78f5fa0481441bdffe2792e1ec3ff0ac4deb0e4f pchan Mon Aug 22 11:38:28 2011 -0700 change arCOG code to link to arCOGs browser instead of local table diff --git src/hg/hgc/lowelab.c src/hg/hgc/lowelab.c index ff3baf9..9d0eef7 100644 --- src/hg/hgc/lowelab.c +++ src/hg/hgc/lowelab.c @@ -1,3898 +1,3939 @@ /* Lowe Lab additions for Archaea and Bacterial details pages*/ #include "common.h" #include "obscure.h" #include "hCommon.h" #include "hash.h" #include "bits.h" #include "memgfx.h" #include "portable.h" #include "errabort.h" #include "dystring.h" #include "nib.h" #include "cheapcgi.h" #include "htmshell.h" #include "cart.h" #include "jksql.h" #include "dnautil.h" #include "dnaseq.h" #include "fa.h" #include "fuzzyFind.h" #include "seqOut.h" #include "hdb.h" #include "spDb.h" #include "hui.h" #include "hgRelate.h" #include "htmlPage.h" #include "psl.h" #include "cogs.h" #include "cogsxra.h" #include "bed.h" #include "xenalign.h" #include "isochores.h" #include "genePred.h" #include "genePredReader.h" #include "pepPred.h" #include "wabAli.h" #include "minGeneInfo.h" #include "rnaGene.h" #include "tRNAs.h" #include "snoRNAs.h" #include "gbRNAs.h" #include "hgMaf.h" #include "maf.h" #include "hgConfig.h" #include "web.h" #include "dbDb.h" #include "sample.h" #include "axt.h" #include "gbProtAnn.h" #include "hgSeq.h" #include "chain.h" #include "chainNet.h" #include "chainDb.h" #include "chainToPsl.h" #include "chainToAxt.h" #include "netAlign.h" #include "tigrCmrGene.h" #include "jgiGene.h" #include "lowelabPfamHit.h" #include "lowelabArkinOperonScore.h" #include "lowelabTIGROperonScore.h" #include "sargassoSeaXra.h" #include "codeBlastScore.h" #include "codeBlast.h" #include "tigrOperon.h" #include "easyGene.h" #include "llaInfo.h" #include "blastTab.h" #include "hdb.h" #include "hgc.h" #include "genbank.h" #include "pseudoGeneLink.h" #include "axtLib.h" #include "tfbsCons.h" #include "tfbsConsMap.h" #include "tfbsConsSites.h" #include "tfbsConsFactors.h" #include "simpleNucDiff.h" #include "botDelay.h" #include "bed5FloatScore.h" #include "bed6FloatScore.h" #include "pscreen.h" #include "gapCalc.h" #include "chainConnect.h" #include "ec.h" #include "transMapClick.h" #include "ccdsClick.h" #include "memalloc.h" #include "rnaHybridization.h" #include "cddInfo.h" #include "alignInfo.h" #include "loweutils.h" #include "cddDesc.h" #include "arCOGs.h" #include "arcogdesc.h" #include "megablastInfo.h" #include "geneTree.h" /*#define LISTUI*/ static char const rcsid[] = "$Id: lowelab.c,v 1.50 2010/05/11 01:43:29 kent Exp $"; extern char *uniprotFormat; static void goPrint( struct sqlConnection *conn, char *geneId, char *acc) /* Print out GO annotations. */ { struct sqlConnection *goConn = sqlConnect("go"); char query[512]; struct sqlResult *sr; char **row; static char *aspects[3] = {"F", "P", "C"}; static char *aspectNames[3] = { "Molecular Function", "Biological Process", "Cellular Component", }; int aspectIx; int termCount = 0; if (sqlTableExists(goConn,"goaPart") && sqlTableExists(goConn,"term")) for (aspectIx = 0; aspectIx < ArraySize(aspects); ++aspectIx) { boolean hasFirst = FALSE; safef(query, sizeof(query), "select term.acc,term.name" " from goaPart,term" " where goaPart.dbObjectId = '%s'" " and goaPart.goId = term.acc" " and goaPart.aspect = '%s'" , acc, aspects[aspectIx]); sr = sqlGetResult(goConn, query); while ((row = sqlNextRow(sr)) != NULL) { char *goID = row[0]; char *goTermName = row[1]; if (!hasFirst) { printf("<B>%s:</B><BR>", aspectNames[aspectIx]); hasFirst = TRUE; } printf("<A HREF = \""); printf("http://godatabase.org/cgi-bin/go.cgi?view=details&depth=1&query=%s", goID); printf("\" TARGET=_blank>%s</A> %s<BR>\n", goID, goTermName); termCount++; } if (hasFirst) printf("<BR>"); sqlFreeResult(&sr); } if (termCount == 0) printf("Not available<BR>\n"); sqlDisconnect(&goConn); } void keggOtherGenes(struct sqlConnection *conn, char *geneId, char *table, char *mapId) /* Print out genes linked to a kegg pathway mapId. */ { char query[512], **row; struct sqlResult *sr; char *extraTable = "gbProtCodeXra"; char *keggTable = "keggPathway"; if (hTableExists(database, extraTable)) { safef(query, sizeof(query), "select x.name, x.gene, x.product from %s k1, %s x " "where k1.mapID = '%s' and " "k1.kgID = x.name ;" , keggTable, extraTable, mapId ); sr = sqlGetResult(conn, query); printf("<table>\n"); while ((row = sqlNextRow(sr)) != NULL) { printf("<tr><td>"); hgcAnchorPosition(table,row[0]); printf("%s</A> <BR>\n",row[0]); if (differentString(row[0],row[1]) && differentString(row[1], "none")) printf("</td><td>%s</td><td>%s</td></tr>\n", row[1], row[2]); else printf("</td><td> </td><td>%s</td></tr>\n", row[2]); } sqlFreeResult(&sr); printf("</table>\n"); } } void keggLink(struct sqlConnection *conn, char *geneId, char *table, char *title) /* Print out kegg database link. */ { char query[512], **row; struct sqlResult *sr; struct sqlConnection *conn2 = hAllocConn(database); safef(query, sizeof(query), "select keggPathway.locusID,keggPathway.mapID,keggMapDesc.description" " from keggPathway,keggMapDesc" " where keggPathway.kgID='%s'" " and keggPathway.mapID = keggMapDesc.mapID" , geneId); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { printf("%s",title); printf("<A HREF=\"http://www.genome.ad.jp/dbget-bin/show_pathway?%s+%s\" TARGET=_blank>", row[1], row[0]); printf("%s</A> - %s<BR>", row[1], row[2]); printf("<B>Other Genes in Kegg Pathway: </b><BR>"); keggOtherGenes(conn2, geneId, table, row[1]); printf("<BR>\n"); } sqlFreeResult(&sr); } int keggCount(struct sqlConnection *conn, char *geneId) /* Count up number of hits. */ { char query[256]; char *keggTable = "keggPathway"; if (!hTableExists(database, keggTable)) return 0; safef(query, sizeof(query), "select count(*) from %s where kgID='%s'", keggTable, geneId); return sqlQuickNum(conn, query); } void modBaseAnchor(char *swissProtAcc) /* Print out anchor to modBase. */ { printf("<A HREF=\"http://salilab.org/modbase-cgi/model_search.cgi?searchkw=name&kword=%s\" TARGET=_blank>", swissProtAcc); } float computeGCContent(char* dna, int length) { float percent = 0.0f; int count = 0; int i = 0; for (i = 0; i < length; i++) { if ((dna[i] == 'C') || (dna[i] == 'c') || (dna[i] == 'G') || (dna[i] == 'g')) count++; } percent = (float) count / (float) length * 100.0f; return percent; } int selfBlastpHitCount(struct sqlConnection *conn, char *geneId) /* Count up number of hits. */ { char query[512]; char *blastpHitsTable = "blastpHits"; if (!hTableExists(database, blastpHitsTable)) return 0; safef(query, sizeof(query), "select count(*) from %s where query = '%s' and target like '%s:%%' and target != '%s:%s'", blastpHitsTable, geneId, database, database, geneId); return sqlQuickNum(conn, query); } struct blastTab* loadSelfBlastpHits(struct sqlConnection *conn, char* queryName, int self) /* Load all blastp hits in the same genome of the given query gene into a list */ { char query[512]; struct sqlResult *srBlastpHits = NULL; struct blastTab *list = NULL; struct blastTab *blastpHits; char **row; char blastpHitsTable[] = "blastpHits"; if (hTableExists(database, blastpHitsTable)) { if (self) { sprintf(query, "select * from %s where query = '%s' and target like '%s:%%'", blastpHitsTable, queryName, database); } else { sprintf(query, "select * from %s where query = '%s' and target like '%s:%%' and target != '%s:%s'", blastpHitsTable, queryName, database, database, queryName); } srBlastpHits = sqlGetResult(conn, query); while ((row = sqlNextRow(srBlastpHits)) != NULL) { blastpHits = blastTabLoad(row); slAddTail(&list, blastpHits); } } if (srBlastpHits != NULL) sqlFreeResult(&srBlastpHits); return list; } void printSelfHomologs(struct sqlConnection *conn, struct blastTab *blastpHitsList) /* Print self homologs in refseq */ { char query[512]; struct sqlResult *sr; char **row; char refSeq[50]; char xraTable[50]; char product[255]; struct blastTab *blastpHits; struct minGeneInfo *ginfo; char *blastpTarget[2]; char **buffer = NULL; boolean findTable = FALSE; unsigned int cdsStart = 0; unsigned int cdsEnd = 0; printf("<br>\n"); printf("<b>Homologs within genome</b><BR>\n"); /* Print table */ printf("<table style='width:60%%; background-color:#%s;' border=0 cellpadding=1 cellspacing=0>", HG_COL_BORDER); printf("<tbody><tr><td>\n"); printf("<table style='width:100%%; text-align:left; background-color:#%s;' border=1 cellpadding=2 cellspacing=2>\n", HG_COL_INSIDE); printf("<tbody>\n"); /* Print table column heading */ printf("<tr style=\"vertical-align: top;\">\n"); printf("<td width=\"20%%\"><b>Gene</b></td>\n"); printf("<td><b>Product</b></td>\n"); printf("<td width=\"30%%\"><b>BlastP E-value</b></td>\n"); printf("</tr>\n"); blastpHits = blastpHitsList; while (blastpHits != NULL) { parseDelimitedString(blastpHits->target, ':', blastpTarget, 2); if (hTableExists(blastpTarget[0], "lookup")) { sprintf(query, "select lookupValue from %s.lookup where lookupCode = 'annotRev'", blastpTarget[0]); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { strcpy(refSeq, row[0]); findTable = TRUE; sqlFreeResult(&sr); } } else if (hTableExists(blastpTarget[0], "refSeq")) { strcpy(refSeq, "refSeq"); findTable = TRUE; } if (findTable) { sprintf(query, "select chrom, cdsStart, cdsEnd from %s where name = '%s'", refSeq, blastpTarget[1]); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { cdsStart = strtoul(row[1], buffer, 10); cdsEnd = strtoul(row[2], buffer, 10); printf("<tr style=\"vertical-align: top;\">\n"); printf("<td><a href=\"hgTracks\?position=%s:%u-%u&db=%s\" TARGET=_blank>%s</a></td>\n", row[0], cdsStart, cdsEnd, blastpTarget[0], blastpTarget[1]); } else printf("<td>%s</td>\n", blastpTarget[1]); sqlFreeResult(&sr); } else printf("<td>%s</td>\n", blastpTarget[1]); if (hTableExists(blastpTarget[0], "lookup")) { sprintf(query, "select lookupValue from %s.lookup where lookupCode = 'annotRevXra'", blastpTarget[0]); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { strcpy(xraTable, row[0]); sqlFreeResult(&sr); } else strcpy(product, "N/A"); sprintf(query, "select product from %s where name = '%s'", xraTable, blastpTarget[1]); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { strcpy(product, row[0]); sqlFreeResult(&sr); } else strcpy(product, "N/A"); } else { ginfo = getGbProtCodeInfo(conn, blastpTarget[0], blastpTarget[1]); if (ginfo != NULL && ginfo->product != NULL && differentString(ginfo->product,"none")) strcpy(product, ginfo->product); else strcpy(product, "N/A"); } printf("<td>%s</td>\n", product); printf("<td style=\"text-align: right;\">%0.0e</td>\n", blastpHits->eValue); printf("</tr>\n"); free(blastpTarget[0]); free(blastpTarget[1]); blastpHits = blastpHits->next; } /* Close table */ printf("</tbody>\n"); printf("</table>\n"); printf("</td></tr></tbody>\n"); printf("</table>\n"); } int getGeneTree(struct sqlConnection *conn, char *geneId, char *treeFileName) { int success = 0; char query[256]; char *geneTreeTable = "geneTree"; struct sqlResult *sr; char **row; struct geneTree *genetree; if (!hTableExists(database, geneTreeTable)) return 0; safef(query, sizeof(query), "select * from %s where name = '%s'", geneTreeTable, geneId); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { genetree = geneTreeLoad(row); if (!fileExists(treeFileName)) { FILE *f; f = fopen(treeFileName, "w"); if (f != NULL) { fprintf(f, "%s\n", genetree->tree); fclose(f); success = 1; } } else success = 1; } sqlFreeResult(&sr); geneTreeFree(&genetree); return success; } void doRefSeq(struct trackDb *tdb, char *item, char *pepTable, char *extraTable) /* Handle click on gene track. */ { struct minGeneInfo ginfo; char query[256]; char query2[256]; char *gi = NULL; struct sqlResult *sr, *sr2; struct dnaSeq *sequence; char **row, **row2; char *words[16], *dupe = cloneString(tdb->type); int wordCount, x, length; int num = 0; int hits = 0; struct sqlConnection *conn = hAllocConn(database); struct sqlConnection *conn2; struct sqlConnection *spConn = NULL; struct COG *COG=NULL; struct COGXra *COGXra=NULL; char *temparray[160]; char *giwords[5]; char *spAcc = NULL; struct slName *el, *list; char *table = tdb->table; char *pdb = hPdbFromGdb(database); struct genePred *gpList = NULL, *gp = NULL; char tableName[64]; boolean hasBin; int itemCount = 0; +int arcogCount = 0; +char genome[50] = ""; +char clade[50] = ""; +boolean hasArCOG; char treeFileName[256]; char treeTmpPsFileName[256]; char treePsFileName[256]; char treePngFileName[256]; char treePdfFileName[256]; char command[512]; char buffer[512]; char searchTerm[256]; struct blastTab *blastpHitsList; char pepTableName[64]; char extraTableName[64]; if (startsWith("annotRev", table)) { sprintf(pepTableName, "%s%s", table, pepTable); sprintf(extraTableName, "%s%s", table, extraTable); } else { strcpy(pepTableName, pepTable); strcpy(extraTableName, extraTable); } spConn = sqlConnect( pdb); genericHeader(tdb, item); wordCount = chopLine(dupe, words); if (wordCount > 1) num = atoi(words[1]); if (num < 3) num = 3; if (extraTableName != NULL && hTableExists(database, extraTableName)) { sprintf(query, "select * from %s where name = '%s'", extraTableName, item); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { minGeneInfoStaticLoad(row, &ginfo); gi = cloneString(ginfo.gi); if (ginfo.gene != NULL && differentString(ginfo.gene,"none")) printf("<B>Gene: </B>%s<BR>\n", ginfo.gene); if (ginfo.product != NULL && differentString(ginfo.product,"none")) medlineLinkedLine("Product", ginfo.product, ginfo.product); if (ginfo.note != NULL && differentString(ginfo.note,"none")) printf("<B>Note: </B>%s<BR>\n", ginfo.note); if (ginfo.protein != NULL && differentString(ginfo.protein,"none")) printf("<B>Protein: </B>%s<BR>\n", ginfo.protein); if (ginfo.ec != NULL && differentString(ginfo.ec,"none")) { printf("<B>EC (Enzyme Commission) number:</B> " "<A HREF=\"http://us.expasy.org/enzyme/%s\" " "TARGET=_BLANK>%s</A>\n", ginfo.ec, ginfo.ec); getEcHtml(ginfo.ec); medlineLinkedTermLine("EC PubMed Search", ginfo.ec, ginfo.ec, "EC/RN Number"); printf(" <B>Brenda : </B> <A HREF=\"http://www.brenda.uni-koeln.de/php/result_flat.php4?ecno=%s&organism=\" " "TARGET=_BLANK>%s</A><BR>\n", ginfo.ec, ginfo.ec); } } sqlFreeResult(&sr); } /* lookup swissprot acc */ spAcc = uniProtFindPrimAccFromGene(item, database); if (spAcc != NULL) { printf("<B>UniProtKB:</B> "); printf("<A HREF="); printf(uniprotFormat, spAcc); if (spAcc == NULL) { printf(" TARGET=_blank>%s</A></B><BR>\n", item); } else { printf(" TARGET=_blank>%s</A></B><BR>\n", spAcc); } } /* print table of contents */ printf("<br><hr style='width:100%%; height:2px;'><span style='font-size:larger;'>\n"); printf("<b>[<a href=\"#positions\">Positions and Sequence</a>] \n"); printf("[<a href=\"#COG\">COG</a>] \n"); printf("[<a href=\"#GO\">Gene Ontology</a>] \n"); printf("[<a href=\"#domain\">Protein Domain and Structure Infomation</a>] \n"); printf("[<a href=\"#homology\">Gene Homology</a>] \n"); printf("[<a href=\"#pathway\">Pathway</a>]</b></span> <br>\n"); printf("<hr style=\"width: 100%%; height: 2px;\"><br>\n"); /* Positions and sequence */ printf("<table style=\"text-align: left; width: 99%%;\" border=\"1\" cellpadding=\"5\" cellspacing=\"0\">\n"); printf("<tbody><tr><td style=\"background-color:#eee9e9;\">\n"); printf("<a name=\"positions\"></a><b>Positions and Sequence</b><br></td></tr>\n"); printf("<tr><td>\n"); hFindSplitTable(database, seqName, table, tableName, &hasBin); safef(query, sizeof(query), "name = \"%s\"", item); gpList = genePredReaderLoadQuery(conn, tableName, query); for (gp = gpList; gp != NULL; gp = gp->next) { sequence = hDnaFromSeq(database, gp->chrom, gp->txStart, gp->txEnd, dnaUpper); if (sequence != NULL) printf("<B>GC content:</B> %0.2f%%<BR>\n", computeGCContent(sequence->dna, sequence->size)); } geneShowPosAndLinks(item, item, tdb, pepTableName, "htcTranslatedProtein", "htcGeneMrna", "htcGeneInGenome", "Predicted mRNA"); genePredFreeList(&gpList); printf("</td></tr></tbody></table><br>\n"); /* COG */ printf("<table style=\"text-align: left; width: 99%%;\" border=\"1\" cellpadding=\"5\" cellspacing=\"0\">\n"); printf("<tbody><tr><td style=\"background-color:#eee9e9;\">\n"); printf("<a name=\"COG\"></a><b>COG</b><br></td></tr>\n"); printf("<tr><td>\n"); /* cog description */ itemCount = 0; if (hTableExists(database, "COG")) { sprintf(query, "select * from COG where name = '%s'", item); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { COG = COGLoad(row); if(COG!