\n");
- printf("\n", HG_COL_INSIDE);
+ printf("\n", HG_COL_INSIDE);
printf("\n");
/* Print table column heading */
printf("\n");
printf("| Gene 1 | \n");
printf("Gene 2 | \n");
printf("Confidence | \n");
printf("Number of Conserved Genomes | \n");
printf(" \n");
sprintf(query, "select * from lowelabTIGROperonScore where name = '%s'", tigrOperonName);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
tigrOperonScore = lowelabTIGROperonScoreLoad(row);
printf("\n");
printf("| %s | \n", tigrOperonScore->gene1);
printf("%s | \n", tigrOperonScore->gene2);
printf("%d | \n", tigrOperonScore->confidence);
printf("%d | \n", tigrOperonScore->ortholog_link, tigrOperonScore->ortholog);
printf(" \n");
tigrOperonScore = tigrOperonScore->next;
}
sqlFreeResult(&sr);
/* Close table */
printf("\n");
printf(" \n");
printf("\n");
printf(" \n");
printf("
Note:\n");
printf("
Confidence - an estimation of the lower boundary of the probability that the two corresponding genes are located in the same operon\n");
printf("
Number of Conserved Genomes - number of other genomes that have the same pair of genes located in the same directon (a set of consecutive genes on the same DNA strand)\n");
bedFree(&tigrOperon);
lowelabTIGROperonScoreFree(&tigrOperonScore);
hFreeConn(&conn);
printTrackHtml(tdb);
}
void doArkinOperons(struct trackDb *tdb, char *arkinOperonName)
/* Handle the Arkin operons track. */
{
struct bed *arkinOperon;
struct lowelabArkinOperonScore *arkinOperonScore;
char query[512];
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr;
char *dupe, *words[16];
char **row;
int wordCount;
int rowOffset;
int bedSize = 0;
genericHeader(tdb, arkinOperonName);
dupe = cloneString(tdb->type);
wordCount = chopLine(dupe, words);
if (wordCount > 1)
bedSize = atoi(words[1]);
if (bedSize < 3) bedSize = 3;
rowOffset = hOffsetPastBin(database, seqName, tdb->table);
sprintf(query, "select * from %s where name = '%s'", tdb->table, arkinOperonName);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
arkinOperon = bedLoadN(row+rowOffset, bedSize);
printf("Arkin operon name: %s
\n",arkinOperonName);
printf("
Position: "
"",
hgTracksPathAndSettings(), database, arkinOperon->chrom, arkinOperon->chromStart + 1, arkinOperon->chromEnd);
printf("%s:%d-%d
\n", arkinOperon->chrom, arkinOperon->chromStart + 1, arkinOperon->chromEnd);
printf("Strand: %s
\n", arkinOperon->strand);
printf("Genomic size: %d nt
\n", (arkinOperon->chromEnd - arkinOperon->chromStart));
if (arkinOperon->next != NULL)
printf("
\n");
}
sqlFreeResult(&sr);
printf("
Arkin operon predicted gene pairs
\n");
/* Print table */
printf("", HG_COL_BORDER);
printf("\n");
- printf("\n", HG_COL_INSIDE);
+ printf("\n", HG_COL_INSIDE);
printf("\n");
/* Print table column heading */
printf("\n");
printf("| Gene 1 | \n");
printf("Gene 2 | \n");
printf("Probability of the Same Operon | \n");
printf("Gene neighbor score | \n");
printf(" \n");
sprintf(query, "select * from lowelabArkinOperonScore where name = '%s'", arkinOperonName);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
arkinOperonScore = lowelabArkinOperonScoreLoad(row);
printf("\n");
printf("| %s | \n", arkinOperonScore->gene1);
printf("%s | \n", arkinOperonScore->gene2);
printf("%0.3f | \n", arkinOperonScore->prob);
printf("%0.3f | \n", arkinOperonScore->gnMinus);
printf(" \n");
arkinOperonScore = arkinOperonScore->next;
}
sqlFreeResult(&sr);
/* Close table */
printf("\n");
printf(" \n");
printf("\n");
printf(" \n");
printf("
Note:\n");
printf("
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("
Gene neighbor score - An indicator of conservation (gene neighbor score, surprisal subtracted). Positive scores indicate conservation, and scores above 5 are generally strongly indicative of operons\n");
