf("Development stage: %s
\n", development);
printf("Cell line: %s
\n", cell);
printf("Sex: %s
\n", sex);
printf("Library: %s
\n", library);
printf("Clone: %s
\n", clone);
if (isEst)
{
printf("Read direction: ");
if (direction[0] != '0')
printf("%s' (guessed from GenBank description)
\n", direction);
else
printf("unknown (can't guess from GenBank description)
");
}
else
printf("CDS: %s
\n", cds);
printf("Date: %s
\n", date);
if (hasVersion)
{
printf("Version: %s
\n", version);
}
/* print RGD EST Report link if it is Rat genome and it has a link to RGD */
if (sameWord(organism, "Rat"))
{
if (hTableExists(database, "rgdEstLink"))
{
snprintf(query, sizeof(query),
"select id from %s.rgdEstLink where name = '%s';", database, acc);
if (sqlQuickQuery(conn2, query, rgdEstId, sizeof(rgdEstId)) != NULL)
{
tdbRgdEst = hashFindVal(trackHash, "rgdEst");
printf("RGD EST Report: ");
printf("", tdbRgdEst->url, rgdEstId);
printf("RGD:%s
\n", rgdEstId);
}
}
}
printStanSource(acc, type);
if (isEst && hTableExists(database, "estOrientInfo") && (psl != NULL))
{
int estOrient = getEstTranscriptionDir(conn2, psl);
if (estOrient != 0)
printf("EST transcribed from %c strand (supported by %d splice sites).
\n",
(estOrient > 0 ? '+' : '-' ), abs(estOrient));
}
if (hGenBankHaveSeq(database, acc, NULL))
{
printf("%s sequence: ", type);
hgcAnchorSomewhere("htcDisplayMrna", acc, tdb->track, seqName);
printf("%s
\n", acc);
}
}
else
{
warn("Couldn't find %s in gbCdnaInfo table", acc);
}
if (end != 0 && differentString(chrom,"0") && isNotEmpty(chrom))
{
printf("Position: "
"",
hgTracksPathAndSettings(), database, chrom, start+1, end);
printf("%s:%d-%d
\n", chrom, start+1, end);
}
gbWarnFree(&gbWarn);
sqlFreeResult(&sr);
freeDyString(&dy);
hFreeConn(&conn);
hFreeConn(&conn2);
}
static boolean isPslToPrintByClick(struct psl *psl, int startFirst, boolean isClicked)
/* Determine if a psl should be printed based on if it was or was not the one that was clicked
* on.
*/
{
return ((psl->tStart == startFirst) && sameString(psl->tName, seqName)) == isClicked;
}
void printAlignmentsSimple(struct psl *pslList, int startFirst, char *hgcCommand,
char *tableName, char *itemIn)
/* Print list of mRNA alignments, don't add extra textual link when
* doesn't honor hgcCommand. */
{
struct psl *psl;
int aliCount = slCount(pslList);
boolean isClicked;
if (pslList == NULL || tableName == NULL)
return;
if (aliCount > 1)
printf("The alignment you clicked on is first in the table below.
\n");
printf("");
if (startsWith("chr", pslList->tName))
printf("BROWSER | SIZE IDENTITY CHROMOSOME STRAND START END QUERY START END TOTAL\n");
else
printf("BROWSER | SIZE IDENTITY SCAFFOLD STRAND START END QUERY START END TOTAL\n");
printf("-----------------------------------------------------------------------------------------------------\n");
for (isClicked = 1; isClicked >= 0; isClicked -= 1)
{
for (psl = pslList; psl != NULL; psl = psl->next)
{
if (isPslToPrintByClick(psl, startFirst, isClicked))
{
char otherString[512];
safef(otherString, sizeof(otherString), "%d&aliTable=%s", psl->tStart, tableName);
printf("browser | ",
hgTracksPathAndSettings(), database, psl->tName, psl->tStart+1, psl->tEnd);
hgcAnchorSomewhere(hgcCommand, itemIn, otherString, psl->tName);
printf("%5d %5.1f%% %9s %s %9d %9d %20s %5d %5d %5d",
psl->match + psl->misMatch + psl->repMatch,
100.0 - pslCalcMilliBad(psl, TRUE) * 0.1,
skipChr(psl->tName), psl->strand, psl->tStart + 1, psl->tEnd,
psl->qName, psl->qStart+1, psl->qEnd, psl->qSize);
printf("\n");
}
}
}
printf("");
}
void printAlignments(struct psl *pslList, int startFirst, char *hgcCommand,
char *tableName, char *itemIn)
/* Print list of mRNA alignments. */
{
if (pslList == NULL || tableName == NULL)
return;
printAlignmentsSimple(pslList, startFirst, hgcCommand, tableName, itemIn);
struct psl *psl = pslList;
for (psl = pslList; psl != NULL; psl = psl->next)
{
if ( pslTrimToTargetRange(psl, winStart, winEnd) != NULL
&&
!startsWith("xeno", tableName)
&& !(startsWith("user", tableName) && pslIsProtein(psl))
&& psl->tStart == startFirst
&& sameString(psl->tName, seqName)
)
{
char otherString[512];
safef(otherString, sizeof(otherString), "%d&aliTable=%s",
psl->tStart, tableName);
hgcAnchorSomewhere("htcCdnaAliInWindow", cgiEncode(psl->qName),
otherString, psl->tName);
printf("
View details of parts of alignment within browser window.