=NULL) { length=chopString(COG->COG, "," , temparray, 999); for(x=0; x<length; x++) { conn2 = hAllocConn(database); sprintf(query2, "select * from COGXra where name = '%s'", temparray[x]); sr2 = sqlGetResult(conn2, query2); while ((row2 = sqlNextRow(sr2)) != NULL) { COGXra=COGXraLoad(row2); if(COGXra!=NULL) printf("<B>COG:</B> " - "<A HREF=\"http://www.ncbi.nlm.nih.gov/COG/grace/wiew.cgi?%s\" " + "<A HREF=\"http://www.ncbi.nlm.nih.gov/COG/grace/wiew.cgi?%s\" target=\"_blank\" " ">%s</A> " - "<A HREF=\"http://www.ncbi.nlm.nih.gov/COG/grace/wiew.cgi?fun=%s\" " + "<A HREF=\"http://www.ncbi.nlm.nih.gov/COG/grace/wiew.cgi?fun=%s\" target=\"_blank\" " ">Code %s</A> \n", COGXra->name, COGXra->name, COG->code,COG->code); printf(" %s<BR>\n", COGXra->info); itemCount++; } sqlFreeResult(&sr2); hFreeConn(&conn2); } } } sqlFreeResult(&sr); //hFreeConn(&conn2); } +/* if (hTableExists(database, "arCOGs")) { struct arCOGs *infoload = NULL; struct arcogdesc *description = NULL; int rowOffset = hOffsetPastBin(database, seqName, "arCOGs"); //infoload = arCOGsLoad(row); row = NULL; sprintf(query, "select * from arCOGs where gene = '%s'", item); sr = sqlGetResult(conn, query); conn2 = hAllocConn(database); while ((row = sqlNextRow(sr)) != NULL) { infoload = arCOGsLoad(row+rowOffset); if(infoload!=NULL) { sprintf(query2, "select * from mgCommonDb.arcogdesc where name = '%s'",infoload->name ); sr2 = sqlGetResult(conn2, query2); while ((row2 = sqlNextRow(sr2)) != NULL) { description=arcogdescLoad(row2); if(description!=NULL) { printf("<B>arCOG:</B> %s Code %s",infoload->name, description->code); printf(" %s<BR/>\n", description->description); itemCount++; } } sqlFreeResult(&sr2); hFreeConn(&conn2); } } } +*/ + +arcogCount = 0; +hasArCOG = false; +row = NULL; +sprintf(query, "show databases like 'arCogsDb'"); +sr = sqlGetResult(conn, query); +if ((row = sqlNextRow(sr)) != NULL) +{ + hasArCOG = true; +} +sqlFreeResult(&sr); + +if (hasArCOG) +{ + /* Get species info */ + memset(genome, 0, 50); + memset(clade, 0, 50); + getGenomeClade(conn, database, genome, clade); + + sprintf(query, "select distinct a.arcog_id, a.anntation, c.class_id from arCogsDb.arcogDef a, arCogsDb.arcog b, arCogsDb.arcogFun c where a.arcog_id = b.arcog_id and a.arcog_id = c.arcog_id and db_name = '%s' and name = '%s'", + database, item); + sr = sqlGetResult(conn, query); + while ((row = sqlNextRow(sr)) != NULL) + { + printf("<B>arCOG:</B> <A HREF=\"/arCOGsBrowser/#Tax_Tree;ArcogsId=%s\" target=\"_blank\">%s</A> <A HREF=\"/arCOGsBrowser/#MainAdvance;Genome=%s,FunId=%s,Limit=50,Index=0,Load=true\" target=\"_blank\">Code %s</A> ", + row[0], row[0], genome, row[2], row[2]); + printf(" %s<BR/>\n", row[1]); + arcogCount++; + itemCount++; + } + sqlFreeResult(&sr); + if (arcogCount > 0) + printf("<A HREF=\"/arCOGsBrowser/#MainGene;Genome=%s,Gene=%s\" target=\"_blank\">arCOG Gene Annotation</A><BR/>", genome, item); +} + if (itemCount == 0) printf("Not available\n"); printf("</td></tr></tbody></table><br>\n"); /* GO */ printf("<table style=\"text-align: left; width: 99%%;\" border=\"1\" cellpadding=\"5\" cellspacing=\"0\">\n"); printf("<tbody><tr><td style=\"background-color:#eee9e9;\">\n"); printf("<a name=\"GO\"></a><b>Gene Ontology</b><br></td></tr>\n"); printf("<tr><td>\n"); /* print go terms */ goPrint( conn, item, spAcc); printf("</td></tr></tbody></table><br>\n"); /* Protein domain and structure information */ printf("<table style=\"text-align: left; width: 99%%;\" border=\"1\" cellpadding=\"5\" cellspacing=\"0\">\n"); printf("<tbody><tr><td style=\"background-color:#eee9e9;\">\n"); printf("<a name=\"domain\"></a><b>Protein Domain and Structure Information</b><br></td></tr>\n"); printf("<tr><td>\n"); /* interpro domains */ list = spExtDbAcc1List(spConn, spAcc, "InterPro"); if (list != NULL) { char query[256], **row, **row2; struct sqlResult *sr, *sr2; printf("<B>InterPro Domains: </B> "); printf("<A HREF=\"http://www.ebi.ac.uk/interpro/ISpy?mode=single&ac=%s\" TARGET=_blank>", spAcc); printf("Graphical view of domain structure</A><BR>"); safef(query, sizeof(query), "select extAcc1,extAcc2 from extDbRef,extDb" " where extDbRef.acc = '%s'" " and extDb.val = 'Interpro' and extDb.id = extDbRef.extDb" , spAcc); sr = sqlGetResult(spConn, query); while ((row = sqlNextRow(sr)) != NULL) { char interPro[256]; char *pdb = hPdbFromGdb(database); safef(interPro, 128, "%s.interProXref", pdb); if (hTableExists(database, interPro)) { safef(query, sizeof(query), "select description from %s where accession = '%s' and interProId = '%s'", interPro, spAcc, row[0]); sr2 = sqlGetResult(conn, query); if ((row2 = sqlNextRow(sr2)) != NULL) { printf("<A HREF=\"http://www.ebi.ac.uk/interpro/IEntry?ac=%s\" TARGET=_blank>", row[0]); printf("%s</A> - %s <BR>\n", row[0], row2[0]); } sqlFreeResult(&sr2); } else { printf("<A HREF=\"http://www.ebi.ac.uk/interpro/IEntry?ac=%s\" TARGET=_blank>", row[0]); printf("%s</A> - %s<BR>\n", row[0], row[1]); } } printf("<BR>\n"); slFreeList(&list); } /* pfam domains */ list = spExtDbAcc1List(spConn, spAcc, "Pfam"); if (list != NULL) { printf("<B>Pfam Domains:</B><BR>"); for (el = list; el != NULL; el = el->next) { char query[256]; char *description; safef(query, sizeof(query), "select description from proteome.pfamDesc where pfamAC='%s'", el->name); description = sqlQuickString(spConn, query); if (description == NULL) { safef(query, sizeof(query), "select extDbRef.extAcc1 from extDbRef,extDb " "where extDbRef.acc = '%s' " "and extDbRef.extDb = extDb.id " "and extDb.val = '%s'" , spAcc,el->name); printf("%s\n", query); description = sqlQuickString(spConn, query); } if (description == NULL) description = cloneString("n/a"); printf("<A HREF=\"http://pfam.sanger.ac.uk/family?acc=%s\" TARGET=_blank>", el->name); printf("%s</A> - %s<BR>\n", el->name, description); freez(&description); } slFreeList(&list); printf("<BR>\n"); } list = spExtDbAcc1List(spConn, spAcc, "PDB"); if (list != NULL) { char query[256], **row; struct sqlResult *sr; int column = 0, maxColumn=4, rowCount=0; printf("<B>Protein Data Bank (PDB) 3-D Structure</B><BR>"); safef(query, sizeof(query), "select extAcc1,extAcc2 from extDbRef,extDb" " where extDbRef.acc = '%s'" " and extDb.val = 'PDB' and extDb.id = extDbRef.extDb" , spAcc); sr = sqlGetResult(spConn, query); printf("<TABLE><TR>\n"); while ((row = sqlNextRow(sr)) != NULL) { if (++column > maxColumn) { printf("</TR><TR>"); column = 1; if (rowCount == 0) { printf("<TD ALIGN=CENTER COLSPAN=4><I>To conserve bandwidth, only the images from the first %d structures are shown.</I>", maxColumn); printf("</TR><TR>"); } ++rowCount; } printf("<TD>"); printf("<A HREF=\"http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=%s\" TARGET=_blank>", row[0]); if (rowCount < 1) printf("<IMG SRC=\"http://www.rcsb.org/pdb/images/%s_bio_r_80.jpg\"><BR>", row[0]); printf("%s</A> - %s<BR>\n", row[0], row[1]); printf("</TD>"); } printf("</TR></TABLE>\n"); printf("<BR>\n"); slFreeList(&list); } /* Do modBase link. */ { printf("<B>ModBase Predicted Comparative 3D Structure on "); modBaseAnchor(spAcc); printf("%s", spAcc); printf("</A></B><BR>\n"); printf("<TABLE><TR>"); printf("<TD>"); modBaseAnchor(spAcc); printf("\n<IMG SRC=\"http://salilab.org/modbaseimages/image/modbase.jpg?database_id=%s\"></A></TD>", spAcc); printf("<TD>"); modBaseAnchor(spAcc); printf("\n<IMG SRC=\"http://salilab.org/modbaseimages/image/modbase.jpg?database_id=%s&axis=x°ree=90\"></A></TD>", spAcc); printf("<TD>"); modBaseAnchor(spAcc); printf("\n<IMG SRC=\"http://salilab.org/modbaseimages/image/modbase.jpg?database_id=%s&axis=y°ree=90\"></A></TD>", spAcc); printf("</TR><TR>\n"); printf("<TD ALIGN=CENTER>Front</TD>"); printf("<TD ALIGN=CENTER>Top</TD>"); printf("<TD ALIGN=CENTER>Side</TD>"); printf("</TR></TABLE>\n"); printf("<I>The pictures above may be empty if there is no " "ModBase structure for the protein. The ModBase structure " "frequently covers just a fragment of the protein. You may " "be asked to log onto ModBase the first time you click on the " "pictures. It is simplest after logging in to just click on " "the picture again to get to the specific info on that model.</I><p>"); } printf("</td></tr></tbody></table><br>\n"); /* Gene Homology */ printf("<table style=\"text-align: left; width: 99%%;\" border=\"1\" cellpadding=\"5\" cellspacing=\"0\">\n"); printf("<tbody><tr><td style=\"background-color:#eee9e9;\">\n"); printf("<a name=\"homology\"></a><b>Gene Homology</b><br></td></tr>\n"); printf("<tr><td>\n"); /* ncbi blast hits */ hits = chopString(gi,":",giwords,sizeof(giwords)); if (hits > 0) { printf("<B>NCBI Blast Hits:</B> " "<A HREF=\"http://www.ncbi.nlm.nih.gov/sutils/blink.cgi?pid=%s\" " "TARGET=_BLANK>%s</A><BR>\n", (hits == 2) ? giwords[1] : giwords[0], (hits == 2) ? giwords[1] : giwords[0]); } /* Gene tree */ safef(treeFileName, sizeof(treeFileName), "../trash/geneTree/geneTree_%s.txt", item); if (getGeneTree(conn, item, treeFileName)) { safef(treeTmpPsFileName, sizeof(treeTmpPsFileName), "../trash/geneTree/tmp_geneTree_%s.ps", item); safef(treePsFileName, sizeof(treePsFileName), "../trash/geneTree/geneTree_%s.ps", item); safef(treePngFileName, sizeof(treePngFileName), "../trash/geneTree/geneTree_%s.png", item); safef(treePdfFileName, sizeof(treePdfFileName), "../trash/geneTree/geneTree_%s.pdf", item); safef(searchTerm, sizeof(searchTerm), ".%s) show\n", item); if (!fileExists(treePsFileName)) { safef(command, sizeof(command), "../bin/draw_tree -b %s | grep -v translate | sed '5 i 10 530 translate' | sed '6 i 0.33 0.33 scale' | sed 's/findfont 12/findfont 24/' > %s", treeFileName, treeTmpPsFileName); mustSystem(command); FILE *fi = mustOpen(treeTmpPsFileName, "r"); FILE *fo = mustOpen(treePsFileName, "w"); if ((fi != NULL) && (fo != NULL)) { mustGetLine(fi, buffer, 512); while (!sameWord(buffer, "")) { if (endsWith(buffer, searchTerm)) { fprintf(fo, "255 0 0 setrgbcolor\n"); fprintf(fo, "%s", buffer); fprintf(fo, "0 0 0 setrgbcolor\n"); } else fprintf(fo, "%s", buffer); mustGetLine(fi, buffer, 512); } fclose(fo); fclose(fi); } safef(command, sizeof(command), "rm -f %s", treeTmpPsFileName); mustSystem(command); } if (!fileExists(treePngFileName)) { safef(command, sizeof(command), "pstoimg -scale 0.4 -aaliastext -type png -density 300 -out %s %s", treePngFileName, treePsFileName); mustSystem(command); } if (!fileExists(treePdfFileName)) { safef(command, sizeof(command), "ps2pdf %s %s", treePsFileName, treePdfFileName); mustSystem(command); } printf("<BR><B>Phylogenetic tree with homologous genes:</B> View as \n"); printf("<A HREF=\"%s\" TARGET=_BLANK>Postscript</A> \n", treePsFileName); printf("<A HREF=\"%s\" TARGET=_BLANK>PNG</A> \n", treePngFileName); printf("<A HREF=\"%s\" TARGET=_BLANK>PDF</A> \n", treePdfFileName); printf("<A HREF=\"%s\" TARGET=_BLANK>Text</A> <BR>\n", treeFileName); printf("<BR>The 20 highest scoring homologous genes of this protein were retrieved by BLASTP from the genomes available in the UCSC microbial genome browser. "); printf("The alignments of the protein sequences, made by <A HREF=\"http://www.drive5.com/muscle/\" TARGET=_BLANK>MUSCLE</A>, "); printf("were used to construct the phylogenetic tree. This maximum likelihood unrooted tree was computed by using "); printf("<A HREF=\"http://www.atgc-montpellier.fr/phyml/\" TARGET=_BLANK>PHYML</A> with the Jones Taylor Thornton model of sequence evolution, "); printf("by including a Gamma-correction (eight categories of evolutionary rates, "); printf("an estimated alpha-parameter and an estimated proportion of invariant sites).