bedFree(&arkinOperon);
lowelabArkinOperonScoreFree(&arkinOperonScore);
hFreeConn(&conn);
printTrackHtml(tdb);
}
struct bed * getBlastpTrackRecord(struct sqlConnection *conn, struct trackDb *tdb, char *targetName)
/* Get blastp track record clicked by user*/
{
struct bed *blastpTrack = NULL;
char *dupe, *words[16];
int wordCount;
int bedSize = 0;
char query[512];
struct sqlResult *sr;
char **row;
int rowOffset;
int start = cartInt(cart, "o");
int end = cartInt(cart, "t");
char *chrom = cartString(cart, "c");
dupe = cloneString(tdb->type);
wordCount = chopLine(dupe, words);
if (wordCount > 1)
bedSize = atoi(words[1]);
if (bedSize < 3) bedSize = 3;
rowOffset = hOffsetPastBin(database, seqName, tdb->table);
sprintf(query, "select distinct * from %s where name = '%s' and chrom = '%s' and chromStart = %d and chromEnd = %d",
tdb->table, targetName, chrom, start, end);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
blastpTrack = bedLoadN(row+rowOffset, bedSize);
freez(&dupe);
sqlFreeResult(&sr);
return blastpTrack;
}
void printQueryGeneInfo(struct sqlConnection *conn, struct bed *blastpTrack, char *queryName, unsigned int *querySeqLength, char *queryTable)
/* Get and print blastp query gene info */
{
char query[512];
struct sqlResult *srRefSeq;
char **row;
int geneCount;
char **buffer = NULL;
char *targetGeneName[2];
struct minGeneInfo* ginfo;
char blastpHits[] = "blastpHits";
unsigned int queryStart = 0;
unsigned int queryEnd = 0;
parseDelimitedString(blastpTrack->name, ':', targetGeneName, 2);
if (hTableExists(database, queryTable) && hTableExists(database, blastpHits))
{
/* Get query gene from refSeq */
sprintf(query, "select count(*) from %s where chrom = '%s' and strand = '%s' and cdsStart <= %u and cdsEnd >= %u",
queryTable, blastpTrack->chrom, blastpTrack->strand, blastpTrack->chromStart, blastpTrack->chromEnd);
srRefSeq = sqlGetResult(conn, query);
if ((row = sqlNextRow(srRefSeq)) != NULL)
{
geneCount = atoi(row[0]);
sqlFreeResult(&srRefSeq);
if (geneCount == 1)
{
sprintf(query, "select name, cdsStart, cdsEnd from %s where chrom = '%s' and strand = '%s' and cdsStart <= %u and cdsEnd >= %u",
queryTable, blastpTrack->chrom, blastpTrack->strand, blastpTrack->chromStart, blastpTrack->chromEnd);
srRefSeq = sqlGetResult(conn, query);
if ((row = sqlNextRow(srRefSeq)) != NULL)
{
strcpy(queryName, row[0]);
queryStart = strtoul(row[1], buffer, 10);
queryEnd = strtoul(row[2], buffer, 10);
}
sqlFreeResult(&srRefSeq);
}
else
{
/* Check blastpHits if more than 1 query gene is found within the region */
sprintf(query, "select a.name, a.cdsStart, a.cdsEnd from %s a, %s b where a.chrom = '%s' and a.strand = '%s' and a.cdsStart <= %u and a.cdsEnd >= %u and a.name = b.query and b.target like '%%%s'",
queryTable, blastpHits,
blastpTrack->chrom, blastpTrack->strand, blastpTrack->chromStart, blastpTrack->chromEnd, targetGeneName[0]);
srRefSeq = sqlGetResult(conn, query);
if ((row = sqlNextRow(srRefSeq)) != NULL)
{
strcpy(queryName, row[0]);
queryStart = strtoul(row[1], buffer, 10);
queryEnd = strtoul(row[2], buffer, 10);
}
sqlFreeResult(&srRefSeq);
}
if ((queryStart == 0) && (queryEnd == 0))
printf("Query gene not found for %s at %s:%u-%u\n", blastpTrack->name, blastpTrack->chrom, blastpTrack->chromStart, blastpTrack->chromEnd);
else
{
*querySeqLength = queryEnd - queryStart;
/* Print query gene info */
printf("Gene: %s
\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("Position: "
"",
hgTracksPathAndSettings(), database, blastpTrack->chrom, queryStart + 1, queryEnd);
printf("%s:%d-%d
\n", blastpTrack->chrom, queryStart + 1, queryEnd);
printf("Strand: %s
\n", blastpTrack->strand);
printf("Genomic size: %d nt
\n", (queryEnd - queryStart));
}
}
else
printf("