\n");
}
}
}
struct psl *getAlignments(struct sqlConnection *conn, char *table, char *acc)
/* get the list of alignments for the specified acc */
{
struct sqlResult *sr = NULL;
char **row;
struct psl *psl, *pslList = NULL;
boolean hasBin;
char splitTable[64];
char query[256];
if (!hFindSplitTable(database, seqName, table, splitTable, &hasBin))
errAbort("can't find table %s or %s_%s", table, seqName, table);
safef(query, sizeof(query), "select * from %s where qName = '%s'", splitTable, acc);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
psl = pslLoad(row+hasBin);
slAddHead(&pslList, psl);
}
sqlFreeResult(&sr);
slReverse(&pslList);
return pslList;
}
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;
}
void doHgRna(struct trackDb *tdb, char *acc)
/* Click on an individual RNA. */
{
char *track = tdb->track;
char *table = tdb->table;
struct sqlConnection *conn = hAllocConn(database);
char *type;
int start = cartInt(cart, "o");
struct psl *pslList = NULL;
if (sameString("xenoMrna", track) || sameString("xenoBestMrna", track) || sameString("xenoEst", track) || sameString("sim4", track) )
{
char temp[256];
sprintf(temp, "non-%s RNA", organism);
type = temp;
}
else if ( sameWord("blatzHg17KG", track) )
{
type = "Human mRNA";
}
else if (stringIn("estFiltered",track))
{
type = "EST";
}
else if (stringIn("est", track) || stringIn("Est", track))
{
type = "EST";
// table = "all_est"; // Should fall out of wash now
}
else if (startsWith("psu", track))
{
type = "Pseudo & Real Genes";
table = "psu";
}
else if (sameWord("xenoBlastzMrna", track) )
{
type = "Blastz to foreign mRNA";
}
else if (startsWith("mrnaBlastz",track ))
{
type = "mRNA";
}
else if (startsWith("pseudoMrna",track) || startsWith("pseudoGeneLink",track))
{
type = "mRNA";
table = "pseudoMrna";
}
else if (startsWith("celeraMrna",track))
{
type = "mRNA";
}
else if (startsWith("all_mrnaFiltered",track))
{
type = "mRNA";
}
else
{
type = "mRNA";
// table = "all_mrna"; // should fall out of wash now
}
/* Print non-sequence info. */
cartWebStart(cart, database, "%s", acc);
printRnaSpecs(tdb, acc, pslList);
/* Get alignment info. */
pslList = getAlignments(conn, table, acc);
if (pslList == NULL)
{
/* this was not actually a click on an aligned item -- we just
* want to display RNA info, so leave here */
hFreeConn(&conn);
htmlHorizontalLine();
printf("mRNA %s alignment does not meet minimum alignment criteria on this assembly.", acc);
return;
}
htmlHorizontalLine();
printf("%s/Genomic Alignments
", type);
if (startsWith("mrnaBlastz",tdb->table))
slSort(&pslList, pslCmpScoreDesc);
printAlignments(pslList, start, "htcCdnaAli", table, acc);
printTrackHtml(tdb);
hFreeConn(&conn);
}
void printPslFormat(struct sqlConnection *conn, struct trackDb *tdb, char *item, int start, char *subType)
/* Handles click in affyU95 or affyU133 tracks */
{
struct psl *pslList = getAlignments(conn, tdb->table, item);
struct psl *psl;
char *face = "Times"; /* specifies font face to use */
char *fsize = "+1"; /* specifies font size */
/* check if there is an alignment available for this sequence. This checks
* both genbank sequences and other sequences in the seq table. If so,
* set it up so they can click through to the alignment. */
if (hGenBankHaveSeq(database, item, NULL))
{
printf("%s/Genomic Alignments
", item);
printAlignments(pslList, start, "htcCdnaAli", tdb->table, item);
}
else
{
/* print out the psls */
printf("");
printf("\n", face, fsize);
for (psl = pslList; psl != NULL; psl = psl->next)
{
pslOutFormat(psl, stdout, '\n', '\n');
}
printf("\n");
}
pslFreeList(&pslList);
}
void doAffy(struct trackDb *tdb, char *item, char *itemForUrl)
/* Display information for Affy tracks*/
{
char *dupe, *type, *words[16];
char *orthoTable = trackDbSetting(tdb, "orthoTable");
char *otherDb = trackDbSetting(tdb, "otherDb");
int wordCount;
int start = cartInt(cart, "o");
char query[256];
char **row;
struct sqlResult *sr = NULL;
struct sqlConnection *conn = hAllocConn(database);
struct sqlConnection *conn2 = hAllocConn(database);
if (itemForUrl == NULL)
itemForUrl = item;
dupe = cloneString(tdb->type);
genericHeader(tdb, item);
wordCount = chopLine(dupe, words);
printCustomUrl(tdb, itemForUrl, item == itemForUrl);
/* If this is the affyZebrafish track, check for human ortholog information */
if (sameString("affyZebrafish", tdb->table))
{
if (orthoTable != NULL && hTableExists(database, orthoTable))
{