<BR>"); } /* Self Homologs */ if (selfBlastpHitCount(conn, item) > 0) { blastpHitsList = loadSelfBlastpHits(conn, item, 0); printSelfHomologs(conn, blastpHitsList); } printf("</td></tr></tbody></table><br>\n"); /* Pathway */ printf("<table style=\"text-align: left; width: 99%%;\" border=\"1\" cellpadding=\"5\" cellspacing=\"0\">\n"); printf("<tbody><tr><td style=\"background-color:#eee9e9;\">\n"); printf("<a name=\"pathway\"></a><b>Pathway</b><br></td></tr>\n"); printf("<tr><td>\n"); /* kegg pathway links */ if (keggCount(conn, item) > 0) { keggLink(conn, item, table, "<B>Kegg Pathway: </b><BR>"); } else printf("Not available\n"); printf("</td></tr></tbody></table><br>\n"); /* Do SAM-T02 sub-section */ //doSamT02(spAcc, database); printTrackHtml(tdb); hFreeConn(&conn); } /*Code to display Sargasso Sea Information*/ void doSargassoSea(struct trackDb *tdb, char *trnaName) { struct bed *cb=NULL; struct sargassoSeaXra *cbs=NULL, *cbs2, *list=NULL; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char query[512]; char *dupe, *words[16]; char **row; char tempstring[255]=""; int flag, z, dashes, wordCount, rowOffset; int start = cartInt(cart, "o"), num = 0, flag2=0; float sequenceLength, dashlength=60; genericHeader(tdb,trnaName); dupe = cloneString(tdb->type); wordCount = chopLine(dupe, words); if (wordCount > 1) num = atoi(words[1]); if (num < 3) num = 3; genericBedClick(conn, tdb, trnaName, start, num); rowOffset = hOffsetPastBin(database, seqName, tdb->table); sprintf(query, "select * from %s where name = '%s'", tdb->table, trnaName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) cb=bedLoadN(row+1, 6); sequenceLength=(cb->chromEnd - cb->chromStart); if(sequenceLength<0){ sequenceLength=sequenceLength*-1;} sequenceLength=sequenceLength/3; dashlength=sequenceLength/60; /*Query the database for the extrainfo file for sargassoSea*/ conn=hAllocConn(database);/*sqlConnect(dupe);*/ safef(tempstring, sizeof(tempstring),"select * from sargassoSeaXra where qname = '%s'", trnaName); sr = sqlGetResult(conn, tempstring); /*Load the required data from the database*/ while ((row = sqlNextRow(sr)) != NULL) { cbs=sargassoSeaXraLoad(row); slAddHead(&list, cbs); } slReverse(&list); flag=0; flag2=0; /*Print out table with Blast information*/ printf(" </tbody>\n</table>\n<br><br>"); printf("<table cellpadding=\"2\" cellspacing=\"2\" border=\"1\" style=\"text-align: left; width: 100%%;\">"); printf(" <tbody>\n <tr>\n"); printf(" <td style=\"vertical-align: top;\"><b>Organism</b>"); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<b>Nucleotides \naligned begin</b>"); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<b>Nucelotides \naligned end</b>"); printf("<br>\n </td>\n <td style=\"vertical-align: top;\"><b>NCBI Link</b>"); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<b>Evalue</b>"); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<b>Percent Identity</b>"); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<b>Alignment Length</b>"); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<b>Gap openings</b>"); printf("</td>\n </tr>\n <tr>"); flag=0; for(cbs2=list;cbs2!=NULL;cbs2=cbs2->next) { printf("\n \n <td style=\"vertical-align: top;\">"); printf("<a name=\"%i-desc\"></a>",cbs2->GI); printf("<a\nhref=\"#%i-align\">%s</a>",cbs2->GI,cbs2->species); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("%i",cbs2->thisseqstart); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("%i",cbs2->thisseqend); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=%i\">NCBI Link</a>",cbs2->GI); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("%s",cbs2->evalue); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("%.2f",cbs2->PI); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("%i",cbs2->length); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("%i",cbs2->gap); printf("<br></td>\n </tr>\n"); flag=0; } /* printf(" <br><br></tbody>\n</table> \n"); */ /*Print out the table for the alignments*/ printf("<table cellpadding=\"2\" cellspacing=\"2\" border=\"1\" style=\"width: 100%%;\">"); printf(" <tbody>\n <tr>\n"); printf(" <td style=\"vertical-align: top;\"><b>Organism</b>"); printf("<br>\n </td>\n <td style=\"vertical-align: top;\"><b>Alignment</b>"); printf("</td>\n </tr>\n <tr>"); printf(" <td style=\"vertical-align: top;\">%s where each plus(+) is approx. %.1f amino acids", trnaName, dashlength); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<code>\n"); for(z=0; z<60; z++) { printf("+"); } printf("</code>"); printf("</td>\n </tr>\n <tr>"); flag=0; flag2=0; for(cbs2=list;cbs2!=NULL;cbs2=cbs2->next) { printf("\n </td>\n <td style=\"vertical-align: top;\">"); dashes=cbs2->queryseqstart-cbs2->queryseqend; if(dashes<0) dashes=dashes*-1; printf("<a name=\"%i-align\"></a>",cbs2->GI); printf("<a\nhref=\"#%i-desc\">%s</a>, %s",cbs2->GI, cbs2->species,cbs2->qName); printf("\n </td>\n <td style=\"vertical-align: top;\">"); printf("<code>\n"); dashes=dashes/dashlength; if(cbs2->queryseqstart>cbs2->queryseqend) for(z=0; z<((cbs2->queryseqend)/dashlength); z++) { printf(" "); } else for(z=0; z<((cbs2->queryseqstart)/dashlength); z++) { printf(" "); } if(dashes<1) printf("+"); for(z=0; z<dashes; z++) printf("+"); printf("</code>"); printf("</td>\n </tr>\n"); flag=0; } /*Free the data*/ hFreeConn(&conn); sargassoSeaXraFree(&cbs); printTrackHtml(tdb); } /*Function to print out full code name from code letter*/ void printCode(char code) { switch(code) { case 'a': printf("Aerobe"); break; case 'b': printf("Bacteria"); break; case 'c': printf("Crenarchaea"); break; case 'd': printf("Acidophile"); break; case 'e': printf("Euryarchaea"); break; case 'g': printf("Within Genus"); break; case 'h': printf("Hyperthermophile"); break; case 'm': printf("Methanogen"); break; case 'n': printf("Anaerobe"); break; case 'o': printf("Nanoarchaea"); break; case 't': printf("Thermophile"); break; case 'u': printf("Eukarya"); break; case 'v': printf("Viral"); break; case 'k': printf("Alkaliphile"); break; case 'l': printf("Halophile"); break; case 'r': printf("Facultative Aerobe"); break; default: break; } } void doTrnaGenes(struct trackDb *tdb, char *trnaName) { struct tRNAs *trna; char query[512]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char *dupe, *words[16]; char **row; int wordCount; int rowOffset; char* chrom = cartString(cart, "c"); genericHeader(tdb,trnaName); dupe = cloneString(tdb->type); wordCount = chopLine(dupe, words); rowOffset = hOffsetPastBin(database, seqName, tdb->table); sprintf(query, "select * from %s where chrom = '%s' and name = '%s'", tdb->table, chrom, trnaName); sr = sqlGetResult(conn, query); printf("<TABLE>\n"); while ((row = sqlNextRow(sr)) != NULL) { printf("<TR>\n"); printf("<TD valign=top>\n"); trna = tRNAsLoad(row+rowOffset); printf("<B>tRNA name: </B> %s<BR>\n",trna->name); printf("<B>tRNA Isotype: </B> %s<BR>\n",trna->aa); printf("<B>tRNA anticodon: </B> %s<BR>\n",trna->ac); printf("<B>tRNAscan-SE score: </B> %.2f<BR>\n",trna->trnaScore); printf("<B>Intron(s): </B> %s<BR>\n",trna->intron); printf("<B>Genomic size: </B> %d nt<BR>\n",trna->chromEnd-trna->chromStart); printf("<B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, trna->chrom, trna->chromStart+1, trna->chromEnd); printf("%s:%d-%d</A><BR>\n", trna->chrom, trna->chromStart+1, trna->chromEnd); printf("<B>Strand:</B> %s<BR>\n", trna->strand); if (!sameString(trna->genomeUrl, "")) { printf("<BR><A HREF=\"%s\" TARGET=_blank>View summary of all genomic tRNA predictions</A><BR>\n", trna->genomeUrl); printf("<BR><A HREF=\"%s\" TARGET=_blank>View tRNA alignments</A><BR>\n", trna->trnaUrl); } if (trna->next != NULL) printf("<hr>\n"); printf("</TD>\n"); printf("<TD>\n"); if (startsWith(trna->chrom, trna->name)) printf("<img align=right src=\"../RNA-img/%s/%s-%s.gif\" alt='tRNA secondary structure for %s'>\n", database,database,trna->name,trna->name); else printf("<img align=right src=\"../RNA-img/%s/%s-%s-%s.gif\" alt='tRNA secondary structure for %s'>\n", database,database,trna->chrom,trna->name,trna->name); printf("</TD>"); printf("</TR>"); } printf("</TABLE>"); sqlFreeResult(&sr); hFreeConn(&conn); printTrackHtml(tdb); tRNAsFree(&trna); } void doSnornaGenes(struct trackDb *tdb, char *snornaName) { struct snoRNAs *snorna; char query[512]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char *dupe, *words[16]; char **row; int wordCount; int rowOffset; genericHeader(tdb,snornaName); dupe = cloneString(tdb->type); wordCount = chopLine(dupe, words); rowOffset = hOffsetPastBin(database, seqName, tdb->table); sprintf(query, "select * from %s where name = '%s'", tdb->table, snornaName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { snorna = snoRNAsLoad(row+rowOffset); printf("<B>sRNA name: </B> %s<BR>\n",snorna->name); printf("<B>Snoscan score: </B> %.2f<BR>\n",snorna->snoScore); printf("<B>HMM snoRNA score: </B> %.2f<BR>\n",snorna->hmmScore); printf("<B>Predicted targets: </B> %s<BR>\n",snorna->targetList); printf("<B>Predicted guide interactions:</B><pre>%s</pre>\n",snorna->guideStr); printf("<B>Possible sRNA homolog(s): </B> %s<BR>\n",snorna->orthologs); printf("<BR><B>Genomic size: </B> %d nt<BR>\n",snorna->chromEnd-snorna->chromStart); printf("<B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, snorna->chrom, snorna->chromStart+1, snorna->chromEnd); printf("%s:%d-%d</A><BR>\n", snorna->chrom, snorna->chromStart+1, snorna->chromEnd); printf("<B>Strand:</B> %s<BR><BR>\n", snorna->strand); printf("<B>Snoscan program output: </B><BR><pre> %s</pre><BR>\n",snorna->snoscanOutput); if (snorna->next != NULL) printf("<hr>\n"); } sqlFreeResult(&sr); hFreeConn(&conn); printTrackHtml(tdb); snoRNAsFree(&snorna); } void doGbRnaGenes(struct trackDb *tdb, char *gbRnaName) { struct gbRNAs *gbRna; char query[512]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char *dupe, *words[16]; char **row; int wordCount; int rowOffset; genericHeader(tdb,gbRnaName); dupe = cloneString(tdb->type); wordCount = chopLine(dupe, words); rowOffset = hOffsetPastBin(database, seqName, tdb->table); sprintf(query, "select * from %s where name = '%s'", tdb->table, gbRnaName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { gbRna = gbRNAsLoad(row+rowOffset); printf("<B>Genbank ncRNA name: </B> %s<BR>\n",gbRna->name); printf("<B>Product Description/Note: </B> %s<BR>\n",gbRna->product); printf ("<B>Intron(s): </B> %s<BR>\n",gbRna->intron); printf("<BR><B>Genomic size: </B> %d nt<BR>\n",gbRna->chromEnd-gbRna->chromStart); printf("<B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, gbRna->chrom, gbRna->chromStart+1, gbRna->chromEnd); printf("%s:%d-%d</A><BR>\n", gbRna->chrom, gbRna->chromStart+1, gbRna->chromEnd); printf("<B>Strand:</B> %s<BR>\n", gbRna->strand); if (gbRna->next != NULL) printf("<hr>\n"); } sqlFreeResult(&sr); hFreeConn(&conn); printTrackHtml(tdb); gbRNAsFree(&gbRna); } void doEasyGenes(struct trackDb *tdb, char *egName) { struct easyGene *egList = NULL, *eg; char query[512]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; int rowOffset; genericHeader(tdb,egName); rowOffset = hOffsetPastBin(database, seqName, tdb->table); sprintf(query, "select * from %s where name = '%s'", tdb->table, egName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) slAddTail(&egList,easyGeneLoad(row+rowOffset)); slReverse(&egList); sqlFreeResult(&sr); hFreeConn(&conn); for (eg = egList; eg != NULL; eg = eg->next) { if (eg->genbank[0] == 'Y') printf("<span style='color:#FF0000;'>\n"); else printf("<span style='color:#000000;'>\n"); printf("<B>Item:</B> %s<BR>\n",eg->name); printf("<B>Feature identifier:</B> %s<BR>\n",eg->feat); printf("<B>Start codon:</B> %s<BR>\n",eg->startCodon); printf("<B>EasyGene descriptor:</B> %s<BR>\n",eg->descriptor); if (eg->R >= 0.001) printf("<B>R value:</B> %.3f<BR>\n",eg->R); else printf("<B>R value:</B> %.2e<BR>\n",eg->R); printf("<B>Log-odds :</B> %.1f<BR>\n",eg->logOdds); printf("<B>Frame:</B> %d<BR>\n",eg->frame); printf("<B>Swiss-Prot match:</B> %s<BR>\n",eg->swissProt); printf("<B>ORF identifier:</B> %s<BR>\n",eg->orf); printPos(eg->chrom, eg->chromStart, eg->chromEnd, eg->strand, TRUE, eg->name); printf("</span>\n"); if (eg->next != NULL) printf("<hr>\n"); } printTrackHtml(tdb); easyGeneFreeList(&egList); } void doCodeBlast(struct trackDb *tdb, char *trnaName) { struct pepPred *pp=NULL; struct codeBlast *cb=NULL; struct codeBlastScore *cbs=NULL, *cbs2, *list=NULL; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char query[512]; char *dupe, *words[16]; char **row; char tempstring[255]=""; int flag, z, dashes, wordCount, rowOffset, currentGI=0; int start = cartInt(cart, "o"), num = 0, flag2=0; float sequenceLength, dashlength=60; genericHeader(tdb,trnaName); dupe = cloneString(tdb->type); wordCount = chopLine(dupe, words); if (wordCount > 1) num = atoi(words[1]); if (num < 3) num = 3; genericBedClick(conn, tdb, trnaName, start, num); rowOffset = hOffsetPastBin(database, seqName, tdb->table); sprintf(query, "select * from %s where name = '%s'", tdb->table, trnaName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { cb=codeBlastLoad(row); } sequenceLength=(cb->chromEnd - cb->chromStart); if(sequenceLength<0){ sequenceLength=sequenceLength*-1;} sequenceLength=sequenceLength/3; dashlength=sequenceLength/60; conn=hAllocConn(database);/*sqlConnect(dupe);*/ sprintf(query, "select * from gbProtCodePep where name = '%s'", trnaName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { pp=pepPredLoad(row); } /*Query the database for the extrainfo file for codeBlast*/ conn=hAllocConn(database);/*sqlConnect(dupe);*/ safef(tempstring, sizeof(tempstring), "select * from codeBlastScore where qname = '%s'", trnaName); sr = sqlGetResult(conn, tempstring); /*Load the required data from the database*/ while ((row = sqlNextRow(sr)) != NULL) { cbs=codeBlastScoreLoad(row); slAddHead(&list, cbs); } if (pp!=NULL) printf( "<br><a\nhref=\"http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi?ALIGNMENTS=250&ALIGNMENT_VIEW=Pairwise&AUTO_FORMAT=Semiauto&CDD_SEARCH=on&CLIENT=web&DATABASE=nr&DESCRIPTIONS=500&ENTREZ_QUERY=All+organisms&EXPECT=10&FILTER=L&FORMAT_BLOCK_ON_RESPAGE=None&FORMAT_ENTREZ_QUERY=All+organisms&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&GAPCOSTS=11+1&GET_SEQUENCE=on&I_THRESH=0.005&LAYOUT=TwoWindows&MASK_CHAR=0&MASK_COLOR=0&MATRIX_NAME=BLOSUM62&NCBI_GI=on&NEW_FORMATTER=on&PAGE=Proteins&PROGRAM=blastp&QUERY=%s&SERVICE=plain&SET_DEFAULTS=Yes&SET_DEFAULTS.x=25&SET_DEFAULTS.y=11&SHOW_LINKOUT=on&SHOW_OVERVIEW=on&WORD_SIZE=3&END_OF_HTTPGET=Yes\">Query NCBI Blast",pp->seq); /*Print out table with Blast information*/ printf(" </tbody>\n</table>\n<br><br><table cellpadding=\"2\" cellspacing=\"2\" border=\"1\" style=\"text-align: left; width: 100%%;\">"); printf(" <tbody>\n <tr>\n"); printf(" <td style=\"vertical-align: top;\"><b>Organism</b>"); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<b>Phylogenetic/Functional Category</b>"); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<b>Gene Name</b>"); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<b>Product</b>"); printf("<br>\n </td>\n <td style=\"vertical-align: top;\"><b>NCBI Entry</b>"); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<b>Evalue</b>"); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<b>Percent Identity</b>"); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<b>Alignment Length(AA)</b>"); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<b>Gap openings</b>"); printf("</td>\n </tr>\n <tr>"); flag=0; for(cbs2=list;cbs2!=NULL;cbs2=cbs2->next) { if(sameString(trnaName, cbs2->qName)) { if(flag==0) { currentGI=cbs2->GI; printf("\n \n <td style=\"vertical-align: top;\">"); printf("<a name=\"%i-desc\"></a>",cbs2->GI); printf("<a\nhref=\"#%i-align\">%s</a>",cbs2->GI,cbs2->species); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); flag=1; } if((cbs2->next!