Query gene not found for %s at %s:%u-%u
\n", blastpTrack->name, blastpTrack->chrom, blastpTrack->chromStart, blastpTrack->chromEnd);
}
sqlFreeResult(&srRefSeq);
free(targetGeneName[0]);
free(targetGeneName[1]);
}
struct slName* getAllClades(struct sqlConnection *conn)
/* Get all available clades in database */
{
char query[512];
struct sqlResult *srDb;
char **rowDb;
struct slName *list = NULL;
char clade[50];
sprintf(query, "select label from %s.clade", cfgOption("central.db"));
srDb = sqlGetResult(conn, query);
while ((rowDb = sqlNextRow(srDb)) != NULL)
{
strcpy(clade, rowDb[0]);
slNameAddTail(&list, clade);
}
sqlFreeResult(&srDb);
return list;
}
struct blastTab* loadBlastpHits(struct sqlConnection *conn, char* queryName)
/* Load all blastp hits of the given query gene into a list */
{
char query[512];
struct sqlResult *srBlastpHits = NULL;
struct blastTab *list = NULL;
struct blastTab *blastpHits;
char **row;
char blastpHitsTable[] = "blastpHits";
if (hTableExists(database, blastpHitsTable))
{
sprintf(query, "select * from %s where query = '%s'", blastpHitsTable, queryName);
srBlastpHits = sqlGetResult(conn, query);
while ((row = sqlNextRow(srBlastpHits)) != NULL)
{
blastpHits = blastTabLoad(row);
slAddTail(&list, blastpHits);
}
}
if (srBlastpHits != NULL)
sqlFreeResult(&srBlastpHits);
return list;
}
void printBlastpResult(struct sqlConnection *conn, struct blastTab *blastpHitsList, unsigned int querySeqLength)
/* Print Blastp result of given clade */
{
char query[512];
struct sqlResult *sr;
char **row;
char refSeq[50];
char xraTable[50];
char product[255];
struct blastTab *blastpHits;
struct minGeneInfo *ginfo;
char *blastpTarget[2];
char *clades[2];
int cladePortionCount = 0;
char genome[50] = "";
char clade[50] = "";
unsigned int hitStart = 0;
unsigned int hitEnd = 0;
char **buffer = NULL;
boolean findTable = FALSE;
int tStart = cartInt(cart, "o");
int tEnd = cartInt(cart, "t");
char *tChrom = cartString(cart, "c");
printf("
\n");
/* Print table */
printf("", HG_COL_BORDER);
printf("\n");
- printf("\n", HG_COL_INSIDE);
+ printf("\n", HG_COL_INSIDE);
printf("\n");
/* Print table column heading */
printf("\n");
printf("| Organism | \n");
printf("Clade | \n");
printf("Gene | \n");
printf("Product | \n");
printf("Percent Length of Full Protein | \n");
printf("Position in Source Protein | \n");
printf("Protein Identity (%%) | \n");
printf("E-value | \n");
printf("Log of E-value | \n");
printf("Bit Score | \n");
printf("Protein Alignment Length | \n");
printf("Protein Mismatches | \n");
printf("Alignment Gaps | \n");
printf(" \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("\n");
printf("| %s | \n", blastpTarget[1], tChrom, tStart, tEnd, genome);
if (cladePortionCount == 1)
printf("%s | \n", clades[0]);
else if (cladePortionCount == 2)
printf("%s
%s | \n", clades[0], clades[1]);
/* Get target gene position from refSeq */
strcpy(refSeq, blastpTarget[0]);
strcat(refSeq, ".");
if (hDbExists(blastpTarget[0]))
{
if (hTableExists(blastpTarget[0], "lookup"))
{
sprintf(query, "select lookupValue from %s.lookup where lookupCode = 'annotRev'", blastpTarget[0]);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
{
strcat(refSeq, row[0]);
findTable = TRUE;
sqlFreeResult(&sr);
}
}
else if (hTableExists(blastpTarget[0], "refSeq"))
{
strcat(refSeq, "refSeq");
findTable = TRUE;
}
if (findTable)
{
sprintf(query, "select chrom, cdsStart, cdsEnd from %s where name = '%s'",
refSeq, blastpTarget[1]);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
{
hitStart = strtoul(row[1], buffer, 10) + blastpHits->tStart * 3 + 1;
hitEnd = strtoul(row[1], buffer, 10) + blastpHits->tEnd * 3;
printf("%s | \n",
row[0], hitStart, hitEnd, blastpTarget[0], blastpTarget[1]);
}
else
printf("%s | \n", blastpTarget[1]);