safef(query, sizeof(query), "select geneSymbol, description from %s where name = '%s' ", orthoTable, item);
sr = sqlMustGetResult(conn, query);
row = sqlNextRow(sr);
if (row != NULL)
{
printf("
\n\n");
printf("Human %s Ortholog:
%s Ortholog Description: %s
\n");
}
}
}
if (wordCount > 0)
{
type = words[0];
if (sameString(type, "psl"))
{
char *subType = ".";
if (wordCount > 1)
subType = words[1];
printPslFormat(conn2, tdb, item, start, subType);
}
}
printTrackHtml(tdb);
freez(&dupe);
hFreeConn(&conn);
hFreeConn(&conn2);
}
void doZfishRHmap(struct trackDb *tdb, char *itemName)
/* Put up Radiation Hybrid map information for Zebrafish */
{
char *dupe, *type, *words[16];
char query[256];
struct sqlResult *sr = NULL;
char **row = NULL;
struct rhMapZfishInfo *rhInfo = NULL;
int wordCount;
int start = cartInt(cart, "o");
struct sqlConnection *conn = hAllocConn(database);
struct sqlConnection *conn1 = hAllocConn(database);
boolean rhMapInfoExists = sqlTableExists(conn, "rhMapZfishInfo");
dupe = cloneString(tdb->type);
wordCount = chopLine(dupe, words);
genericHeader(tdb, itemName);
/* Print out RH map information if available */
if (rhMapInfoExists)
{
sprintf(query, "SELECT * FROM rhMapZfishInfo WHERE name = '%s'", itemName);
sr = sqlMustGetResult(conn, query);
row = sqlNextRow(sr);
if (row != NULL)
{
rhInfo = rhMapZfishInfoLoad(row);
if (rhInfo != NULL)
{
printf("Information on %s
\n", itemName);
if (!sameString(rhInfo->zfinId, ""))
{
printf("");
printCustomUrl(tdb, rhInfo->zfinId, TRUE);
printf("
\n");
}
printf("
\n\n");
printf("Linkage group: %s Position on linkage group: %d Distance (cR): %d Marker type: %s Marker source: %s Mapping institution: %s Forward Primer: %s Reverse Primer: %s
\n");
}
}
}
dupe = cloneString(tdb->type);
wordCount = chopLine(dupe, words);
if (wordCount > 0)
{
type = words[0];
if (sameString(type, "psl"))
{
char *subType = ".";
if (wordCount > 1)
subType = words[1];
printPslFormat(conn1, tdb, itemName, start, subType);
}
}
printTrackHtml(tdb);
freez(&dupe);
hFreeConn(&conn);
hFreeConn(&conn1);
}
void doRikenRna(struct trackDb *tdb, char *item)
/* Put up Riken RNA stuff. */
{
char query[512];
struct sqlResult *sr;
char **row;
struct sqlConnection *conn = sqlConnect("mgsc");
genericHeader(tdb, item);
sprintf(query, "select * from rikenMrna where qName = '%s'", item);
sr = sqlGetResult(conn, query);
printf("\n");
printf("#match\tmisMatches\trepMatches\tnCount\tqNumInsert\tqBaseInsert\ttNumInsert\tBaseInsert\tstrand\tqName\tqSize\tqStart\tqEnd\ttName\ttSize\ttStart\ttEnd\tblockCount\tblockSizes\tqStarts\ttStarts\n");
while ((row = sqlNextRow(sr)) != NULL)
{
struct psl *psl = pslLoad(row+1);
pslTabOut(psl, stdout);
}
printf("\n");
sqlDisconnect(&conn);
printTrackHtml(tdb);
}
void doYaleTars(struct trackDb *tdb, char *item, char *itemForUrl)
/* Display information for Affy tracks*/
{
char *dupe, *type, *words[16], *chrom = NULL, *strand = NULL;
char *item2 = NULL;
int wordCount, end = 0;
int start = cartInt(cart, "o");
char query[256];
char **row;
struct sqlResult *sr = NULL;
struct sqlConnection *conn = hAllocConn(database);
struct sqlConnection *conn2 = hAllocConn(database);
if (itemForUrl == NULL)
{
if (startsWith("TAR", item))
{
/* Remove TAR prefix from item */
item2 = strchr(item, 'R');
item2++;
itemForUrl = item2;
}
else
itemForUrl = item;
}
dupe = cloneString(tdb->type);
genericHeader(tdb, item);
wordCount = chopLine(dupe, words);
printCustomUrl(tdb, itemForUrl, item == itemForUrl);
safef(query, sizeof(query), "select tName, tEnd, strand from %s where qName='%s' and tStart=%d;", tdb->table, item, start);
sr = sqlMustGetResult(conn, query);
row = sqlNextRow(sr);
/* load PSL into struct */
if (row != NULL)
{
chrom = cloneString(row[0]);
end = sqlUnsigned(row[1]);
strand = cloneString(row[2]);
}
printPos(chrom, start, end, strand, TRUE, item);
if (wordCount > 0)
{
type = words[0];
if (sameString(type, "psl"))
{
char *subType = ".";
if (wordCount > 1)
subType = words[1];
printPslFormat(conn2, tdb, item, start, subType);
}
}
printTrackHtml(tdb);
freez(&dupe);
hFreeConn(&conn);
hFreeConn(&conn2);
}
void printPcrTargetMatch(struct targetDb *target, struct psl *tpsl,
boolean mustGetItem)
/* Show the non-genomic target PCR result and its genomic mapping. */
{
char *acc = pcrResultItemAccession(tpsl->tName);
char *name = pcrResultItemName(tpsl->tName);
char niceName[256];
if (name == NULL || sameString(acc, name))
safecpy(niceName, sizeof(niceName), acc);
else