=NULL) && (currentGI== cbs2->GI) && (currentGI== cbs2->next->GI) ) { printCode(cbs2->code[0]); printf(", "); } else { printCode(cbs2->code[0]); /*See which database to link to*/ if((sameString(cbs2->species, "Pyrococcus furiosus"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=pyrFur2&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Pyrococcus abyssi"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=pyrAby1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Pyrococcus horikoshii"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=pyrHor1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Thermococcus kodakaraensis"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=therKoda1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Sulfolobus solfataricus"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=sulSol1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Sulfolobus tokodaii"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=sulfToko1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Sulfolobus acidocaldarius"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=sulfAcid1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Pyrobaculum aerophilum"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=pyrAer1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Nanoarchaeum equitans"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=nanEqu1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Methanosarcina acetivorans"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=metAce1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Methanosarcina barkeri"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=methBark1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Methanosarcina mazei"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=methMaze1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Methanothermobacter thermautotrophicus"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=methTher1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Methanococcoides burtonii"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=methBurt1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Methanopyrus kandleri"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=methKand1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Haloarcula marismortui"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=halMar1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Halobacterium sp."))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=haloHalo1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Aeropyrum pernix"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=aerPer1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Archaeoglobus fulgidus"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=archFulg1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Thermoplasma acidophilum"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=therAcid1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Thermoplasma volcanium"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=therVolc1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Methanocaldococcus jannaschii"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=methJann1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Methanococcus maripaludis"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=metMar1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Methanosphaera stadtmanae"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=methStad1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Methanospirillum hungatei"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=methHung1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Aquifex aeolicus"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=aquiAeol1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Thermotoga maritima"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=therMari1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Escherichia coli K12"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=eschColi_K12_1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Bacillus subtilis"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=baciSubt1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else if((sameString(cbs2->species, "Shewanella oneidensis"))){ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"%s?db=shewOnei1&position=%s\">%s</a>",hgTracksName(),cbs2->name,cbs2->name); } else{ printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("%s",cbs2->name); } printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("%s",cbs2->product); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<a\nhref=\"http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=%i\">NCBI Link</a>",cbs2->GI); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("%s",cbs2->evalue); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("%.2f",cbs2->PI); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("%i",cbs2->length); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("%i",cbs2->gap); printf("<br></td>\n </tr>\n"); flag=0; } } } /*Print out the table for the alignments*/ printf("</td></td></td><br>\n<table cellpadding=\"2\" cellspacing=\"2\" border=\"1\" style=\"width: 100%%;\">"); printf(" <tbody>\n <tr>\n"); printf(" <td style=\"vertical-align: top;\"><b>Organism</b>"); printf("<br>\n </td>\n <td style=\"vertical-align: top;\"><b>Alignment</b>"); printf("</td>\n </tr>\n <tr>"); printf(" <td style=\"vertical-align: top;\">%s where each plus(+) is approx. %f amino acids", trnaName, dashlength); printf("<br>\n </td>\n <td style=\"vertical-align: top;\">"); printf("<code>\n"); for(z=0; z<60; z++) { printf("+"); } printf("</code>"); printf("</td>\n </tr>\n <tr>"); flag=0; flag2=0; for(cbs2=list;cbs2!=NULL;cbs2=cbs2->next) { if(sameString(trnaName, cbs2->qName)); { if(flag==0) { currentGI=cbs2->GI; printf("\n </td>\n <td style=\"vertical-align: top;\">"); flag=1; } if((cbs2->next!=NULL) && (currentGI== cbs2->GI) && (currentGI== cbs2->next->GI) ) { } else { dashes=cbs2->seqend-cbs2->seqstart; if(cbs2->length<dashes/2){dashes=dashes/3;} if(dashes<0) dashes=dashes*-1; printf("<a name=\"%i-align\"></a>",cbs2->GI); printf("<a\nhref=\"#%i-desc\">%s</a>, %s",cbs2->GI, cbs2->species, cbs2->name); printf("\n </td>\n <td style=\"vertical-align: top;\">"); printf("<code>\n"); dashes=dashes/dashlength; if(cbs2->seqstart>cbs2->seqend) for(z=0; z<((cbs2->seqend)/dashlength); z++) { printf(" "); } else for(z=0; z<((cbs2->seqstart)/dashlength); z++) { printf(" "); } if(dashes<1) printf("+"); for(z=0; z<dashes; z++) printf("+"); printf("</code>"); printf("</td>\n </tr>\n"); flag=0; } } } printf(" <br><br></tbody>\n</table> \n"); /*\printf(" </tbody>\n</table> \n"); */ /*Free the data*/ hFreeConn(&conn); codeBlastScoreFree(&cbs); codeBlastFree(&cb); printTrackHtml(tdb); } void llDoCodingGenes(struct trackDb *tdb, char *item, char *pepTable, char *extraTable) /* Handle click on gene track. */ { struct minGeneInfo ginfo; char query[256]; char query2[256]; struct sqlResult *sr, *sr2; char **row, **row2; char *words[16], *dupe = cloneString(tdb->type); int wordCount, x, length; int start = cartInt(cart, "o"), num = 0; struct sqlConnection *conn = hAllocConn(database); struct sqlConnection *conn2; struct COG *COG=NULL; struct COGXra *COGXra=NULL; char *temparray[160]; genericHeader(tdb, item); wordCount = chopLine(dupe, words); if (wordCount > 1) num = atoi(words[1]); if (num < 3) num = 3; genericBedClick(conn, tdb, item, start, num); if (pepTable != NULL && hTableExists(database, pepTable)) { char *pepNameCol = sameString(pepTable, "gbSeq") ? "acc" : "name"; conn = hAllocConn(database); /* simple query to see if pepName has a record in pepTable: */ safef(query, sizeof(query), "select 0 from %s where %s = '%s'", pepTable, pepNameCol, item); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { hgcAnchorSomewhere("htcTranslatedProtein", item, pepTable, seqName); printf("Predicted Protein</A> <BR>\n"); } sqlFreeResult(&sr); } if (extraTable != NULL && hTableExists(database, extraTable)) { conn = hAllocConn(database); sprintf(query, "select * from %s where name = '%s'", extraTable, item); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { minGeneInfoStaticLoad(row, &ginfo); printf("<B>Product: </B>%s<BR>\n", ginfo.product); printf("<B>Note: </B>%s<BR>\n", ginfo.note); } sqlFreeResult(&sr); } if (hTableExists(database, "COG")) { conn = hAllocConn(database); sprintf(query, "select * from COG where name = '%s'", item); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { COG = COGLoad(row); if(COG!=NULL) { length=chopString(COG->COG, "," , temparray, 999); for(x=0; x<length; x++) { conn2 = hAllocConn(database); sprintf(query2, "select * from COGXra where name = '%s'", temparray[x]); sr2 = sqlGetResult(conn2, query2); while ((row2 = sqlNextRow(sr2)) != NULL) { COGXra=COGXraLoad(row2); if(COGXra!=NULL) printf("<B>COG: </B>%s <B>INFO: </B>%s<BR>\n", COGXra->name, COGXra->info); } sqlFreeResult(&sr2); hFreeConn(&conn2); } } } } printTrackHtml(tdb); hFreeConn(&conn); } /*void doTigrOperons(struct trackDb *tdb, char *opName)*/ /* track handler for the TIGR operon predictions */ /*{ struct tigrOperon *op; char query[512]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char *dupe, *words[16]; char **row; int wordCount; int start = cartInt(cart, "o"), num = 0; genericHeader(tdb,opName); dupe = cloneString(tdb->type); wordCount = chopLine(dupe, words); if (wordCount > 1) num = atoi(words[1]); if (num < 3) num = 3; genericBedClick(conn, tdb, opName, start, num); sprintf(query, "select * from %sInfo where name = '%s'", tdb->table, opName); sr = sqlGetResult(conn, query);*/ /* Make the operon table like on the TIGR web page. */ /*if ((row = sqlNextRow(sr)) != NULL) { int i,j; char *infos[30]; op = tigrOperonLoad(row); chopCommas(op->info,infos); printf("<P>\n<TABLE BORDER=1 ALIGN=\"CENTER\">\n"); for (i = 0; i <= op->size; i++) { printf(" <TR ALIGN=\"CENTER\">"); for (j = 0; j <= op->size; j++) { printf("<TD>"); if ((i == 0 || j == 0) && !(i == 0 && j == 0)) (i > j) ? printf("%s",op->genes[i-1]) : printf("%s",op->genes[j-1]); else if (i + j > 0) { char *data = infos[((i-1)*op->size)+(j-1)]; if (!sameString(data,"---")) { char *n, *conf; n = chopPrefixAt(data,'|'); conf = data; printf("confidence = %.2f, n = %d",atof(conf),atoi(n)); } else printf("%s",data); } printf("</TD>"); } printf("</TR>\n"); } printf("</TABLE>\n</P>\n"); } printTrackHtml(tdb);*/ /* clean up */ /*sqlFreeResult(&sr); hFreeConn(&conn); tigrOperonFree(&op); } */ void doTigrCmrGene(struct trackDb *tdb, char *tigrName) /* Handle the TIRG CMR gene track. */ { struct tigrCmrGene *tigr; char query[512]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char *dupe, *words[16]; char **row; int wordCount; int rowOffset; /* int start = cartInt(cart, "o"), num = 0; */ genericHeader(tdb,tigrName); dupe = cloneString(tdb->type); wordCount = chopLine(dupe, words); rowOffset = hOffsetPastBin(database, seqName, tdb->table); sprintf(query, "select * from %s where name = '%s'", tdb->table, tigrName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { tigr = tigrCmrGeneLoad(row); if (tigr != NULL) { printf("<B>TIGR locus name: </B> %s<BR>\n",tigrName); printf("<B>TIGR gene description: </B> %s<BR>\n",tigr->tigrCommon); printf("<B>Alternate TIGR gene name: </B> "); if (strlen(tigr->tigrGene) >0) { printf("%s<BR>\n",tigr->tigrGene); } else { printf("None<BR>"); } printf("<B>Genbank locus name: </B> %s<BR>\n",tigr->primLocus); printf("<B>Protein length: </B> %d aa<BR>\n",tigr->tigrPepLength); if (strlen(tigr->tigrECN)>0) { printf("<B>Enzyme comission number: </B> %s<BR>\n",tigr->tigrECN); } printf("<B>Main role: </B> %s<BR>\n",tigr->tigrMainRole); printf("<B>Subrole: </B> %s<BR>\n",tigr->tigrSubRole); if (tigr->tigrMw > 0) { printf("<B>Molecular weight: </B> %.2f Da<BR>\n",tigr->tigrMw); } if (tigr->tigrPi > 0) { printf("<B>Isoelectric point: </B> %.2f<BR>\n",tigr->tigrPi); } printf("<B>GC content: </B> %.2f %%<BR>\n",tigr->tigrGc); printf("<BR><B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, tigr->chrom, tigr->chromStart, tigr->chromEnd); printf("%s:%d-%d</A><BR>\n", tigr->chrom, tigr->chromStart, tigr->chromEnd); printf("<B>Strand:</B> %s<BR>\n", tigr->strand); printf("<B>Genomic size: </B> %d nt<BR>\n",tigr->tigrLength); if (tigr->next != NULL) printf("<hr>\n"); } } sqlFreeResult(&sr); hFreeConn(&conn); printTrackHtml(tdb); tigrCmrGeneFree(&tigr); } void doJgiGene(struct trackDb *tdb, char *jgiName) /* Handle the JGI gene track. */ { struct jgiGene *jgi; char query[512]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char *dupe, *words[16]; char **row; int wordCount; int rowOffset; genericHeader(tdb,jgiName); dupe = cloneString(tdb->type); wordCount = chopLine(dupe, words); rowOffset = hOffsetPastBin(database, seqName, tdb->table); sprintf(query, "select * from %s where name = '%s'", tdb->table, jgiName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { jgi = jgiGeneLoad(row+rowOffset); printf("<B>JGI locus name: </B> %s<BR>\n",jgiName); printf("<B>JGI gene symbol: </B> %s<BR>\n",jgi->jgiSymbol); printf("<B>JGI gene description: </B> %s<BR>\n",jgi->jgiDescription); printf("<B>JGI gene id:</B> " "<A HREF=\"http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=%s\" TARGET=_blank>", jgi->jgiGeneId); printf("%s</A><BR>\n", jgi->jgiGeneId); printf("<B>GC content: </B> %.0f %%<BR>\n",jgi->jgiGc); printf("<BR><B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, jgi->chrom, jgi->chromStart + 1, jgi->chromEnd); printf("%s:%d-%d</A><BR>\n", jgi->chrom, jgi->chromStart + 1, jgi->chromEnd); printf("<B>Strand:</B> %s<BR>\n", jgi->strand); printf("<B>Genomic size: </B> %d nt<BR>\n", (jgi->chromEnd - jgi->chromStart)); if (jgi->next != NULL) printf("<hr>\n"); } sqlFreeResult(&sr); hFreeConn(&conn); printTrackHtml(tdb); jgiGeneFree(&jgi); } void doPfamHit(struct trackDb *tdb, char *hitName) /* Handle the Pfam hits track. */ { struct lowelabPfamHits *pfamHit; char query[512]; struct sqlConnection *conn = hAllocConn(database); struct sqlConnection *spConn = NULL; struct sqlResult *sr; char *dupe, *words[16]; char **row; int wordCount; int rowOffset; char *description; int start = cartInt(cart, "o"); char *pdb = hPdbFromGdb(database); spConn = sqlConnect(pdb); genericHeader(tdb,hitName); dupe = cloneString(tdb->type); wordCount = chopLine(dupe, words); rowOffset = hOffsetPastBin(database, seqName, tdb->table); sprintf(query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", tdb->table, hitName,seqName,start); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { pfamHit = lowelabPfamHitsLoad(row+rowOffset); safef(query, sizeof(query), "select description from proteome.pfamDesc where pfamAC='%s'", pfamHit->pfamAC); if (!sqlTableExists(spConn,"proteome.pfamDesc")) { safef(query, sizeof(query), "select extDbRef.extAcc1 from extDbRef,extDb " "where extDbRef.acc = '%s' " "and extDbRef.extDb = extDb.id " "and extDb.val = '%s'" , pfamHit->pfamAC,pfamHit->pfamID); } description = sqlQuickString(spConn, query); if (description == NULL) description = cloneString("n/a"); printf("<A HREF=\"http://pfam.sanger.ac.uk/family?acc=%s\" TARGET=_blank>", pfamHit->pfamAC ); printf("%s</A> - %s<BR><BR>\n", pfamHit->pfamAC, description); freez(&description); printf("<B>Domain assignment based on %d%% identity BlastP hit to Pfam-A SwissProt Sequence:</B><BR>\n" "<A HREF=\"http://www.expasy.org/uniprot/%s\">%s</A> (%s, %d%% full-length alignment) " "<BR><A HREF=\"http://www.sanger.ac.uk/cgi-bin/Pfam/swisspfamget.pl?name=%s\">[Pfam Domain Structure]</A><BR>\n", pfamHit->ident,pfamHit->swissAC,pfamHit->swissAC,pfamHit->protCoord,pfamHit->percLen,pfamHit->swissAC); printf("<BR><B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, pfamHit->chrom, pfamHit->chromStart + 1, pfamHit->chromEnd); printf("%s:%d-%d</A><BR>\n", pfamHit->chrom, pfamHit->chromStart + 1, pfamHit->chromEnd); printf("<B>Strand:</B> %s<BR>\n", pfamHit->strand); printf("<B>Genomic size: </B> %d nt<BR>\n", (pfamHit->chromEnd - pfamHit->chromStart)); if (pfamHit->next != NULL) printf("<hr>\n"); } sqlFreeResult(&sr); hFreeConn(&conn); printTrackHtml(tdb); lowelabPfamHitsFree(&pfamHit); } void doTigrOperons(struct trackDb *tdb, char *tigrOperonName) /* Handle the TIGR operons track. */ { struct bed *tigrOperon; struct lowelabTIGROperonScore *tigrOperonScore; char query[512]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char *dupe, *words[16]; char **row; int wordCount; int rowOffset; int bedSize = 0; genericHeader(tdb, tigrOperonName); dupe = cloneString(tdb->type); wordCount = chopLine(dupe, words); if (wordCount > 1) bedSize = atoi(words[1]); if (bedSize < 3) bedSize = 3; rowOffset = hOffsetPastBin(database, seqName, tdb->table); sprintf(query, "select * from %s where name = '%s'", tdb->table, tigrOperonName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { tigrOperon = bedLoadN(row+rowOffset, bedSize); printf("<B>Operon name: </B> %s<BR>\n",tigrOperonName); printf("<BR><B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, tigrOperon->chrom, tigrOperon->chromStart + 1, tigrOperon->chromEnd); printf("%s:%d-%d</A><BR>\n", tigrOperon->chrom, tigrOperon->chromStart + 1, tigrOperon->chromEnd); printf("<B>Strand:</B> %s<BR>\n", tigrOperon->strand); printf("<B>Genomic size: </B> %d nt<BR>\n", (tigrOperon->chromEnd - tigrOperon->chromStart)); if (tigrOperon->next != NULL) printf("<hr>\n"); } sqlFreeResult(&sr); printf("<br><B>OperonDB predicted gene pairs</B><br>\n"); /* Print table */ printf("<table style=\"width: 50%%;\" bgcolor=\"#%s\" border=\"0\" cellpadding=\"1\" cellspacing=\"0\">", HG_COL_BORDER); printf("<tbody><tr><td>\n"); printf("<table style='width:100%%; text-align:left; background-color:#%s;' border=1 cellpadding=2 cellspacing=2>\n", HG_COL_INSIDE); printf("<tbody>\n"); /* Print table column heading */ printf("<tr style=\"vertical-align: top;\">\n"); printf("<td width=\"25%%\"><b>Gene 1</b></td>\n"); printf("<td width=\"25%%\"><b>Gene 2</b></td>\n"); printf("<td width=\"25%%\"><b>Confidence</b></td>\n"); printf("<td width=\"25%%\"><b>Number of Conserved Genomes</b></td>\n"); printf("</tr>\n"); sprintf(query, "select * from lowelabTIGROperonScore where name = '%s'", tigrOperonName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { tigrOperonScore = lowelabTIGROperonScoreLoad(row); printf("<tr style=\"vertical-align: top;\">\n"); printf("<td>%s</td>\n", tigrOperonScore->gene1); printf("<td>%s</td>\n", tigrOperonScore->gene2); printf("<td style=\"text-align: right;\">%d</td>\n", tigrOperonScore->confidence); printf("<td style=\"text-align: right;\"><A HREF=\"%s\">%d</A></td>\n", tigrOperonScore->ortholog_link, tigrOperonScore->ortholog); printf("</tr>\n"); tigrOperonScore = tigrOperonScore->next; } sqlFreeResult(&sr); /* Close table */ printf("</tbody>\n"); printf("</table>\n"); printf("</td></tr></tbody>\n"); printf("</table>\n"); printf("<br>Note:\n"); printf("<br>Confidence - an estimation of the lower boundary of the probability that the two corresponding genes are located in the same operon\n"); printf("<br>Number of Conserved Genomes - number of other genomes that have the same pair of genes located in the same directon (a set of consecutive genes on the same DNA strand)\n"); bedFree(&tigrOperon); lowelabTIGROperonScoreFree(&tigrOperonScore); hFreeConn(&conn); printTrackHtml(tdb); } void doArkinOperons(struct trackDb *tdb, char *arkinOperonName) /* Handle the Arkin operons track. */ { struct bed *arkinOperon; struct lowelabArkinOperonScore *arkinOperonScore; char query[512]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char *dupe, *words[16]; char **row; int wordCount; int rowOffset; int bedSize = 0; genericHeader(tdb, arkinOperonName); dupe = cloneString(tdb->type); wordCount = chopLine(dupe, words); if (wordCount > 1) bedSize = atoi(words[1]); if (bedSize < 3) bedSize = 3; rowOffset = hOffsetPastBin(database, seqName, tdb->table); sprintf(query, "select * from %s where name = '%s'", tdb->table, arkinOperonName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { arkinOperon = bedLoadN(row+rowOffset, bedSize); printf("<B>Arkin operon name: </B> %s<BR>\n",arkinOperonName); printf("<BR><B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, arkinOperon->chrom, arkinOperon->chromStart + 1, arkinOperon->chromEnd); printf("%s:%d-%d</A><BR>\n", arkinOperon->chrom, arkinOperon->chromStart + 1, arkinOperon->chromEnd); printf("<B>Strand:</B> %s<BR>\n", arkinOperon->strand); printf("<B>Genomic size: </B> %d nt<BR>\n", (arkinOperon->chromEnd - arkinOperon->chromStart)); if (arkinOperon->next != NULL) printf("<hr>\n"); } sqlFreeResult(&sr); printf("<br><B>Arkin operon predicted gene pairs</B><br>\n"); /* Print table */ printf("<table style=\"width: 50%%;\" bgcolor=\"#%s\" border=\"0\" cellpadding=\"1\" cellspacing=\"0\">", HG_COL_BORDER); printf("<tbody><tr><td>\n"); printf("<table style='width:100%%; text-align:left; background-color:#%s;' border=1 cellpadding=2 cellspacing=2>\n", HG_COL_INSIDE); printf("<tbody>\n"); /* Print table column heading */ printf("<tr style=\"vertical-align: top;\">\n"); printf("<td width=\"25%%\"><b>Gene 1</b></td>\n"); printf("<td width=\"25%%\"><b>Gene 2</b></td>\n"); printf("<td width=\"25%%\"><b>Probability of the Same Operon</b></td>\n"); printf("<td width=\"25%%\"><b>Gene neighbor score</b></td>\n"); printf("</tr>\n"); sprintf(query, "select * from lowelabArkinOperonScore where name = '%s'", arkinOperonName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { arkinOperonScore = lowelabArkinOperonScoreLoad(row); printf("<tr style=\"vertical-align: top;\">\n"); printf("<td>%s</td>\n", arkinOperonScore->gene1); printf("<td>%s</td>\n", arkinOperonScore->gene2); printf("<td style=\"text-align: right;\">%0.3f</td>\n", arkinOperonScore->prob); printf("<td style=\"text-align: right;\">%0.3f</td>\n", arkinOperonScore->gnMinus); printf("</tr>\n"); arkinOperonScore = arkinOperonScore->next; } sqlFreeResult(&sr); /* Close table */ printf("</tbody>\n"); printf("</table>\n"); printf("</td></tr></tbody>\n"); printf("</table>\n"); printf("<br>Note:\n"); printf("<br>Probability of the Same Operon - Estimated probability that the pair is in the same operon. Values near 1 or 0 are confident predictions of being in the same operon or not, while values near 0.5 are low-confidence predictions.\n"); printf("<br>Gene neighbor score - An indicator of conservation (gene neighbor score, surprisal subtracted). Positive scores indicate conservation, and scores above 5 are generally strongly indicative of operons\n"); bedFree(&arkinOperon); lowelabArkinOperonScoreFree(&arkinOperonScore); hFreeConn(&conn); printTrackHtml(tdb); } struct bed * getBlastpTrackRecord(struct sqlConnection *conn, struct trackDb *tdb, char *targetName) /* Get blastp track record clicked by user*/ { struct bed *blastpTrack = NULL; char *dupe, *words[16]; int wordCount; int bedSize = 0; char query[512]; struct sqlResult *sr; char **row; int rowOffset; int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); char *chrom = cartString(cart, "c"); dupe = cloneString(tdb->type); wordCount = chopLine(dupe, words); if (wordCount > 1) bedSize = atoi(words[1]); if (bedSize < 3) bedSize = 3; rowOffset = hOffsetPastBin(database, seqName, tdb->table); sprintf(query, "select distinct * from %s where name = '%s' and chrom = '%s' and chromStart = %d and chromEnd = %d", tdb->table, targetName, chrom, start, end); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) blastpTrack = bedLoadN(row+rowOffset, bedSize); freez(&dupe); sqlFreeResult(&sr); return blastpTrack; } void printQueryGeneInfo(struct sqlConnection *conn, struct bed *blastpTrack, char *queryName, unsigned int *querySeqLength, char *queryTable) /* Get and print blastp query gene info */ { char query[512]; struct sqlResult *srRefSeq; char **row; int geneCount; char **buffer = NULL; char *targetGeneName[2]; struct minGeneInfo* ginfo; char blastpHits[] = "blastpHits"; unsigned int queryStart = 0; unsigned int queryEnd = 0; parseDelimitedString(blastpTrack->name, ':', targetGeneName, 2); if (hTableExists(database, queryTable) && hTableExists(database, blastpHits)) { /* Get query gene from refSeq */ sprintf(query, "select count(*) from %s where chrom = '%s' and strand = '%s' and cdsStart <= %u and cdsEnd >= %u", queryTable, blastpTrack->chrom, blastpTrack->strand, blastpTrack->chromStart, blastpTrack->chromEnd); srRefSeq = sqlGetResult(conn, query); if ((row = sqlNextRow(srRefSeq)) != NULL) { geneCount = atoi(row[0]); sqlFreeResult(&srRefSeq); if (geneCount == 1) { sprintf(query, "select name, cdsStart, cdsEnd from %s where chrom = '%s' and strand = '%s' and cdsStart <= %u and cdsEnd >= %u", queryTable, blastpTrack->chrom, blastpTrack->strand, blastpTrack->chromStart, blastpTrack->chromEnd); srRefSeq = sqlGetResult(conn, query); if ((row = sqlNextRow(srRefSeq)) != NULL) { strcpy(queryName, row[0]); queryStart = strtoul(row[1], buffer, 10); queryEnd = strtoul(row[2], buffer, 10); } sqlFreeResult(&srRefSeq); } else { /* Check blastpHits if more than 1 query gene is found within the region */ sprintf(query, "select a.name, a.cdsStart, a.cdsEnd from %s a, %s b where a.chrom = '%s' and a.strand = '%s' and a.cdsStart <= %u and a.cdsEnd >= %u and a.name = b.query and b.target like '%%%s'", queryTable, blastpHits, blastpTrack->chrom, blastpTrack->strand, blastpTrack->chromStart, blastpTrack->chromEnd, targetGeneName[0]); srRefSeq = sqlGetResult(conn, query); if ((row = sqlNextRow(srRefSeq)) != NULL) { strcpy(queryName, row[0]); queryStart = strtoul(row[1], buffer, 10); queryEnd = strtoul(row[2], buffer, 10); } sqlFreeResult(&srRefSeq); } if ((queryStart == 0) && (queryEnd == 0)) printf("Query gene not found for %s at %s:%u-%u\n", blastpTrack->name, blastpTrack->chrom, blastpTrack->chromStart, blastpTrack->chromEnd); else { *querySeqLength = queryEnd - queryStart; /* Print query gene info */ printf("<B>Gene: </B>%s<BR>\n", queryName); ginfo = getGbProtCodeInfo(conn, database, queryName); if (ginfo != NULL) { if (ginfo->product != NULL && differentString(ginfo->product,"none")) medlineLinkedLine("Product", ginfo->product, ginfo->product); } printf("<B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, blastpTrack->chrom, queryStart + 1, queryEnd); printf("%s:%d-%d</A><BR>\n", blastpTrack->chrom, queryStart + 1, queryEnd); printf("<B>Strand:</B> %s<BR>\n", blastpTrack->strand); printf("<B>Genomic size: </B> %d nt<BR>\n", (queryEnd - queryStart)); } } else printf("<BR>Query gene not found for %s at %s:%u-%u<BR>\n", blastpTrack->name, blastpTrack->chrom, blastpTrack->chromStart, blastpTrack->chromEnd); } sqlFreeResult(&srRefSeq); free(targetGeneName[0]); free(targetGeneName[1]); } struct slName* getAllClades(struct sqlConnection *conn) /* Get all available clades in database */ { char query[512]; struct sqlResult *srDb; char **rowDb; struct slName *list = NULL; char clade[50]; sprintf(query, "select label from %s.clade", cfgOption("central.db")); srDb = sqlGetResult(conn, query); while ((rowDb = sqlNextRow(srDb)) != NULL) { strcpy(clade, rowDb[0]); slNameAddTail(&list, clade); } sqlFreeResult(&srDb); return list; } struct blastTab* loadBlastpHits(struct sqlConnection *conn, char* queryName) /* Load all blastp hits of the given query gene into a list */ { char query[512]; struct sqlResult *srBlastpHits = NULL; struct blastTab *list = NULL; struct blastTab *blastpHits; char **row; char blastpHitsTable[] = "blastpHits"; if (hTableExists(database, blastpHitsTable)) { sprintf(query, "select * from %s where query = '%s'", blastpHitsTable, queryName); srBlastpHits = sqlGetResult(conn, query); while ((row = sqlNextRow(srBlastpHits)) != NULL) { blastpHits = blastTabLoad(row); slAddTail(&list, blastpHits); } } if (srBlastpHits != NULL) sqlFreeResult(&srBlastpHits); return list; } void printBlastpResult(struct sqlConnection *conn, struct blastTab *blastpHitsList, unsigned int querySeqLength) /* Print Blastp result of given clade */ { char query[512]; struct sqlResult *sr; char **row; char refSeq[50]; char xraTable[50]; char product[255]; struct blastTab *blastpHits; struct minGeneInfo *ginfo; char *blastpTarget[2]; char *clades[2]; int cladePortionCount = 0; char genome[50] = ""; char clade[50] = ""; unsigned int hitStart = 0; unsigned int hitEnd = 0; char **buffer = NULL; boolean findTable = FALSE; int tStart = cartInt(cart, "o"); int tEnd = cartInt(cart, "t"); char *tChrom = cartString(cart, "c"); printf("<br>\n"); /* Print table */ printf("<table style=\"width: 100%%;\" bgcolor=\"#%s\" border=\"0\" cellpadding=\"1\" cellspacing=\"0\">", HG_COL_BORDER); printf("<tbody><tr><td>\n"); printf("<table style='width:100%%; text-align:left; background-color:#%s;' border=1 cellpadding=2 cellspacing=2>\n", HG_COL_INSIDE); printf("<tbody>\n"); /* Print table column heading */ printf("<tr style=\"vertical-align: top;\">\n"); printf("<td width=\"18%%\"><b>Organism</b></td>\n"); printf("<td width=\"7%%\"><b>Clade</b></td>\n"); printf("<td width=\"7%%\"><b>Gene</b></td>\n"); printf("<td><b>Product</b></td>\n"); printf("<td width=\"5%%\"><b>Percent Length of Full Protein</b></td>\n"); printf("<td width=\"8%%\"><b>Position in Source Protein</b></td>\n"); printf("<td width=\"5%%\"><b>Protein Identity (%%)</b></td>\n"); printf("<td width=\"5%%\"><b>E-value</b></td>\n"); printf("<td width=\"5%%\"><b>Log of E-value</b></td>\n"); printf("<td width=\"5%%\"><b>Bit Score</b></td>\n"); printf("<td width=\"6%%\"><b>Protein Alignment Length</b></td>\n"); printf("<td width=\"5%%\"><b>Protein Mismatches</b></td>\n"); printf("<td width=\"5%%\"><b>Alignment Gaps</b></td>\n"); printf("</tr>\n"); blastpHits = blastpHitsList; while (blastpHits != NULL) { parseDelimitedString(blastpHits->target, ':', blastpTarget, 2); /* Get species info */ memset(genome, 0, 50); memset(clade, 0, 50); getGenomeClade(conn, blastpTarget[0], genome, clade); if ((strcmp(genome , "") != 0) && (strcmp(clade, "") != 0)) { cladePortionCount = parseDelimitedString(clade, '-', clades, 2); printf("<tr style=\"vertical-align: top;\">\n"); printf("<td><a name=\"%s:%s:%u-%u\"><i>%s</i></td>\n", blastpTarget[1], tChrom, tStart, tEnd, genome); if (cladePortionCount == 1) printf("<td>%s</td>\n", clades[0]); else if (cladePortionCount == 2) printf("<td>%s<br>%s</td>\n", clades[0], clades[1]); /* Get target gene position from refSeq */ strcpy(refSeq, blastpTarget[0]); strcat(refSeq, "."); if (hDbExists(blastpTarget[0])) { if (hTableExists(blastpTarget[0], "lookup")) { sprintf(query, "select lookupValue from %s.lookup where lookupCode = 'annotRev'", blastpTarget[0]); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { strcat(refSeq, row[0]); findTable = TRUE; sqlFreeResult(&sr); } } else if (hTableExists(blastpTarget[0], "refSeq")) { strcat(refSeq, "refSeq"); findTable = TRUE; } if (findTable) { sprintf(query, "select chrom, cdsStart, cdsEnd from %s where name = '%s'", refSeq, blastpTarget[1]); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { hitStart = strtoul(row[1], buffer, 10) + blastpHits->tStart * 3 + 1; hitEnd = strtoul(row[1], buffer, 10) + blastpHits->tEnd * 3; printf("<td><a href=\"hgTracks\?position=%s:%u-%u&db=%s\" TARGET=_blank>%s</a></td>\n", row[0], hitStart, hitEnd, blastpTarget[0], blastpTarget[1]); } else printf("<td>%s</td>\n", blastpTarget[1]); sqlFreeResult(&sr); } else printf("<td>%s</td>\n", blastpTarget[1]); } else printf("<td>%s</td>\n", blastpTarget[1]); /* Get target gene product annotation */ if (hDbExists(blastpTarget[0])) { if (hTableExists(blastpTarget[0], "lookup")) { sprintf(query, "select lookupValue from %s.lookup where lookupCode = 'annotRevXra'", blastpTarget[0]); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { strcpy(xraTable, row[0]); sqlFreeResult(&sr); } else strcpy(product, "N/A"); sprintf(query, "select product from %s.