sqlFreeResult(&sr);
}
else
printf("%s | \n", blastpTarget[1]);
}
else
printf("%s | \n", blastpTarget[1]);
/* Get target gene product annotation */
if (hDbExists(blastpTarget[0]))
{
if (hTableExists(blastpTarget[0], "lookup"))
{
sprintf(query, "select lookupValue from %s.lookup where lookupCode = 'annotRevXra'", blastpTarget[0]);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
{
strcpy(xraTable, row[0]);
sqlFreeResult(&sr);
}
else
strcpy(product, "N/A");
sprintf(query, "select product from %s.%s where name = '%s'", blastpTarget[0], xraTable, blastpTarget[1]);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
{
strcpy(product, row[0]);
sqlFreeResult(&sr);
}
else
strcpy(product, "N/A");
}
else
{
ginfo = getGbProtCodeInfo(conn, blastpTarget[0], blastpTarget[1]);
if (ginfo != NULL && ginfo->product != NULL && differentString(ginfo->product,"none"))
strcpy(product, ginfo->product);
else
strcpy(product, "N/A");
}
printf("%s | \n", product);
}
else
printf("%s | \n", "N/A");
printf("%0.f | \n", ((double) (blastpHits->qEnd - blastpHits->qStart) / ((double) (querySeqLength-3) / 3.0f)) * 100.0f);
printf("%u - %u | \n", blastpHits->qStart + 1, blastpHits->qEnd);
printf("%0.1f | \n", blastpHits->identity);
printf("%0.0e | \n", blastpHits->eValue);
printf("e%0.0f | \n", (blastpHits->eValue == 0)? 0 : log(blastpHits->eValue) / log(10));
printf("%0.1f | \n", blastpHits->bitScore);
printf("%u | \n", blastpHits->aliLength);
printf("%u | \n", blastpHits->mismatch);
printf("%u | \n", blastpHits->gapOpen);
printf(" \n");
}
free(blastpTarget[0]);
free(blastpTarget[1]);
blastpHits = blastpHits->next;
}
/* Close table */
printf("\n");
printf(" \n");
printf("\n");
printf(" \n");
}
void doBlastP(struct trackDb *tdb, char *targetName)
/* Handle the BlastP Archaea and BlastP Bacteria tracks. */
{
char queryName[50];
char queryTable[50];
unsigned int querySeqLength = 0;
struct sqlConnection *conn = hAllocConn(database);
struct bed *blastpTrack;
struct blastTab *blastpHitsList;
char query[512];
struct sqlResult *sr;
char **row;
cartWebStart(cart, database, "%s", "BlastP Alignment Hits");
blastpTrack = getBlastpTrackRecord(conn, tdb, targetName);
if (hTableExists(database, "lookup"))
{
sprintf(query, "select lookupValue from lookup where lookupCode = 'annotRev'");
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
{
strcpy(queryTable, row[0]);
sqlFreeResult(&sr);
}
}
else
strcpy(queryTable, "refSeq");
printQueryGeneInfo(conn, blastpTrack, queryName, &querySeqLength, queryTable);
blastpHitsList = loadBlastpHits(conn, queryName);
printBlastpResult(conn, blastpHitsList, querySeqLength);
printf("
Note: All measurements are counted by the number of amino acids.
\n");
printf("
\n");
hFreeConn(&conn);
printTrackHtml(tdb);
}
void doSelfHomologs(struct trackDb *tdb, char *targetName)
/* Handle the Self Homologs tracks. */
{
char queryName[50];
char queryTable[50];
unsigned int querySeqLength = 0;
struct sqlConnection *conn = hAllocConn(database);
struct bed *blastpTrack;
struct blastTab *blastpHitsList;
char query[512];
struct sqlResult *sr;
char **row;
cartWebStart(cart, database, "%s", "Homologs Within Genome by BlastP Search");
blastpTrack = getBlastpTrackRecord(conn, tdb, targetName);
if (hTableExists(database, "lookup"))
{
sprintf(query, "select lookupValue from lookup where lookupCode = 'annotRev'");
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
{
strcpy(queryTable, row[0]);
sqlFreeResult(&sr);
}
}
else
strcpy(queryTable, "refSeq");
printQueryGeneInfo(conn, blastpTrack, queryName, &querySeqLength, queryTable);
blastpHitsList = loadSelfBlastpHits(conn, queryName, 1);
printBlastpResult(conn, blastpHitsList, querySeqLength);
printf("
Note: All measurements are counted by the number of amino acids.