safef(niceName, sizeof(niceName), "%s (%s)", name, acc);
printf("Position in %s: %s"
":%d-%d
\n",
target->description, hgTracksName(), cartSidUrlString(cart), database,
acc, niceName, tpsl->tStart+1, tpsl->tEnd);
printf("Size in %s: %d
\n", niceName,
tpsl->tEnd - tpsl->tStart);
if (tpsl->strand[0] == '-')
printf(" "
"Warning: the match is on the reverse strand of %s
\n",
niceName);
struct psl *itemPsl = NULL, *otherPsls = NULL, *gpsl;
int itemStart = cartInt(cart, "o");
int itemEnd = cartInt(cart, "t");
int rowOffset = hOffsetPastBin(database, seqName, target->pslTable);
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr;
char **row;
char query[2048];
safef(query, sizeof(query), "select * from %s where qName = '%s'",
target->pslTable, acc);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
gpsl = pslLoad(row+rowOffset);
struct psl *pslTrimmed = pslTrimToQueryRange(gpsl, tpsl->tStart,
tpsl->tEnd);
if (sameString(gpsl->tName, seqName) &&
((gpsl->tStart == itemStart && gpsl->tEnd == itemEnd) ||
(pslTrimmed->tStart == itemStart && pslTrimmed->tEnd == itemEnd)))
itemPsl = pslTrimmed;
else
slAddHead(&otherPsls, pslTrimmed);
pslFree(&gpsl);
}
hFreeConn(&conn);
if (mustGetItem && itemPsl == NULL)
errAbort("Did not find record for amplicon in %s at %s:%d-%d",
niceName, seqName, itemStart, itemEnd);
char strand[2];
strand[1] = '\0';
if (itemPsl != NULL)
{
if (itemPsl->strand[1] == '\0')
strand[0] = itemPsl->strand[0];
else if (itemPsl->strand[0] != itemPsl->strand[1])
strand[0] = '-';
else
strand[0] = '+';
if (itemPsl != NULL)
printPosOnChrom(itemPsl->tName, itemPsl->tStart, itemPsl->tEnd,
strand, FALSE, tpsl->tName);
}
slSort(&otherPsls, pslCmpTarget);
if (itemPsl != NULL && otherPsls != NULL)
printf("Other matches in genomic alignments of %s:
\n",
niceName);
for (gpsl = otherPsls; gpsl != NULL; gpsl = gpsl->next)
{
if (gpsl->strand[1] == '\0')
strand[0] = gpsl->strand[0];
else if (gpsl->strand[0] != gpsl->strand[1])
strand[0] = '-';
else
strand[0] = '+';
printPosOnChrom(gpsl->tName, gpsl->tStart, gpsl->tEnd, strand, FALSE,
tpsl->tName);
}
pslFree(&itemPsl);
pslFreeList(&otherPsls);
}
static void upperMatch(char *dna, char *primer, int size)
/* Uppercase DNA where it matches primer. -- copied from gfPcrLib.c. */
{
int i;
for (i=0; itEnd - psl->tStart;
char *ffPrimer = cloneString(fPrimer);
char *rrPrimer = cloneString(rPrimer);
int rPrimerSize = strlen(rPrimer);
struct dnaSeq *seq;
if (target != NULL)
{
/* Use seq+extFile if specified; otherwise just retrieve from seqFile. */
if (isNotEmpty(target->seqTable) && isNotEmpty(target->extFileTable))
{
struct sqlConnection *conn = hAllocConn(database);
seq = hDnaSeqGet(database, psl->tName, target->seqTable,
target->extFileTable);
hFreeConn(&conn);
char *dna = cloneStringZ(seq->dna + psl->tStart, productSize);
freeMem(seq->dna);
seq->dna = dna;
}
else
{
struct twoBitFile *tbf = twoBitOpen(target->seqFile);
seq = twoBitReadSeqFrag(tbf, psl->tName, psl->tStart,
psl->tEnd);
twoBitClose(&tbf);
}
}
else
seq = hChromSeq(database, psl->tName, psl->tStart, psl->tEnd);
char *dna = seq->dna;
tolowers(dna);
if (psl->strand[0] == '-')
reverseComplement(dna, productSize);
printf("");
/* The rest of this is loosely copied from gfPcrLib.c:outputFa(): */
char *tNameForPos = (target != NULL ? pcrResultItemAccession(psl->tName) : psl->tName);
printf(">tStart+1, psl->tEnd);
printf("\">%s:%d%c%d %dbp %s %s\n",
psl->tName, psl->tStart+1, psl->strand[0], psl->tEnd,
productSize, fPrimer, rPrimer);
/* Flip reverse primer to be in same direction and case as sequence, to
* compare with sequence: */
reverseComplement(rrPrimer, rPrimerSize);
tolowers(rrPrimer);
tolowers(ffPrimer);
/* Capitalize where sequence and primer match, and write out sequence. */
upperMatch(dna, ffPrimer, strlen(ffPrimer));
upperMatch(dna + productSize - rPrimerSize, rrPrimer, rPrimerSize);
faWriteNext(stdout, NULL, dna, productSize);
printf("");
}
void doPcrResult(char *track, char *item)
/* Process click on PCR of user's primers. */
{
struct trackDb *tdb = pcrResultFakeTdb();
char *pslFileName, *primerFileName;
struct targetDb *target;
cartWebStart(cart, database, "PCR Results");
if (! pcrResultParseCart(database, cart, &pslFileName, &primerFileName, &target))
errAbort("PCR Result track has disappeared!");
char *fPrimer, *rPrimer;
pcrResultGetPrimers(primerFileName, &fPrimer, &rPrimer);
printf("PCR Results (%s %s)
\n", fPrimer, rPrimer);
printf("Forward primer: 5' %s 3'
\n", fPrimer);