%s where name = '%s'", blastpTarget[0], xraTable, blastpTarget[1]); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { strcpy(product, row[0]); sqlFreeResult(&sr); } else strcpy(product, "N/A"); } else { ginfo = getGbProtCodeInfo(conn, blastpTarget[0], blastpTarget[1]); if (ginfo != NULL && ginfo->product != NULL && differentString(ginfo->product,"none")) strcpy(product, ginfo->product); else strcpy(product, "N/A"); } printf("<td>%s</td>\n", product); } else printf("<td>%s</td>\n", "N/A"); printf("<td style=\"text-align: center;\">%0.f</td>\n", ((double) (blastpHits->qEnd - blastpHits->qStart) / ((double) (querySeqLength-3) / 3.0f)) * 100.0f); printf("<td style=\"text-align: center;\">%u - %u</td>\n", blastpHits->qStart + 1, blastpHits->qEnd); printf("<td style=\"text-align: right;\">%0.1f</td>\n", blastpHits->identity); printf("<td style=\"text-align: right;\">%0.0e</td>\n", blastpHits->eValue); printf("<td style=\"text-align: right;\">e%0.0f</td>\n", (blastpHits->eValue == 0)? 0 : log(blastpHits->eValue) / log(10)); printf("<td style=\"text-align: right;\">%0.1f</td>\n", blastpHits->bitScore); printf("<td style=\"text-align: right;\">%u</td>\n", blastpHits->aliLength); printf("<td style=\"text-align: right;\">%u</td>\n", blastpHits->mismatch); printf("<td style=\"text-align: right;\">%u</td>\n", blastpHits->gapOpen); printf("</tr>\n"); } free(blastpTarget[0]); free(blastpTarget[1]); blastpHits = blastpHits->next; } /* Close table */ printf("</tbody>\n"); printf("</table>\n"); printf("</td></tr></tbody>\n"); printf("</table>\n"); } void doBlastP(struct trackDb *tdb, char *targetName) /* Handle the BlastP Archaea and BlastP Bacteria tracks. */ { char queryName[50]; char queryTable[50]; unsigned int querySeqLength = 0; struct sqlConnection *conn = hAllocConn(database); struct bed *blastpTrack; struct blastTab *blastpHitsList; char query[512]; struct sqlResult *sr; char **row; cartWebStart(cart, database, "%s", "BlastP Alignment Hits"); blastpTrack = getBlastpTrackRecord(conn, tdb, targetName); if (hTableExists(database, "lookup")) { sprintf(query, "select lookupValue from lookup where lookupCode = 'annotRev'"); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { strcpy(queryTable, row[0]); sqlFreeResult(&sr); } } else strcpy(queryTable, "refSeq"); printQueryGeneInfo(conn, blastpTrack, queryName, &querySeqLength, queryTable); blastpHitsList = loadBlastpHits(conn, queryName); printBlastpResult(conn, blastpHitsList, querySeqLength); printf("<BR>Note: All measurements are counted by the number of amino acids.<BR>\n"); printf("<hr>\n"); hFreeConn(&conn); printTrackHtml(tdb); } void doSelfHomologs(struct trackDb *tdb, char *targetName) /* Handle the Self Homologs tracks. */ { char queryName[50]; char queryTable[50]; unsigned int querySeqLength = 0; struct sqlConnection *conn = hAllocConn(database); struct bed *blastpTrack; struct blastTab *blastpHitsList; char query[512]; struct sqlResult *sr; char **row; cartWebStart(cart, database, "%s", "Homologs Within Genome by BlastP Search"); blastpTrack = getBlastpTrackRecord(conn, tdb, targetName); if (hTableExists(database, "lookup")) { sprintf(query, "select lookupValue from lookup where lookupCode = 'annotRev'"); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { strcpy(queryTable, row[0]); sqlFreeResult(&sr); } } else strcpy(queryTable, "refSeq"); printQueryGeneInfo(conn, blastpTrack, queryName, &querySeqLength, queryTable); blastpHitsList = loadSelfBlastpHits(conn, queryName, 1); printBlastpResult(conn, blastpHitsList, querySeqLength); printf("<BR>Note: All measurements are counted by the number of amino acids.<BR>\n"); printf("<hr>\n"); hFreeConn(&conn); printTrackHtml(tdb); } void printQuerySequenceInfo(struct sqlConnection *conn, struct bed *blastxTrack, char *queryName, unsigned int *querySeqLength, char *queryTable) /* Get and print blastx query sequence info */ { char query[512]; struct sqlResult *srQuerySeq; char **row; int seqCount; char **buffer = NULL; char *targetGeneName[2]; char blastxHits[] = "blastxHits"; unsigned int queryStart = 0; unsigned int queryEnd = 0; parseDelimitedString(blastxTrack->name, ':', targetGeneName, 2); if (hTableExists(database, queryTable) && hTableExists(database, blastxHits)) { /* Get query sequence from query table */ sprintf(query, "select count(*) from %s where chrom = '%s' and chromStart <= %u and chromEnd >= %u", queryTable, blastxTrack->chrom, blastxTrack->chromStart, blastxTrack->chromEnd); srQuerySeq = sqlGetResult(conn, query); if ((row = sqlNextRow(srQuerySeq)) != NULL) { seqCount = atoi(row[0]); sqlFreeResult(&srQuerySeq); if (seqCount == 1) { sprintf(query, "select name, chromStart, chromEnd from %s where chrom = '%s' and chromStart <= %u and chromEnd >= %u", queryTable, blastxTrack->chrom, blastxTrack->chromStart, blastxTrack->chromEnd); srQuerySeq = sqlGetResult(conn, query); if ((row = sqlNextRow(srQuerySeq)) != NULL) { strcpy(queryName, row[0]); queryStart = strtoul(row[1], buffer, 10); queryEnd = strtoul(row[2], buffer, 10); } sqlFreeResult(&srQuerySeq); } else { /* Check blastxHits if more than 1 query sequence is found within the region */ sprintf(query, "select a.name, a.chromStart, a.chromEnd from %s a, %s b where a.chrom = '%s' and a.chromStart <= %u and a.chromEnd >= %u and a.name = b.query and b.target like '%%%s'", queryTable, blastxHits, blastxTrack->chrom, blastxTrack->chromStart, blastxTrack->chromEnd, targetGeneName[0]); srQuerySeq = sqlGetResult(conn, query); if ((row = sqlNextRow(srQuerySeq)) != NULL) { strcpy(queryName, row[0]); queryStart = strtoul(row[1], buffer, 10); queryEnd = strtoul(row[2], buffer, 10); } sqlFreeResult(&srQuerySeq); } if ((queryStart == 0) && (queryEnd == 0)) printf("Query sequence not found for %s at %s:%u-%u\n", blastxTrack->name, blastxTrack->chrom, blastxTrack->chromStart, blastxTrack->chromEnd); else { *querySeqLength = (blastxTrack->chromEnd - blastxTrack->chromStart); /* Print query sequence info */ printf("<B>Query sequence: </B>%s<BR>\n", queryName); printf("<B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, blastxTrack->chrom, queryStart + 1, queryEnd); printf("%s:%d-%d</A><BR>\n", blastxTrack->chrom, queryStart + 1, queryEnd); printf("<B>Genomic size: </B> %d nt<BR><BR>\n", (queryEnd - queryStart)); printf("<B>BlastX hit position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, blastxTrack->chrom, blastxTrack->chromStart + 1, blastxTrack->chromEnd); printf("%s:%d-%d</A><BR>\n", blastxTrack->chrom, blastxTrack->chromStart + 1, blastxTrack->chromEnd); printf("<B>BlastX hit position relative to query sequence: </B> %d-%d<BR>\n", blastxTrack->chromStart - queryStart + 1, blastxTrack->chromEnd - queryStart); printf("<B>BlastX hit genomic size: </B> %d nt<BR>\n", (blastxTrack->chromEnd - blastxTrack->chromStart)); } } else printf("<BR>Query sequence not found for %s at %s:%u-%u<BR>\n", blastxTrack->name, blastxTrack->chrom, blastxTrack->chromStart, blastxTrack->chromEnd); } sqlFreeResult(&srQuerySeq); free(targetGeneName[0]); free(targetGeneName[1]); } struct blastTab* loadBlastxHits(struct sqlConnection *conn, char* queryName, char* queryTable, struct bed *blastxTrack) /* Load all blastx hits of the given query region into a list */ { char query[512]; struct sqlResult *srBlastxHits = NULL; struct blastTab *list = NULL; struct blastTab *blastxHits; struct sqlResult *srQuery = NULL; struct bed *queryTrack = NULL; char **rowQuery; int rowOffset; char **row; char blastxHitsTable[] = "blastxHits"; unsigned int queryStart = 0; unsigned int queryEnd = 0; unsigned int qStart = 0; unsigned int qEnd = 0; if (hTableExists(database, queryTable) && hTableExists(database, blastxHitsTable)) { rowOffset = hOffsetPastBin(database, seqName, queryTable); sprintf(query, "select * from %s where name = '%s'", queryTable, queryName); srQuery = sqlGetResult(conn, query); if ((rowQuery = sqlNextRow(srQuery)) != NULL) { queryTrack = bedLoadN(rowQuery+rowOffset, 6); queryStart = blastxTrack->chromStart - queryTrack->chromStart + 1; queryEnd = blastxTrack->chromEnd - queryTrack->chromStart; } sqlFreeResult(&srQuery); srQuery = NULL; sprintf(query, "select * from %s where query = '%s'", blastxHitsTable, queryName); srBlastxHits = sqlGetResult(conn, query); while ((row = sqlNextRow(srBlastxHits)) != NULL) { blastxHits = blastTabLoad(row); if (blastxHits->qStart < blastxHits->qEnd) { qStart = blastxHits->qStart; qEnd = blastxHits->qEnd; } else { qStart = blastxHits->qEnd; qEnd = blastxHits->qStart; } if (((qStart <= queryStart) && (qEnd >= queryEnd)) || ((qStart >= queryStart) && (qStart <= queryEnd)) || ((qEnd >= queryStart) && (qEnd <= queryEnd))) slAddTail(&list, blastxHits); } } if (srQuery != NULL) sqlFreeResult(&srQuery); if (srBlastxHits != NULL) sqlFreeResult(&srBlastxHits); return list; } void printBlastxResult(struct sqlConnection *conn, struct blastTab *blastxHitsList, unsigned int querySeqLength) /* Print Blastx result of given clade */ { char query[512]; struct sqlResult *sr; char **row; char refSeq[50]; struct blastTab *blastxHits; struct minGeneInfo *ginfo; char *blastxTarget[2]; char *clades[2]; int cladePortionCount = 0; char genome[50] = ""; char clade[50] = ""; unsigned int targetProteinStart = 0; unsigned int targetProteinEnd = 0; unsigned int hitStart = 0; unsigned int hitEnd = 0; char **buffer = NULL; int tStart = cartInt(cart, "o"); int tEnd = cartInt(cart, "t"); char *tChrom = cartString(cart, "c"); printf("<br>\n"); /* Print table */ printf("<table style=\"width: 100%%;\" bgcolor=\"#%s\" border=\"0\" cellpadding=\"1\" cellspacing=\"0\">", HG_COL_BORDER); printf("<tbody><tr><td>\n"); printf("<table style='width:100%%; text-align:left; background-color:#%s;' border=1 cellpadding=2 cellspacing=2>\n", HG_COL_INSIDE); printf("<tbody>\n"); /* Print table column heading */ printf("<tr style=\"vertical-align: top;\">\n"); printf("<td width=\"10%%\"><b>Organism</b></td>\n"); printf("<td width=\"7%%\"><b>Clade</b></td>\n"); printf("<td width=\"7%%\"><b>Gene</b></td>\n"); printf("<td><b>Product</b></td>\n"); printf("<td width=\"7%%\"><b>Position in Query Genomic Sequence</b></td>\n"); printf("<td width=\"7%%\"><b>Position in Target Protein</b></td>\n"); printf("<td width=\"7%%\"><b>Percent Length of Target Protein</b></td>\n"); printf("<td width=\"5%%\"><b>Protein Identity (%%)</b></td>\n"); printf("<td width=\"5%%\"><b>E-value</b></td>\n"); printf("<td width=\"5%%\"><b>Log of E-value</b></td>\n"); printf("<td width=\"5%%\"><b>Bit Score</b></td>\n"); printf("<td width=\"8%%\"><b>Protein Alignment Length</b></td>\n"); printf("<td width=\"8%%\"><b>Protein Mismatches</b></td>\n"); printf("<td width=\"8%%\"><b>Alignment Gaps</b></td>\n"); printf("</tr>\n"); blastxHits = blastxHitsList; while (blastxHits != NULL) { parseDelimitedString(blastxHits->target, ':', blastxTarget, 2); /* Get species info */ memset(genome, 0, 50); memset(clade, 0, 50); getGenomeClade(conn, blastxTarget[0], genome, clade); if ((strcmp(genome , "") != 0) && (strcmp(clade, "") != 0)) { cladePortionCount = parseDelimitedString(clade, '-', clades, 2); printf("<tr style=\"vertical-align: top;\">\n"); printf("<td><a name=\"%s:%s:%u-%u\"><i>%s</i></td>\n", blastxTarget[1], tChrom, tStart, tEnd, genome); if (cladePortionCount == 1) printf("<td>%s</td>\n", clades[0]); else if (cladePortionCount == 2) printf("<td>%s<br>%s</td>\n", clades[0], clades[1]); /* Get target gene position from refSeq */ strcpy(refSeq, blastxTarget[0]); strcat(refSeq, ".refSeq"); if (hDbExists(blastxTarget[0]) && hTableExists(blastxTarget[0], "refSeq")) { sprintf(query, "select chrom, cdsStart, cdsEnd from %s where name = '%s'", refSeq, blastxTarget[1]); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { targetProteinStart = strtoul(row[1], buffer, 10); targetProteinEnd = strtoul(row[2], buffer, 10); hitStart = targetProteinStart + blastxHits->tStart * 3 + 1; hitEnd = targetProteinStart + blastxHits->tEnd * 3; printf("<td><a href=\"hgTracks\?position=%s:%u-%u&db=%s\" TARGET=_blank>%s</a></td>\n", row[0], hitStart, hitEnd, blastxTarget[0], blastxTarget[1]); } else printf("<td>%s</td>\n", blastxTarget[1]); sqlFreeResult(&sr); } else printf("<td>%s</td>\n", blastxTarget[1]); /* Get target gene product annotation */ if (hDbExists(blastxTarget[0])) { ginfo = getGbProtCodeInfo(conn, blastxTarget[0], blastxTarget[1]); if (ginfo != NULL && ginfo->product != NULL && differentString(ginfo->product,"none")) printf("<td>%s</td>\n", ginfo->product); else printf("<td>%s</td>\n", "N/A"); } else printf("<td>%s</td>\n", "N/A"); printf("<td style=\"text-align: center;\">%u - %u</td>\n", blastxHits->qStart + 1, blastxHits->qEnd); printf("<td style=\"text-align: center;\">%u - %u</td>\n", blastxHits->tStart + 1, blastxHits->tEnd); if ((targetProteinStart == 0) || (targetProteinEnd == 0)) printf("<td style=\"text-align: center;\">N/A</td>\n"); else printf("<td style=\"text-align: center;\">%0.f</td>\n", ((double) (blastxHits->tEnd - blastxHits->tStart) / ((double) (targetProteinEnd-targetProteinStart-3) / 3.0f)) * 100.0f); printf("<td style=\"text-align: right;\">%0.1f</td>\n", blastxHits->identity); printf("<td style=\"text-align: right;\">%0.0e</td>\n", blastxHits->eValue); printf("<td style=\"text-align: right;\">e%0.0f</td>\n", (blastxHits->eValue == 0)? 