src/hg/hgc/lowelab.c 1.32
1.32 2009/05/08 21:15:26 pchan
fix hTableExist call for blastp track; change code to use centraldb name from hg.conf; add code to support blastx track
Index: src/hg/hgc/lowelab.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgc/lowelab.c,v
retrieving revision 1.31
retrieving revision 1.32
diff -b -B -U 1000000 -r1.31 -r1.32
--- src/hg/hgc/lowelab.c 30 Jan 2009 23:47:45 -0000 1.31
+++ src/hg/hgc/lowelab.c 8 May 2009 21:15:26 -0000 1.32
@@ -1,2672 +1,3004 @@
/* 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"
static char const rcsid[] = "$Id$";
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;
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);
}
if (hasFirst)
printf("<BR>");
sqlFreeResult(&sr);
}
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;
}
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];
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->tableName;
char *pdb = hPdbFromGdb(database);
struct genePred *gpList = NULL, *gp = NULL;
char tableName[64];
boolean hasBin;
spConn = sqlConnect( pdb);
genericHeader(tdb, item);
wordCount = chopLine(dupe, words);
if (wordCount > 1)
num = atoi(words[1]);
if (num < 3) num = 3;
if (extraTable != NULL && hTableExists(database, extraTable))
{
sprintf(query, "select * from %s where name = '%s'", extraTable, item);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
minGeneInfoStaticLoad(row, &ginfo);
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);
}
}
/* ncbi blast hits */
hits = chopString(ginfo.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]);
}
/* cog description */
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\" "
">%s</A> "
"<A HREF=\"http://www.ncbi.nlm.nih.gov/COG/grace/wiew.cgi?fun=%s\" "
">Code %s</A> \n",
COGXra->name, COGXra->name, COG->code,COG->code);
printf(" %s<BR><BR>\n", COGXra->info);
}
sqlFreeResult(&sr2);
hFreeConn(&conn2);
}
}
}
}
/* 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);
- if (!sqlTableExists(spConn,"pfamDesc"))
+ 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/cgi/pdbImage.cgi/%sx150.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);
}
/* kegg pathway links */
if (keggCount(conn, item) > 0)
{
keggLink(conn, item, table, "<B>Kegg Pathway: </b><BR>");
}
/* Do SAM-T02 sub-section */
//doSamT02(spAcc, database);
/* print go terms */
goPrint( conn, item, spAcc);
/* 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>");
}
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, pepTable, "htcTranslatedProtein",
"htcGeneMrna", "htcGeneInGenome", "Predicted mRNA");
genePredFreeList(&gpList);
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 *track = tdb->tableName;
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, track);
sprintf(query, "select * from %s where name = '%s'", track, 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)
{
char *track = tdb->tableName;
struct tRNAs *trna;
char query[512];
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr;
char *dupe, *words[16];
char **row;
int wordCount;
int rowOffset;
genericHeader(tdb,trnaName);
dupe = cloneString(tdb->type);
wordCount = chopLine(dupe, words);
rowOffset = hOffsetPastBin(database, seqName, track);
sprintf(query, "select * from %s where name = '%s'", track, trnaName);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
trna = tRNAsLoad(row+rowOffset);
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("<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("<BR><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 (trna->next != NULL)
printf("<hr>\n");
}
sqlFreeResult(&sr);
hFreeConn(&conn);
printTrackHtml(tdb);
tRNAsFree(&trna);
}
void doSnornaGenes(struct trackDb *tdb, char *snornaName)
{
char *track = tdb->tableName;
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, track);
sprintf(query, "select * from %s where name = '%s'", track, 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)
{
char *track = tdb->tableName;
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, track);
sprintf(query, "select * from %s where name = '%s'", track, 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)
{
char *track = tdb->tableName;
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, track);
sprintf(query, "select * from %s where name = '%s'", track, 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("<FONT COLOR=\"#FF0000\">\n");
else
printf("<FONT 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("</FONT>\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 *track = tdb->tableName;
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, track);
sprintf(query, "select * from %s where name = '%s'", track, 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 */
/*{
char *track = tdb->tableName;
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'", track, 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. */
{
char *track = tdb->tableName;
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, track);
sprintf(query, "select * from %s where name = '%s'", track, 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. */
{
char *track = tdb->tableName;
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, track);
sprintf(query, "select * from %s where name = '%s'", track, 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. */
{
char *track = tdb->tableName;
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, track);
sprintf(query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", track, 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,"pfamDesc"))
+ 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. */
{
char *track = tdb->tableName;
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, track);
sprintf(query, "select * from %s where name = '%s'", track, 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;\" bgcolor=\"%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. */
{
char *track = tdb->tableName;
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, track);
sprintf(query, "select * from %s where name = '%s'", track, 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;\" bgcolor=\"%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);
}
int parseDelimitedString(char *inString, char delimiter, char *outString[], int outSize)
{
int arrayCount = 0;
int charCount = 0;
int start = 0;
char *out = NULL;
for (charCount = 0; charCount < strlen(inString); charCount++)
{
if (inString[charCount] == delimiter)
{
if (arrayCount < outSize)
{