printf("Reverse primer: 5' %s 3'
\n", rPrimer);
if (target != NULL)
printf("Search target: %s
\n", target->description);
struct psl *itemPsl = NULL, *otherPsls = NULL, *psl;
if (target != NULL)
{
/* item (from hgTracks) is |-separated: target sequence name,
* amplicon start offset in target sequence, and amplicon end offset. */
char *words[3];
int wordCount = chopByChar(cloneString(item), '|', words, ArraySize(words));
if (wordCount != 3)
errAbort("doPcrResult: expected 3 |-sep'd words but got '%s'", item);
char *targetSeqName = words[0];
if (endsWith(targetSeqName, "__"))
targetSeqName[strlen(targetSeqName)-2] = '\0';
int ampStart = atoi(words[1]), ampEnd = atoi(words[2]);
pcrResultGetPsl(pslFileName, target, targetSeqName, seqName, ampStart, ampEnd,
&itemPsl, &otherPsls);
printPcrTargetMatch(target, itemPsl, TRUE);
}
else
{
pcrResultGetPsl(pslFileName, target, item,
seqName, cartInt(cart, "o"), cartInt(cart, "t"),
&itemPsl, &otherPsls);
printPosOnChrom(itemPsl->tName, itemPsl->tStart, itemPsl->tEnd,
itemPsl->strand, FALSE, NULL);
}
if (otherPsls != NULL)
{
puts("
");
printf("Other matches for these primers:
\n");
for (psl = otherPsls; psl != NULL; psl = psl->next)
{
puts("
");
if (target != NULL)
printPcrTargetMatch(target, psl, FALSE);
else
printPosOnChrom(psl->tName, psl->tStart, psl->tEnd,
psl->strand, FALSE, NULL);
}
puts("
");
}
printPcrSequence(target, itemPsl, fPrimer, rPrimer);
puts("
");
printTrackHtml(tdb);
}
void doUserPsl(char *track, char *item)
/* Process click on user-defined alignment. */
{
int start = cartInt(cart, "o");
struct lineFile *lf;
struct psl *pslList = NULL, *psl;
char *pslName, *faName, *qName;
char *encItem = cgiEncode(item);
enum gfType qt, tt;
cartWebStart(cart, database, "BLAT Search Alignments");
printf("BLAT Search Alignments
\n");
printf("Click on a line to see detailed letter-by-letter display
");
parseSs(item, &pslName, &faName, &qName);
pslxFileOpen(pslName, &qt, &tt, &lf);
while ((psl = pslNext(lf)) != NULL)
{
if (sameString(psl->qName, qName))
{
slAddHead(&pslList, psl);
}
else
{
pslFree(&psl);
}
}
slReverse(&pslList);
lineFileClose(&lf);
printAlignments(pslList, start, "htcUserAli", "user", encItem);
pslFreeList(&pslList);
webIncludeHelpFile(USER_PSL_TRACK_NAME, TRUE);
}
void doHgGold(struct trackDb *tdb, char *fragName)
/* Click on a fragment of golden path. */
{
struct sqlConnection *conn = hAllocConn(database);
struct sqlConnection *conn2 = hAllocConn(database);
struct sqlConnection *conn3 = hAllocConn(database);
char query[256];
struct sqlResult *sr;
char **row;
char query2[256];
struct sqlResult *sr2;
char **row2;
char query3[256];
struct sqlResult *sr3;
char **row3;
struct agpFrag frag;
struct contigAcc contigAcc;
int start = cartInt(cart, "o");
boolean hasBin;
char splitTable[64];
char *chp;
char *accession1, *accession2, *spanner, *evaluation, *variation, *varEvidence,
*contact, *remark, *comment;
char *secondAcc, *secondAccVer;
char *tmpString;
int first;
cartWebStart(cart, database, "%s", fragName);
hFindSplitTable(database, seqName, tdb->table, splitTable, &hasBin);
sprintf(query, "select * from %s where frag = '%s' and chromStart = %d",
splitTable, fragName, start);
sr = sqlMustGetResult(conn, query);
row = sqlNextRow(sr);
agpFragStaticLoad(row+hasBin, &frag);
printf("Clone Fragment ID: %s
\n", frag.frag);
printf("Clone Fragment Type: %s
\n", frag.type);
printf("Clone Bases: %d-%d
\n", frag.fragStart+1, frag.fragEnd);
if (hTableExists(database, "contigAcc"))
{
sprintf(query2, "select * from contigAcc where contig = '%s'", frag.frag);
if ((sr2 = sqlGetResult(conn2, query2)))
{
row = sqlNextRow(sr2);
if (row)
{
contigAccStaticLoad(row, &contigAcc);
printf("Genbank Accession: %s
\n", contigAcc.acc);
}
sqlFreeResult(&sr2);
}
}
printPos(frag.chrom, frag.chromStart, frag.chromEnd, frag.strand, FALSE, NULL);
if (hTableExists(database, "certificate"))
{
first = 1;
again:
tmpString = cloneString(frag.frag);
chp = strstr(tmpString, ".");
if (chp != NULL) *chp = '\0';
if (first)
{
sprintf(query2,"select * from certificate where accession1='%s';", tmpString);
}
else
{
sprintf(query2,"select * from certificate where accession2='%s';", tmpString);
}
sr2 = sqlMustGetResult(conn2, query2);
row2 = sqlNextRow(sr2);
while (row2 != NULL)
{
printf("
");
accession1 = row2[0];
accession2 = row2[1];
spanner = row2[2];
evaluation = row2[3];
variation = row2[4];
varEvidence = row2[5];
contact = row2[6];
remark = row2[7];