0 : log(blastxHits->eValue) / log(10)); printf("<td style=\"text-align: right;\">%0.1f</td>\n", blastxHits->bitScore); printf("<td style=\"text-align: right;\">%u</td>\n", blastxHits->aliLength); printf("<td style=\"text-align: right;\">%u</td>\n", blastxHits->mismatch); printf("<td style=\"text-align: right;\">%u</td>\n", blastxHits->gapOpen); printf("</tr>\n"); } free(blastxTarget[0]); free(blastxTarget[1]); blastxHits = blastxHits->next; } /* Close table */ printf("</tbody>\n"); printf("</table>\n"); printf("</td></tr></tbody>\n"); printf("</table>\n"); } void doBlastX(struct trackDb *tdb, char *targetName) /* Handle the BlastX Archaea and BlastX Bacteria tracks. */ { char queryName[50]; char queryTable[50]; unsigned int querySeqLength = 0; struct sqlConnection *conn = hAllocConn(database); struct bed *blastxTrack; struct blastTab *blastxHitsList; cartWebStart(cart, database, "%s", "BlastX Alignment Hits"); blastxTrack = getBlastpTrackRecord(conn, tdb, targetName); /* if (!differentWord(blastxTrack->chrom, "assembly"))*/ if (hTableExists(database, "scaffolds")) strcpy(queryTable, "scaffolds"); else strcpy(queryTable, "igenics"); printQuerySequenceInfo(conn, blastxTrack, queryName, &querySeqLength, queryTable); blastxHitsList = loadBlastxHits(conn, queryName, queryTable, blastxTrack); printBlastxResult(conn, blastxHitsList, querySeqLength); printf("<BR>\n"); printf("<hr>\n"); hFreeConn(&conn); printTrackHtml(tdb); } void doUltraConserved(struct trackDb *tdb, char *item) /* Handle the ultraConserved track. */ { char tableName[65]; int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); struct hashEl* hashItem; struct hashCookie cookie; struct trackDb *multizTrack; struct sqlConnection *conn = hAllocConn(database); cookie = hashFirst(trackHash); hashItem = hashNext(&cookie); while (hashItem != NULL) { memset(tableName, 0, 65); strcpy(tableName, hashItem->name); if (strstr(tableName, "multiz") != NULL) break; hashItem = hashNext(&cookie); } multizTrack = hashFindVal(trackHash, tableName); winStart = start; winEnd = end; genericHeader(tdb, NULL); if (tdb->html != NULL && tdb->html[0] != 0) { puts(tdb->html); htmlHorizontalLine(); } genericMafClick(conn, multizTrack, item, start); printTrackHtml(multizTrack); hFreeConn(&conn); } float computeMolecularWeight(char* dna, int length) { float weight = 0.0f; int count[4] = {0,0,0,0}; int i = 0; for (i = 0; i < length; i++) { if ((dna[i] == 'A') || (dna[i] == 'a')) count[0]++; else if ((dna[i] == 'C') || (dna[i] == 'c')) count[1]++; else if ((dna[i] == 'G') || (dna[i] == 'g')) count[2]++; else if ((dna[i] == 'T') || (dna[i] == 't')) count[3]++; } weight = count[0] * 313.209 + count[1] * 289.184 + count[2] * 329.208 + count[3] * 304.196 - 63.980 + 2.016; return weight; } float computeNMolePerOD(char* dna, int length) { int extCoeff = 0; float nmolePerOD = 0.0f; enum { baseA = 0, baseC, baseG, baseT }; int indExtCoeff[4] = {15400, 7400, 11500, 8700}; int neighborExtCoeff[4][4] = { {27400, 21200, 25000, 22800}, {21200, 14600, 18000, 15200}, {25200, 17600, 21600, 20000}, {23400, 16200, 19000, 16800}}; int i = 0; int *bases = malloc(sizeof(int) * length); for (i = 0; i < length; i++) { if ((dna[i] == 'A') || (dna[i] == 'a')) bases[i] = baseA; else if ((dna[i] == 'C') || (dna[i] == 'c')) bases[i] = baseC; else if ((dna[i] == 'G') || (dna[i] == 'g')) bases[i] = baseG; else if ((dna[i] == 'T') || (dna[i] == 't')) bases[i] = baseT; } for (i = 0; i < (length - 1); i++) extCoeff += neighborExtCoeff[bases[i]][bases[i + 1]]; for (i = 1; i < (length - 1); i++) extCoeff -= indExtCoeff[bases[i]]; nmolePerOD = pow(10, 6) / (float) extCoeff; free(bases); return nmolePerOD; } void doPrimers(struct trackDb *tdb, char *primerName) /* Handle the array primer and GOLD primer tracks. */ { struct bed *primer; struct dnaSeq *sequence; char query[512]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char *dupe, *words[16]; char **row; int wordCount; int rowOffset; int bedSize = 0; int pairCount = 0; boolean forwardPrimer = TRUE; genericHeader(tdb, primerName); if (startsWith("Asn", primerName)) forwardPrimer = FALSE; dupe = cloneString(tdb->type); wordCount = chopLine(dupe, words); if (wordCount > 1) bedSize = atoi(words[1]); if (bedSize < 3) bedSize = 3; rowOffset = hOffsetPastBin(database, seqName, tdb->table); sprintf(query, "select * from %s where name = '%s'", tdb->table, primerName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { primer = bedLoadN(row+rowOffset, bedSize); printf("<B>Primer name: </B> %s<BR>\n",primerName); printf("<BR><B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, primer->chrom, primer->chromStart + 1, primer->chromEnd); printf("%s:%d-%d</A><BR>\n", primer->chrom, primer->chromStart + 1, primer->chromEnd); printf("<B>Strand:</B> %s<BR>\n", primer->strand); printf("<B>Genomic size:</B> %d nt<BR><BR>\n", (primer->chromEnd - primer->chromStart)); sequence = hDnaFromSeq(database, primer->chrom, primer->chromStart, primer->chromEnd, dnaUpper); if (sequence != NULL) { if (strcmp(primer->strand, "-") == 0) reverseComplement(sequence->dna, sequence->size); printf("<B>Sequence:</B> 5' %s 3'<BR>\n", sequence->dna); printf("<B>GC content:</B> %0.2f%%<BR>\n", computeGCContent(sequence->dna, sequence->size)); printf("<B>Molecular weight:</B> %0.1f g/mol<BR>\n", computeMolecularWeight(sequence->dna, sequence->size)); printf("<B>nmole/OD<sub>260</sub>:</B> %0.3f <BR>\n", computeNMolePerOD(sequence->dna, sequence->size)); printf("<B>ug/OD<sub>260</sub>:</B> %0.3f <BR>\n", computeNMolePerOD(sequence->dna, sequence->size) * computeMolecularWeight(sequence->dna, sequence->size) * pow(10,-3)); } if (primer->next != NULL) printf("<hr>\n"); } sqlFreeResult(&sr); printf("<br><B>Primer pairing</B><br>\n"); /* Print table */ printf("<table style=\"width: 90%%;\" bgcolor=\"#%s\" border=\"0\" cellpadding=\"1\" cellspacing=\"0\">", HG_COL_BORDER); printf("<tbody><tr><td>\n"); printf("<table style='width:100%%; text-align:left; background-color:#%s;' border=1 cellpadding=2 cellspacing=2>\n", HG_COL_INSIDE); printf("<tbody>\n"); /* Print table column heading */ printf("<tr style=\"vertical-align: top;\">\n"); printf("<td width=\"20%%\"><b>Primer Name</b></td>\n"); printf("<td width=\"10%%\"><b>Primer Type</b></td>\n"); printf("<td width=\"30%%\"><b>Primer Sequence</b></td>\n"); printf("<td width=\"10%%\"><b>PCR Region</b></td>\n"); printf("<td width=\"10%%\"><b>PCR Length (bp)</b></td>\n"); printf("<td width=\"10%%\"><b>PCR Region<BR>GC Content (%%)</b></td>\n"); printf("</tr>\n"); memset(query, 0, 512); if (strcmp(primer->strand, "+") == 0) { if (hTableExists(database, "genomePcrPrimers")) sprintf(query, "select *, 'Array PCR' primerType from genomePcrPrimers where chrom = '%s' and chromStart > %d and strand = '-'", primer->chrom, primer->chromEnd); if (hTableExists(database, "goldRTprimers")) { if (strcmp(query, "") != 0) sprintf(query, "%s union ", query); sprintf(query, "%sselect *, 'GOLD RT' primerType from goldRTprimers where chrom = '%s' and chromStart > %d and strand = '-'", query, primer->chrom, primer->chromEnd); } sprintf(query, "%s order by chromStart", query); } else { if (hTableExists(database, "genomePcrPrimers")) sprintf(query, "select *, 'Array PCR' primerType from genomePcrPrimers where chrom = '%s' and chromEnd < %d and strand = '+'", primer->chrom, primer->chromStart); if (hTableExists(database, "goldRTprimers")) { if (strcmp(query, "") != 0) sprintf(query, "%s union ", query); sprintf(query, "%sselect *, 'GOLD RT' primerType from goldRTprimers where chrom = '%s' and chromEnd < %d and strand = '+'", query, primer->chrom, primer->chromStart); } sprintf(query, "%s order by chromStart desc", query); } sr = sqlGetResult(conn, query); while (((row = sqlNextRow(sr)) != NULL) && (pairCount < 6)) { if ((forwardPrimer && startsWith("Asn", row[4])) || (!forwardPrimer && startsWith("Sn", row[4]))) { printf("<tr style=\"vertical-align: top;\">\n"); printf("<td>" "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, row[1], atoi(row[2]) + 1, atoi(row[3])); printf("%s</A></td>\n", row[4]); printf("<td>%s</td>\n", row[7]); sequence = hDnaFromSeq(database, row[1], atoi(row[2]), atoi(row[3]), dnaUpper); if (sequence != NULL) { if (strcmp(row[6], "-") == 0) reverseComplement(sequence->dna, sequence->size); printf("<td>5' %s 3'</td>\n", sequence->dna); } else printf("<td>N/A</td>\n"); if (strcmp(primer->strand, "+") == 0) { sequence = hDnaFromSeq(database, primer->chrom, primer->chromStart, atoi(row[3]), dnaUpper); printf("<td>" "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, primer->chrom, primer->chromStart + 1, atoi(row[3])); printf("%s:%d-%d</A></td>\n", primer->chrom, primer->chromStart + 1, atoi(row[3])); } else { sequence = hDnaFromSeq(database, primer->chrom, atoi(row[2]), primer->chromEnd, dnaUpper); printf("<td>" "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, primer->chrom, atoi(row[2]) + 1, primer->chromEnd); printf("%s:%d-%d</A></td>\n", primer->chrom, atoi(row[2])+ 1, primer->chromEnd); } if (sequence != NULL) { printf("<td style=\"text-align: right;\">%d</td>\n", sequence->size); printf("<td style=\"text-align: right;\">%0.2f</td>\n", computeGCContent(sequence->dna, sequence->size)); } else { printf("<td>N/A</td>\n"); printf("<td>N/A</td>\n"); } printf("</tr>\n"); pairCount++; } } sqlFreeResult(&sr); /* Close table */ printf("</tbody>\n"); printf("</table>\n"); printf("</td></tr></tbody>\n"); printf("</table>\n"); bedFree(&primer); hFreeConn(&conn); printTrackHtml(tdb); } void doWiki(char *track, struct trackDb *tdb, char *itemName) { char strand[2]; char wikiea[] = "wikiea"; char wikibme[] = "microbewiki"; char *wiki; if(sameWord(track, "wiki")) wiki = wikiea; else wiki = wikibme; printf("<HEAD>"); if(startsWith("Make", itemName)) { strand[0] = itemName[strlen(itemName)-1]; strand[1] = 0; printf("<META HTTP-EQUIV=\"REFRESH\" content=\"0; URL=http://lowelabwiki.cse.ucsc.edu/index.php/BED:%s:%s:%d-%d:%s\"</META>", database, seqName, winStart, winEnd, strand); } else { printf("<META HTTP-EQUIV=\"REFRESH\" content=\"0; URL=http://lowelabwiki.cse.ucsc.edu/index.php/BED:%s:%s:%s\"</META>", database, seqName, itemName); } printf("</HEAD>"); } void doRNAHybridization(struct trackDb *tdb, char *itemName) { struct sqlConnection *conn = hAllocConn(database); char query[512]; struct sqlResult *sr; char **row; struct rnaHybridization *rnaHyb; char rnaHybridizationTable[] = "rnaHybridization"; char tRNATable[] = "tRNAs"; char jgiTable[] = "jgiGene"; char *saveTableName; int i; cartWebStart(cart, database, "%s", "RNAHybridization Sites"); if (hTableExists(database, rnaHybridizationTable)) { /* Get query gene from refSeq */ sprintf(query, "select * from %s where name='%s'", rnaHybridizationTable, itemName); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { rnaHyb = rnaHybridizationLoad(row); printf("<b>Hybridization Site:</b><br/><br/>"); /* print hybridization site */ printf("<span style='font-family:Courier;'>"); printf("Pattern 5%s3<br>", rnaHyb->patternSeq); printf("         "); for(i=0;i<rnaHyb->matchLength;i++) printf("|"); printf("<br/>"); printf("Target  3%s5", rnaHyb->targetSeq); printf("</span><br/><br/>"); printf("<BR><B>Genomic size: </B> %d nt<BR>\n",rnaHyb->matchLength); printf("<b>Percentage G-C base-pairs:</b> %d<br/>", (int)(rnaHyb->gcContent * 100)); printf("<B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, rnaHyb->chrom, rnaHyb->chromStart+1, rnaHyb->chromEnd); printf("%s:%d-%d</A><BR>\n", rnaHyb->chrom, rnaHyb->chromStart+1, rnaHyb->chromEnd); printf("<B>Strand:</B> %s<BR>\n", rnaHyb->strand); printf("<B>Target Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, rnaHyb->chromTarget, rnaHyb->chromStartTarget+1, rnaHyb->chromEndTarget+1); printf("%s:%d-%d</A><BR>\n", rnaHyb->chromTarget, rnaHyb->chromStartTarget+1, rnaHyb->chromEndTarget+1); printf("<B>Target Strand:</B> %s<BR>\n", rnaHyb->strandTarget); printf("<br/>"); if(strlen(rnaHyb->refSeqTarget) > 0) { printf("<b>Additional information for target<b><br/>"); printf("<hr/>"); doRefSeq(tdb, rnaHyb->refSeqTarget,"gbProtCodePep","gbProtCodeXra"); } if(strlen(rnaHyb->JGITarget) > 0) { saveTableName = tdb->table; tdb->table = jgiTable; printf("<b>Additional information for target<b><br/>"); printf("<hr/>"); doJgiGene(tdb, rnaHyb->JGITarget); tdb->table = saveTableName; } if(strlen(rnaHyb->trnaTarget) > 0) { saveTableName = tdb->table; tdb->table = tRNATable; printf("<b>Additional information for target<b><br/>"); printf("<hr/>"); doTrnaGenes(tdb, rnaHyb->trnaTarget); tdb->table = saveTableName; } freeMem(rnaHyb); } sqlFreeResult(&sr); } hFreeConn(&conn); } void doarCOGs(struct trackDb *tdb, char *itemName) { char query[512]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char *dupe, *words[16]; char **row; int wordCount; int rowOffset; struct arCOGs *infoload; int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); sprintf(query, "select * from mgCommonDb.arcogdesc where name = '%s'", itemName); //sprintf(query, "select * from %s where query = '%s'", blastpHitsTable, queryName); struct sqlResult *srarcogdesc = sqlGetResult(conn, query); struct arcogdesc *description = NULL; while ((row = sqlNextRow(srarcogdesc)) != NULL) { struct arcogdesc *element; element = arcogdescLoad(row); slAddTail(&description, element); } sqlFreeResult(&srarcogdesc); genericHeader(tdb,itemName); dupe = cloneString(tdb->type); wordCount = chopLine(dupe, words); rowOffset = hOffsetPastBin(database,seqName, tdb->table); sprintf(query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d and chromEnd = '%d';", tdb->table, itemName,seqName,start, end); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { infoload = arCOGsLoad(row+rowOffset); printf("<B>Name:</B> %s<BR>\n", infoload->name); printf("<B>Description:</B> %s<BR>\n", description->description); printf("<B>Code:</B> %s<BR>\n", description->code); printf("<B>Gene:</B> %s<BR>\n", infoload->gene); printf("<B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, infoload->chrom, infoload->chromStart + 1, infoload->chromEnd); printf("%s:%d-%d</A><BR>\n", infoload->chrom, infoload->chromStart + 1, infoload->chromEnd); printf("<B>Strand:</B> %s<BR>\n", infoload->strand); printf("<B>Genomic