out = malloc(sizeof(char) * (charCount - start + 1));
memcpy(out, inString + start, sizeof(char) * (charCount - start));
out[charCount - start] = '\0';
outString[arrayCount++] = out;
start = charCount + 1;
}
}
}
if (arrayCount < outSize)
{
out = malloc(sizeof(char) * (charCount - start + 1));
memcpy(out, inString + start, sizeof(char) * (charCount - start));
out[charCount - start] = '\0';
outString[arrayCount++] = out;
}
return arrayCount;
}
struct bed * getBlastpTrackRecord(struct sqlConnection *conn, struct trackDb *tdb, char *targetName)
/* Get blastp track record clicked by user*/
{
char *track = tdb->tableName;
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, track);
sprintf(query, "select distinct * from %s where name = '%s' and chrom = '%s' and chromStart = %d and chromEnd = %d",
track, targetName, chrom, start, end);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
blastpTrack = bedLoadN(row+rowOffset, bedSize);
freez(&dupe);
sqlFreeResult(&sr);
return blastpTrack;
}
struct minGeneInfo* getGbProtCodeInfo(struct sqlConnection *conn, char* dbName, char *geneName)
/* Get refseq protein annotation by given gene name in a given database */
{
char query[512];
- struct sqlResult *sr;
+ struct sqlResult *sr = NULL;
char **row;
struct minGeneInfo* ginfo = NULL;
char gbProtCodeXra[50];
+ if (strcmp(database, dbName) == 0)
+ strcpy(gbProtCodeXra, "gbProtCodeXra");
+ else
+ {
strcpy(gbProtCodeXra, dbName);
strcat(gbProtCodeXra, ".gbProtCodeXra");
- if (hTableExists(database, gbProtCodeXra))
+ }
+ if (hTableExists(dbName, "gbProtCodeXra"))
{
sprintf(query, "select * from %s where name = '%s'", gbProtCodeXra, geneName);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
ginfo = minGeneInfoLoad(row);
}
+ if (sr != NULL)
sqlFreeResult(&sr);
return ginfo;
}
void printQueryGeneInfo(struct sqlConnection *conn, struct bed *blastpTrack, char *queryName, unsigned int *querySeqLength)
/* 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 refSeq[] = "refSeq";
char blastpHits[] = "blastpHits";
unsigned int queryStart = 0;
unsigned int queryEnd = 0;
parseDelimitedString(blastpTrack->name, ':', targetGeneName, 2);
if (hTableExists(database, refSeq) && 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",
refSeq, 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",
refSeq, 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'",
refSeq, 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]);
}
void getGenomeClade(struct sqlConnection *conn, char *dbName, char *genome, char *clade)
/* Get genome and clade for a given database name */
{
char query[512];
struct sqlResult *srDb;
char **rowDb;
+ char *centraldb = cfgOption("central.db");
- sprintf(query, "select count(*) from centraldb.genomeClade a, centraldb.dbDb b, centraldb.clade c where a.genome = b.genome and a.clade = c.name and b.name = '%s'", dbName);
+ sprintf(query, "select count(*) from %s.genomeClade a, %s.dbDb b, %s.clade c where a.genome = b.genome and a.clade = c.name and b.name = '%s'",
+ centraldb, centraldb, centraldb, dbName);
srDb = sqlGetResult(conn, query);
if ((rowDb = sqlNextRow(srDb)) != NULL)
{
sqlFreeResult(&srDb);
- sprintf(query, "select a.genome, c.label from centraldb.genomeClade a, centraldb.dbDb b, centraldb.clade c where a.genome = b.genome and a.clade = c.name and b.name = '%s'", dbName);
+ sprintf(query, "select a.genome, c.label from %s.genomeClade a, %s.dbDb b, %s.clade c where a.genome = b.genome and a.clade = c.name and b.name = '%s'",
+ centraldb, centraldb, centraldb, dbName);
srDb = sqlGetResult(conn, query);
if ((rowDb = sqlNextRow(srDb)) != NULL)
{
strcpy(genome, rowDb[0]);
strcpy(clade, rowDb[1]);
}
}
sqlFreeResult(&srDb);
}
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 centraldb.clade");
+ 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;
+ 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];
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;
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;\" bgcolor=\"%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 Mismatchs</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, ".refSeq");
- if (hDbExists(blastpTarget[0]) && hTableExists(database, refSeq))
+ if (hDbExists(blastpTarget[0]) && hTableExists(blastpTarget[0], "refSeq"))
{
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]);
/* Get target gene product annotation */
if (hDbExists(blastpTarget[0]))
{
ginfo = getGbProtCodeInfo(conn, blastpTarget[0], blastpTarget[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;\">%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];
unsigned int querySeqLength = 0;
struct sqlConnection *conn = hAllocConn(database);
struct bed *blastpTrack;
struct blastTab *blastpHitsList;
cartWebStart(cart, database, "%s", "BlastP Alignment Hits");
blastpTrack = getBlastpTrackRecord(conn, tdb, targetName);
printQueryGeneInfo(conn, blastpTrack, queryName, &querySeqLength);
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 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;\" bgcolor=\"%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"))
+ 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. */
{
char *track = tdb->tableName;
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, track);
sprintf(query, "select * from %s where name = '%s'", track, 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;\" bgcolor=\"%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://lowedev.cse.ucsc.edu/%s/index.php/BED:%s:%s:%d-%d:%s\"</META>", wiki, database, seqName, winStart, winEnd, strand);
}
else
{
printf("<META HTTP-EQUIV=\"REFRESH\" content=\"0; URL=http://lowedev.cse.ucsc.edu/%s/index.php/BED:%s:%s:%s\"</META>", wiki, 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("<font face=\"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("</font><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->tableName;
tdb->tableName = jgiTable;
printf("<b>Additional information for target<b><br/>");
printf("<hr/>");
doJgiGene(tdb, rnaHyb->JGITarget);
tdb->tableName = saveTableName;
}
if(strlen(rnaHyb->trnaTarget) > 0)
{
saveTableName = tdb->tableName;
tdb->tableName = tRNATable;
printf("<b>Additional information for target<b><br/>");
printf("<hr/>");
doTrnaGenes(tdb, rnaHyb->trnaTarget);
tdb->tableName = saveTableName;
}
freeMem(rnaHyb);
}
sqlFreeResult(&sr);
}
hFreeConn(&conn);
}
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 (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
return FALSE;
return TRUE;
}