comment = row2[8];
if (first)
{
secondAcc = accession2;
}
else
{
secondAcc = accession1;
}
sprintf(query3, "select frag from %s where frag like '%s.%c';",
splitTable, secondAcc, '%');
sr3 = sqlMustGetResult(conn3, query3);
row3 = sqlNextRow(sr3);
if (row3 != NULL)
{
secondAccVer = row3[0];
}
else
{
secondAccVer = secondAcc;
}
printf("Non-standard Join Certificate:
\n");
printf("The join between %s and %s is not standard due to a ", frag.frag, secondAccVer);
printf("sub-optimal sequence alignment between the overlapping regions of the ");
printf("clones. The following details are provided by the ");
printf("sequencing center to support the joining of these two clones:
");
printf("Joined with Fragment: %s
\n", secondAccVer);
if (strcmp(spanner, "") != 0) printf("Spanner: %s
\n", spanner);
/* if (strcmp(evaluation, "") != 0) printf("Evaluation: %s
\n", evaluation); */
if (strcmp(variation, "") != 0) printf("Variation: %s
\n", variation);
if (strcmp(varEvidence, "")!= 0) printf("Variation Evidence: %s
\n", varEvidence);
if (strcmp(remark, "") != 0) printf("Remark: %s
\n", remark);
if (strcmp(comment, "") != 0) printf("Comment: %s
\n", comment);
if (strcmp(contact, "") != 0)
printf("Contact: %s
", contact, contact);
sqlFreeResult(&sr3);
row2 = sqlNextRow(sr2);
}
sqlFreeResult(&sr2);
if (first)
{
first = 0;
goto again;
}
}
sqlFreeResult(&sr);
hFreeConn(&conn);
hFreeConn(&conn2);
hFreeConn(&conn3);
printTrackHtml(tdb);
}
void doHgGap(struct trackDb *tdb, char *gapType)
/* Print a teeny bit of info about a gap. */
{
struct sqlConnection *conn = hAllocConn(database);
char query[256];
struct sqlResult *sr;
char **row;
struct agpGap gap;
int start = cartInt(cart, "o");
boolean hasBin;
char splitTable[64];
cartWebStart(cart, database, "Gap in Sequence");
hFindSplitTable(database, seqName, tdb->table, splitTable, &hasBin);
if (sameString(tdb->table, splitTable))
safef(query, sizeof(query), "select * from %s where chrom = '%s' and "
"chromStart = %d",
splitTable, seqName, start);
else
safef(query, sizeof(query), "select * from %s where chromStart = %d",
splitTable, start);
sr = sqlMustGetResult(conn, query);
row = sqlNextRow(sr);
if (row == NULL)
errAbort("Couldn't find gap at %s:%d", seqName, start);
agpGapStaticLoad(row+hasBin, &gap);
printf("Gap Type: %s
\n", gap.type);
printf("Bridged: %s
\n", gap.bridge);
printPos(gap.chrom, gap.chromStart, gap.chromEnd, NULL, FALSE, NULL);
printTrackHtml(tdb);
sqlFreeResult(&sr);
hFreeConn(&conn);
}
void selectOneRow(struct sqlConnection *conn, char *table, char *query,
struct sqlResult **retSr, char ***retRow)
/* Do query and return one row offset by bin as needed. */
{
char fullTable[64];
boolean hasBin;
char **row;
if (!hFindSplitTable(database, seqName, table, fullTable, &hasBin))
errAbort("Table %s doesn't exist in database", table);
*retSr = sqlGetResult(conn, query);
if ((row = sqlNextRow(*retSr)) == NULL)
errAbort("No match to query '%s'", query);
*retRow = row + hasBin;
}
void doHgContig(struct trackDb *tdb, char *ctgName)
/* Click on a contig. */
{
struct sqlConnection *conn = hAllocConn(database);
struct sqlConnection *conn2 = hAllocConn(database);
char query[256], query2[256];
struct sqlResult *sr, *sr2;
char **row;
struct ctgPos *ctg;
struct ctgPos2 *ctg2 = NULL;
int cloneCount;
struct contigAcc contigAcc;
char * ncbiTerm = cgiEncode(ctgName);
safef(query, sizeof(query), "%s%s", NUCCORE_SEARCH, ncbiTerm);
genericHeader(tdb, ctgName);
char *url = tdb->url;
if (sameWord(database,"oryCun2"))
printf("Name: %s
\n", ctgName);
else if (isNotEmpty(url))
{
if (sameWord(url, "none"))
printf("Name: %s
\n", ctgName);
else
printCustomUrl(tdb, ctgName, TRUE);
}
else
printf("Name: %s
\n",
query, ctgName);
freeMem(ncbiTerm);
safef(query, sizeof(query), "select * from %s where contig = '%s'",
tdb->table, ctgName);
selectOneRow(conn, tdb->table, query, &sr, &row);
if (sameString("ctgPos2", tdb->table))
{
ctg2 = ctgPos2Load(row);
printf("Type: %s
\n", ctg2->type);
ctg = (struct ctgPos*)ctg2;
}
else
ctg = ctgPosLoad(row);
sqlFreeResult(&sr);
if (hTableExists(database, "contigAcc"))
{
sprintf(query2, "select * from contigAcc where contig = '%s'", ctgName);
if ((sr2 = sqlGetResult(conn2, query2)))
{
row = sqlNextRow(sr2);
if (row)
{
contigAccStaticLoad(row, &contigAcc);
printf("Genbank Accession: %s
\n", contigAcc.acc);
}
sqlFreeResult(&sr2);
}
}
if (hTableExists(database, "clonePos"))
{
sprintf(query,