size: </B> %d nt<BR>\n", (infoload->chromEnd - infoload->chromStart)); if (infoload->next != NULL) printf("<hr>\n"); } sqlFreeResult(&sr); hFreeConn(&conn); arCOGsFree(&infoload); printTrackHtml(tdb); } void doloweOrthologs(struct trackDb *tdb, char *itemName) { char query[512]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char *dupe, *words[16]; char **row; int wordCount; int rowOffset; struct bed *infoload; int bedSize = 0; int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); dupe = cloneString(tdb->type); wordCount = chopLine(dupe, words); if (wordCount > 1) bedSize = atoi(words[1]); if (bedSize < 3) bedSize = 3; genericHeader(tdb,itemName); dupe = cloneString(tdb->type); wordCount = chopLine(dupe, words); rowOffset = hOffsetPastBin(database,seqName, tdb->table); sprintf(query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d and chromEnd = '%d';", tdb->table, itemName,seqName,start, end); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { infoload = bedLoadN(row+rowOffset, bedSize); printf("<B>Name:</B> %s\n", infoload->name); printf(" <A HREF=\"http://archdev-holmes.cse.ucsc.edu/cgi-bin/hgFrame?track=loweOrthologs&refseq=1&db=%s&name=%s\">List of Orthologs</A><BR>",database,infoload->name); printf("<B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, infoload->chrom, infoload->chromStart + 1, infoload->chromEnd); printf("%s:%d-%d</A><BR>\n", infoload->chrom, infoload->chromStart + 1, infoload->chromEnd); printf("<B>Strand:</B> %s<BR>\n", infoload->strand); printf("<B>Genomic size: </B> %d nt<BR>\n", (infoload->chromEnd - infoload->chromStart)); if (infoload->next != NULL) printf("<hr>\n"); } sqlFreeResult(&sr); hFreeConn(&conn); printTrackHtml(tdb); } void doCddInfo(struct trackDb *tdb, char *itemName) { char query[512]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char *dupe, *words[16]; char **row; int wordCount; int rowOffset; struct cddInfo *infoload; int bedSize = 0; int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); dupe = cloneString(tdb->type); wordCount = chopLine(dupe, words); if (wordCount > 1) bedSize = atoi(words[1]); if (bedSize < 3) bedSize = 3; sprintf(query, "select * from mgCommonDb.cddDesc where accession = '%s'", itemName); //sprintf(query, "select * from %s where query = '%s'", blastpHitsTable, queryName); struct sqlResult *srCddDesc = sqlGetResult(conn, query); struct cddDesc *description = NULL; while ((row = sqlNextRow(srCddDesc)) != NULL) { struct cddDesc *element; element = cddDescLoad(row); slAddTail(&description, element); } sqlFreeResult(&srCddDesc); genericHeader(tdb,itemName); dupe = cloneString(tdb->type); wordCount = chopLine(dupe, words); rowOffset = hOffsetPastBin(database,seqName, tdb->table); sprintf(query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d and chromEnd = '%d';", tdb->table, itemName,seqName,start, end); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { infoload = cddInfoLoad(row+rowOffset); printf("<B>Name:</B> %s<BR>\n", infoload->fullname); printf("<B>Accession:</B> %s<A HREF=\"http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=%s\" TARGET=_blank>", infoload->name, infoload->NCBInum); printf(" Link to NCBI Site</A> <BR>\n"); printf("<B>E-value:</B> %0.0e<BR>\n", infoload->evalue); printf("<B>Description:</B> %s<BR>\n", description->name); printf("<B>Protein Identity:</B> %u%%<BR>\n", infoload->percentident); printf("<B>Percent Length:</B> %u%%<BR>\n", infoload->percentlength); printf("<B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, infoload->chrom, infoload->chromStart + 1, infoload->chromEnd); printf("%s:%d-%d</A><BR>\n", infoload->chrom, infoload->chromStart + 1, infoload->chromEnd); printf("<B>Strand:</B> %s<BR>\n", infoload->strand); printf("<B>Genomic size: </B> %d nt<BR>\n", (infoload->chromEnd - infoload->chromStart)); if (infoload->next != NULL) printf("<hr>\n"); } sqlFreeResult(&sr); hFreeConn(&conn); cddInfoFree(&infoload); printTrackHtml(tdb); } void domegablastInfo(struct trackDb *tdb, char *itemName) { char query[512]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char *dupe, *words[16]; char **row; int wordCount; int rowOffset; struct megablastInfo *infoload; int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); genericHeader(tdb,itemName); dupe = cloneString(tdb->type); wordCount = chopLine(dupe, words); rowOffset = hOffsetPastBin(database,seqName, tdb->table); sprintf(query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d and chromEnd = '%d';", tdb->table, itemName,seqName,start, end); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { infoload = megablastInfoLoad(row+rowOffset); printf("<B>Name:</B> %s<BR>\n", infoload->name); printf("<B>Accession:</B> %s<A HREF=\"http://www.ncbi.nlm.nih.gov/nuccore/%s\" TARGET=_blank>", infoload->name, infoload->name); printf(" Link to NCBI Site</A> <BR>\n"); printf("<B>Description:</B> %s<BR>\n", infoload->fullname); printf("<B>E-value:</B> %0.0e", infoload->evalue); #ifdef LISTUI printf(" <A HREF=\"http://archdev-holmes.cse.ucsc.edu/cgi-bin/hgList?track=megablastInfo&order=evalue&db=%s\">Sort by E-value</A>",database); #endif printf("<BR>\n"); printf("<B>Protein Identity:</B> %u%%\n", infoload->percentident); #ifdef LISTUI printf(" <A HREF=\"http://archdev-holmes.cse.ucsc.edu/cgi-bin/hgList?track=megablastInfo&order=percentident&db=%s\">Sort by Percent Identity</A>",database); #endif printf("<BR>\n"); printf("<B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, infoload->chrom, infoload->chromStart + 1, infoload->chromEnd); printf("%s:%d-%d</A><BR>\n", infoload->chrom, infoload->chromStart + 1, infoload->chromEnd); printf("<B>Strand:</B> %s<BR>\n", infoload->strand); printf("<B>Genomic size: </B> %d nt<BR>\n", (infoload->chromEnd - infoload->chromStart)); if (infoload->next != NULL) printf("<hr>\n"); } sqlFreeResult(&sr); hFreeConn(&conn); megablastInfoFree(&infoload); printTrackHtml(tdb); } void doAlignInfo(struct trackDb *tdb, char *itemName) { char query[512]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char *dupe, *words[16]; char **row; int wordCount; int rowOffset; struct alignInfo *infoload; int bedSize = 0; int start = cartInt(cart, "o"); dupe = cloneString(tdb->type); wordCount = chopLine(dupe, words); if (wordCount > 1) bedSize = atoi(words[1]); if (bedSize < 3) bedSize = 3; genericHeader(tdb,itemName); dupe = cloneString(tdb->type); wordCount = chopLine(dupe, words); rowOffset = hOffsetPastBin(database, seqName, tdb->table); sprintf(query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d;", tdb->table, itemName,seqName,start); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { infoload = alignInfoLoad(row+rowOffset); printf("<B>Name:</B> %s ", infoload->name); linkToOtherBrowserTitle(infoload->orgn, infoload->alignChrom, infoload->alignChromStart + 1, infoload->alignChromEnd, "Aligned Feature"); //printf("<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", //hgTracksPathAndSettings(), infoload->orgn, infoload->alignChrom, infoload->alignChromStart + 1, infoload->alignChromEnd); printf("Link to Feature</A><BR>\n" ); printf("<B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, infoload->chrom, infoload->chromStart + 1, infoload->chromEnd); printf("%s:%d-%d</A><BR>\n", infoload->chrom, infoload->chromStart + 1, infoload->chromEnd); printf("<B>Strand:</B> %s<BR>\n", infoload->strand); printf("<B>Genomic size: </B> %d nt<BR>\n", (infoload->chromEnd - infoload->chromStart)); if (infoload->next != NULL) printf("<hr>\n"); break; } sqlFreeResult(&sr); hFreeConn(&conn); alignInfoFree(&infoload); printTrackHtml(tdb); } void doCRISPRs(struct trackDb *tdb, char *crisprName) /* Handle the CRISPR array track. */ { struct bed *crispr; struct dnaSeq *sequence; char tempSeq[512]; char query[512]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char *dupe, *words[16]; char **row; int wordCount; int rowOffset; int bedSize = 0; int pairCount = 0; genericHeader(tdb, crisprName); dupe = cloneString(tdb->type); wordCount = chopLine(dupe, words); if (wordCount > 1) bedSize = atoi(words[1]); if (bedSize < 3) bedSize = 3; rowOffset = hOffsetPastBin(database, seqName, tdb->table); safef(query, ArraySize(query), "select * from %s where name = '%s'", tdb->table, crisprName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { crispr = bedLoadN(row+rowOffset, bedSize); printf("<B>Name: </B> %s<BR>\n", crisprName); printf("<B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, crispr->chrom, crispr->chromStart + 1, crispr->chromEnd); printf("%s:%d-%d</A><BR>\n", crispr->chrom, crispr->chromStart + 1, crispr->chromEnd); printf("<B>Strand:</B> %s<BR>\n", crispr->strand); printf("<B>Genomic size:</B> %d nt<BR><BR>\n", (crispr->chromEnd - crispr->chromStart)); printf("<B>Number of spacers:</B> %u<BR><BR>\n", crispr->blockCount - 1); sequence = hDnaFromSeq(database, crispr->chrom, crispr->chromStart, crispr->chromEnd, dnaUpper); if (sequence != NULL) { /* Print table */ printf("<table style=\"width: 100%%;\" bgcolor=\"#%s\" border=\"0\" cellpadding=\"1\" cellspacing=\"0\">", HG_COL_BORDER); printf("<tbody><tr><td>\n"); printf("<table style='width:100%%; text-align:left; background-color:#%s;' border=1 cellpadding=2 cellspacing=2>\n", HG_COL_INSIDE); printf("<tbody>\n"); /* Print table column heading */ printf("<tr style=\"vertical-align: top;\">\n"); printf("<td colspan=\"3\"><b>Direct Repeat</b></td>\n"); printf("<td colspan=\"3\"><b>Spacer</b></td>\n"); printf("</tr>\n"); printf("<tr style=\"vertical-align: top;\">\n"); printf("<td width=\"8%%\"><b>Start Pos</b></td>\n"); printf("<td width=\"36%%\"><b>Sequence</b></td>\n"); printf("<td width=\"4%%\"><b>Length</b></td>\n"); printf("<td width=\"8%%\"><b>Start Pos</b></td>\n"); printf("<td><b>Sequence</b></td>\n"); printf("<td width=\"4%%\"><b>Length</b></td>\n"); printf("</tr>\n"); if (strcmp(crispr->strand, "+") == 0) { for (pairCount = 0; pairCount < (int) crispr->blockCount; pairCount++) { printf("<tr style=\"vertical-align: top;\">\n"); memset(tempSeq, '\0', sizeof(tempSeq)); memcpy(tempSeq, sequence->dna + crispr->chromStarts[pairCount], crispr->blockSizes[pairCount]); printf("<td>%d</td><td>%s</td><td>%d</td>\n", crispr->chromStart + 1 + crispr->chromStarts[pairCount], tempSeq, crispr->blockSizes[pairCount]); if (pairCount + 1 < crispr->blockCount) { memset(tempSeq, '\0', sizeof(tempSeq)); memcpy(tempSeq, sequence->dna + crispr->chromStarts[pairCount] + crispr->blockSizes[pairCount], crispr->chromStarts[pairCount+1] - crispr->blockSizes[pairCount] - crispr->chromStarts[pairCount]); printf("<td>%d</td><td>%s</td><td>%d</td>\n", crispr->chromStart + 1 + crispr->chromStarts[pairCount] + crispr->blockSizes[pairCount], tempSeq, crispr->chromStarts[pairCount+1] - crispr->blockSizes[pairCount] - crispr->chromStarts[pairCount]); } else { printf("<td> </td><td> </td><td> </td>\n"); } printf("</tr>\n"); } } else { for (pairCount = ((int)crispr->blockCount - 1); pairCount >= 0; pairCount--) { printf("<tr style=\"vertical-align: top;\">\n"); memset(tempSeq, '\0', sizeof(tempSeq)); memcpy(tempSeq, sequence->dna + crispr->chromStarts[pairCount], crispr->blockSizes[pairCount]); reverseComplement(tempSeq, strlen(tempSeq)); printf("<td>%d</td><td>%s</td><td>%d</td>\n", crispr->chromStart + crispr->chromStarts[pairCount] + crispr->blockSizes[pairCount], tempSeq, crispr->blockSizes[pairCount]); if (pairCount - 1 >= 0) { memset(tempSeq, '\0', sizeof(tempSeq)); memcpy(tempSeq, sequence->dna + crispr->chromStarts[pairCount-1] + crispr->blockSizes[pairCount-1], crispr->chromStarts[pairCount] - crispr->blockSizes[pairCount-1] - crispr->chromStarts[pairCount-1]); reverseComplement(tempSeq, strlen(tempSeq)); printf("<td>%d</td><td>%s</td><td>%d</td>\n", crispr->chromStart + crispr->chromStarts[pairCount], tempSeq, crispr->chromStarts[pairCount] - crispr->blockSizes[pairCount-1] - crispr->chromStarts[pairCount-1]); } else { printf("<td> </td><td> </td><td> </td>\n"); } printf("</tr>\n"); } } /* Close table */ printf("</tbody>\n"); printf("</table>\n"); printf("</td></tr></tbody>\n"); printf("</table>\n"); } if (crispr->next != NULL) printf("<hr>\n"); } sqlFreeResult(&sr); bedFree(&crispr); hFreeConn(&conn); printTrackHtml(tdb); } bool loweLabClick(char *track, char *item, struct trackDb *tdb) /* check if we have one of the lowelab tracks */ { if (sameWord(track, "gbProtCode")) { llDoCodingGenes(tdb, item,"gbProtCodePep","gbProtCodeXra"); } else if (sameWord(track, "refSeq")) { doRefSeq(tdb, item,"gbProtCodePep","gbProtCodeXra"); } else if (startsWith("annotRev", track)) { doRefSeq(tdb, item,"Pep","Xra"); } else if (sameWord(track, "sargassoSea")) { doSargassoSea(tdb, item); } else if (sameWord(track, "tigrCmrORFs")) { doTigrCmrGene(tdb,item); } else if (sameWord(track, "jgiGene")) { doJgiGene(tdb,item); } else if (sameWord(track, "lowelabPfamHits")) { doPfamHit(tdb,item); } /*else if (sameWord(track, "tigrOperons"))*/ else if (sameWord(track, "lowelabTIGROperons")) { doTigrOperons(tdb,item); } else if (sameWord(track, "lowelabArkinOperons")) { doArkinOperons(tdb,item); } else if (sameWord(track,"codeBlast")) { doCodeBlast(tdb, item); } else if (sameWord(track,"gbRNAs")) { doGbRnaGenes(tdb, item); } else if (sameWord(track,"tRNAs")) { doTrnaGenes(tdb, item); } else if (sameWord(track,"snoRNAs")) { doSnornaGenes(tdb, item); } else if (sameWord(track,"easyGene")) { doEasyGenes(tdb, item); } else if (startsWith("BlastP_", track) && differentWord(track, "BlastP_Crenarchaea") && differentWord(track, "BlastP_Nanoarch") && differentWord(track, "BlastP_Euryarch") && differentWord(track, "BlastP_Bacteria")) { doBlastP(tdb, item); } else if (startsWith("BlastX_", track) && differentWord(track, "BlastX_Crenarchaea") && differentWord(track, "BlastX_Nanoarch") && differentWord(track, "BlastX_Euryarch") && differentWord(track, "BlastX_Bacteria")) { doBlastX(tdb, item); } else if (sameWord(track,"ultraConserved")) { doUltraConserved(tdb, item); } else if (sameWord(track,"genomePcrPrimers") || sameWord(track,"goldRTPrimers")) { doPrimers(tdb, item); } else if (sameWord(track,"wiki") || sameWord(track,"wikibme")) { doWiki(track,tdb,item); } else if (sameWord(track,"rnaHybridization")) { doRNAHybridization(tdb, item); } else if (sameWord(track,"cddInfo")) { doCddInfo(tdb, item); } else if (sameWord(track,"alignInfo")) { doAlignInfo(tdb, item); } else if (sameWord(track,"arCOGs")) { doarCOGs(tdb, item); } else if (sameWord(track,"megablastInfo") || sameWord(track,"vecScreenInfo")) { domegablastInfo(tdb, item); } else if (sameWord(track,"loweOrthologs")) { doloweOrthologs(tdb, item); } else if (sameWord(track,"selfHomologs")) { doSelfHomologs(tdb, item); } else if (sameWord(track,"CRISPRs")) { doCRISPRs(tdb, item); } else return FALSE; return TRUE; }