"select count(*) from clonePos where chrom = '%s' and chromEnd >= %d and chromStart <= %d",
ctg->chrom, ctg->chromStart, ctg->chromEnd);
cloneCount = sqlQuickNum(conn, query);
printf("Total Clones: %d
\n", cloneCount);
}
printPos(ctg->chrom, ctg->chromStart, ctg->chromEnd, NULL, TRUE, ctg->contig);
printTrackHtml(tdb);
hFreeConn(&conn);
hFreeConn(&conn2);
}
char *cloneStageName(char *stage)
/* Expand P/D/F. */
{
switch (stage[0])
{
case 'P':
return "predraft (less than 4x coverage shotgun)";
case 'D':
return "draft (at least 4x coverage shotgun)";
case 'F':
return "finished";
default:
return "unknown";
}
}
void doHgCover(struct trackDb *tdb, char *cloneName)
/* Respond to click on clone. */
{
struct sqlConnection *conn = hAllocConn(database);
char query[256];
struct sqlResult *sr;
char **row;
struct clonePos *clone;
int fragCount;
cartWebStart(cart, database, "%s", cloneName);
sprintf(query, "select * from %s where name = '%s'", tdb->table, cloneName);
selectOneRow(conn, tdb->table, query, &sr, &row);
clone = clonePosLoad(row);
sqlFreeResult(&sr);
sprintf(query,
"select count(*) from %s_gl where end >= %d and start <= %d and frag like '%s%%'",
clone->chrom, clone->chromStart, clone->chromEnd, clone->name);
fragCount = sqlQuickNum(conn, query);
printf("Information on %s
\n", cloneName);
printf("GenBank: %s
\n", cloneName);
printf("Status: %s
\n", cloneStageName(clone->stage));
printf("Fragments: %d
\n", fragCount);
printf("Size: %d bases
\n", clone->seqSize);
printf("Chromosome: %s
\n", skipChr(clone->chrom));
printf("
\n");
hFreeConn(&conn);
printTrackHtml(tdb);
}
void doHgClone(struct trackDb *tdb, char *fragName)
/* Handle click on a clone. */
{
char cloneName[128];
fragToCloneVerName(fragName, cloneName);
doHgCover(tdb, cloneName);
}
void doBactigPos(struct trackDb *tdb, char *bactigName)
/* Click on a bactig. */
{
struct bactigPos *bactig;
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr;
char **row;
char query[256];
char goldTable[16];
char ctgStartStr[16];
int ctgStart;
genericHeader(tdb, bactigName);
sprintf(query, "select * from %s where name = '%s'", tdb->table, bactigName);
selectOneRow(conn, tdb->table, query, &sr, &row);
bactig = bactigPosLoad(row);
sqlFreeResult(&sr);
printf("Name: %s
\n", bactigName);
snprintf(goldTable, sizeof(goldTable), "%s_gold", seqName);
puts("First contig:");
if (hTableExists(database, goldTable))
{
snprintf(query, sizeof(query),
"select chromStart from %s where frag = \"%s\"",
goldTable, bactig->startContig);
ctgStart = sqlQuickNum(conn, query);
snprintf(ctgStartStr, sizeof(ctgStartStr), "%d", ctgStart);
hgcAnchor("gold", bactig->startContig, ctgStartStr);
}
printf("%s
\n", bactig->startContig);
puts("Last contig:");
if (hTableExists(database, goldTable))
{
snprintf(query, sizeof(query),
"select chromStart from %s where frag = \"%s\"",
goldTable, bactig->endContig);
ctgStart = sqlQuickNum(conn, query);
snprintf(ctgStartStr, sizeof(ctgStartStr), "%d", ctgStart);
hgcAnchor("gold", bactig->endContig, ctgStartStr);
}
printf("%s
\n", bactig->endContig);
printPos(bactig->chrom, bactig->chromStart, bactig->chromEnd, NULL, FALSE,NULL);
printTrackHtml(tdb);
hFreeConn(&conn);
}
int showGfAlignment(struct psl *psl, bioSeq *qSeq, FILE *f,
enum gfType qType, int qStart, int qEnd, char *qName)
/* Show protein/DNA alignment or translated DNA alignment. */
{
int blockCount;
int tStart = psl->tStart;
int tEnd = psl->tEnd;
char tName[256];
struct dnaSeq *tSeq;
/* protein psl's have a tEnd that isn't quite right */
if ((psl->strand[1] == '+') && (qType == gftProt))
tEnd = psl->tStarts[psl->blockCount - 1] + psl->blockSizes[psl->blockCount - 1] * 3;
tSeq = hDnaFromSeq(database, seqName, tStart, tEnd, dnaLower);
freez(&tSeq->name);
tSeq->name = cloneString(psl->tName);
safef(tName, sizeof(tName), "%s.%s", organism, psl->tName);
if (qName == NULL)
fprintf(f, "Alignment of %s and %s:%d-%d
\n",
psl->qName, psl->tName, psl->tStart+1, psl->tEnd);
else
fprintf(f, "Alignment of %s and %s:%d-%d
\n",
qName, psl->tName, psl->tStart+1, psl->tEnd);
fputs("Click on links in the frame to the left to navigate through "
"the alignment.\n", f);
blockCount = pslShowAlignment(psl, qType == gftProt,
qName, qSeq, qStart, qEnd,
tName, tSeq, tStart, tEnd, f);
freeDnaSeq(&tSeq);
return blockCount;
}
struct ffAli *pslToFfAliAndSequence(struct psl *psl, struct dnaSeq *qSeq,
boolean *retIsRc, struct dnaSeq **retSeq,
int *retTStart)
/* Given psl, dig up target sequence and convert to ffAli.
* Note: if strand is -, this does a pslRc to psl! */
{
int tStart, tEnd, tRcAdjustedStart;
struct dnaSeq *dnaSeq;
tStart = psl->tStart - 100;
if (tStart < 0) tStart = 0;
if (retTStart)
*retTStart = tStart;
tEnd = psl->tEnd + 100;
if (tEnd > psl->tSize) tEnd = psl->tSize;
dnaSeq = hDnaFromSeq(database, seqName, tStart, tEnd, dnaLower);
freez(&dnaSeq->name);
dnaSeq->name = cloneString(psl->tName);
if (retSeq)
*retSeq = dnaSeq;
tRcAdjustedStart = tStart;
if (psl->strand[0] == '-')
{
if (retIsRc)
*retIsRc = TRUE;
reverseComplement(dnaSeq->dna, dnaSeq->size);
pslRc(psl);
tRcAdjustedStart = psl->tSize - tEnd;
}
return pslToFfAli(psl, qSeq, dnaSeq, tRcAdjustedStart);
}
int showPartialDnaAlignment(struct psl *wholePsl,
struct dnaSeq *rnaSeq, FILE *body,
int cdsS, int cdsE, boolean restrictToWindow)
/* Show (part of) alignment for accession. wholePsl is the whole alignment;
* if restrictToWindow then display the part of the alignment in the current
* browser window. */
{
struct dnaSeq *dnaSeq;
int wholeTStart;
int partTStart = wholePsl->tStart, partTEnd = wholePsl->tEnd;
DNA *rna;
int rnaSize;
boolean isRc = FALSE;
struct ffAli *wholeFfAli;
int blockCount;
/* Get RNA sequence and convert psl to ffAli. */
rna = rnaSeq->dna;
rnaSize = rnaSeq->size;
/* Don't forget -- this may change wholePsl! */
wholeFfAli = pslToFfAliAndSequence(wholePsl, rnaSeq, &isRc, &dnaSeq,
&wholeTStart);
if (restrictToWindow)
{
partTStart = max(wholePsl->tStart, winStart);
partTEnd = min(wholePsl->tEnd, winEnd);
}
/* Write body heading info. */
fprintf(body, "Alignment of %s and %s:%d-%d
\n",
wholePsl->qName, wholePsl->tName, partTStart+1, partTEnd);
fprintf(body, "Click on links in the frame to the left to navigate through "
"the alignment.\n");
if (rnaSize != wholePsl->qSize)
{
fprintf(body, "Cannot display alignment. Size of rna %s is %d has changed since alignment was performed when it was %d.\n",
wholePsl->qName, rnaSize, wholePsl->qSize);
return 0;
}
blockCount = ffShAliPart(body, wholeFfAli, wholePsl->qName,
rna, rnaSize, 0,
dnaSeq->name, dnaSeq->dna, dnaSeq->size,
wholeTStart, 8, FALSE, isRc,
FALSE, TRUE, TRUE, TRUE, TRUE,
cdsS, cdsE, partTStart, partTEnd);
return blockCount;
}
void showSomeAlignment(struct psl *psl, bioSeq *oSeq,
enum gfType qType, int qStart, int qEnd,
char *qName, int cdsS, int cdsE)
/* Display protein or DNA alignment in a frame. */
{
int blockCount, i;
struct tempName indexTn, bodyTn;
FILE *index, *body;
trashDirFile(&indexTn, "index", "index", ".html");
trashDirFile(&bodyTn, "body", "body", ".html");
/* Writing body of alignment. */
body = mustOpen(bodyTn.forCgi, "w");
htmStartDirDepth(body, psl->qName, 2);
if (qType == gftRna || qType == gftDna)
blockCount = showPartialDnaAlignment(psl, oSeq, body, cdsS, cdsE, FALSE);
else
blockCount = showGfAlignment(psl, oSeq, body, qType, qStart, qEnd, qName);
htmEnd(body);
fclose(body);
chmod(bodyTn.forCgi, 0666);
/* Write index. */
index = mustOpen(indexTn.forCgi, "w");
if (qName == NULL)
qName = psl->qName;
htmStartDirDepth(index, qName, 2);
fprintf(index, "Alignment of %s
", qName);
fprintf(index, "%s
\n", bodyTn.forCgi, qName);
fprintf(index, "%s.%s
\n", bodyTn.forCgi, hOrganism(database), psl->tName);
for (i=1; i<=blockCount; ++i)
{
fprintf(index, "block%d
\n",
bodyTn.forCgi, i, i);
}
fprintf(index, "together
\n", bodyTn.forCgi);
htmEnd(index);
fclose(index);
chmod(indexTn.forCgi, 0666);
/* Write (to stdout) the main html page containing just the frame info. */
puts("");
puts("