\n");
printf("
\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("Query sequence: %s
\n", queryName);
printf("Position: "
"",
hgTracksPathAndSettings(), database, blastxTrack->chrom, queryStart + 1, queryEnd);
printf("%s:%d-%d
\n", blastxTrack->chrom, queryStart + 1, queryEnd);
printf("Genomic size: %d nt
\n", (queryEnd - queryStart));
printf("BlastX hit position: "
"",
hgTracksPathAndSettings(), database, blastxTrack->chrom, blastxTrack->chromStart + 1, blastxTrack->chromEnd);
printf("%s:%d-%d
\n", blastxTrack->chrom, blastxTrack->chromStart + 1, blastxTrack->chromEnd);
printf("BlastX hit position relative to query sequence: %d-%d
\n", blastxTrack->chromStart - queryStart + 1, blastxTrack->chromEnd - queryStart);
printf("BlastX hit genomic size: %d nt
\n", (blastxTrack->chromEnd - blastxTrack->chromStart));
}
}
else
printf("
Query sequence not found for %s at %s:%u-%u
\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("
\n");
/* Print table */
printf("", HG_COL_BORDER);
printf("\n");
- printf("\n", HG_COL_INSIDE);
+ printf("\n", HG_COL_INSIDE);
printf("\n");
/* Print table column heading */
printf("\n");
printf("| Organism | \n");
printf("Clade | \n");
printf("Gene | \n");
printf("Product | \n");
printf("Position in Query Genomic Sequence | \n");
printf("Position in Target Protein | \n");
printf("Percent Length of Target Protein | \n");
printf("Protein Identity (%%) | \n");
printf("E-value | \n");
printf("Log of E-value | \n");
printf("Bit Score | \n");
printf("Protein Alignment Length | \n");
printf("Protein Mismatches | \n");
printf("Alignment Gaps | \n");
printf(" \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("\n");
printf("| %s | \n", blastxTarget[1], tChrom, tStart, tEnd, genome);
if (cladePortionCount == 1)
printf("%s | \n", clades[0]);
else if (cladePortionCount == 2)
printf("%s
%s | \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("%s | \n",
row[0], hitStart, hitEnd, blastxTarget[0], blastxTarget[1]);
}
else
printf("%s | \n", blastxTarget[1]);
sqlFreeResult(&sr);
}
else
printf("%s | \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("%s | \n", ginfo->product);
else
printf("%s | \n", "N/A");
}
else
printf("%s | \n", "N/A");
printf("%u - %u | \n", blastxHits->qStart + 1, blastxHits->qEnd);
printf("%u - %u | \n", blastxHits->tStart + 1, blastxHits->tEnd);
if ((targetProteinStart == 0) || (targetProteinEnd == 0))
printf("N/A | \n");
else
printf("%0.f | \n", ((double) (blastxHits->tEnd - blastxHits->tStart) /
((double) (targetProteinEnd-targetProteinStart-3) / 3.0f)) * 100.0f);
printf("%0.1f | \n", blastxHits->identity);
printf("%0.0e | \n", blastxHits->eValue);
printf("e%0.0f | \n", (blastxHits->eValue == 0)? 0 : log(blastxHits->eValue) / log(10));
printf("%0.1f | \n", blastxHits->bitScore);
printf("%u | \n", blastxHits->aliLength);
printf("%u | \n", blastxHits->mismatch);
printf("%u | \n", blastxHits->gapOpen);
printf(" \n");
}
free(blastxTarget[0]);
free(blastxTarget[1]);
blastxHits = blastxHits->next;
}
/* Close table */
printf("\n");
printf(" \n");
printf("\n");
printf(" \n");
}
void doBlastX(struct trackDb *tdb, char *targetName)
/* Handle the BlastX Archaea and BlastX Bacteria tracks. */
{
char queryName[50];
char queryTable[50];
unsigned int querySeqLength = 0;
struct sqlConnection *conn = hAllocConn(database);
struct bed *blastxTrack;
struct blastTab *blastxHitsList;
cartWebStart(cart, database, "%s", "BlastX Alignment Hits");
blastxTrack = getBlastpTrackRecord(conn, tdb, targetName);
/* if (!differentWord(blastxTrack->chrom, "assembly"))*/
if (hTableExists(database, "scaffolds"))
strcpy(queryTable, "scaffolds");
else
strcpy(queryTable, "igenics");
printQuerySequenceInfo(conn, blastxTrack, queryName, &querySeqLength, queryTable);
blastxHitsList = loadBlastxHits(conn, queryName, queryTable, blastxTrack);
printBlastxResult(conn, blastxHitsList, querySeqLength);
printf("
\n");
printf("
\n");
hFreeConn(&conn);
printTrackHtml(tdb);
}
void doUltraConserved(struct trackDb *tdb, char *item)
/* Handle the ultraConserved track. */
{
char tableName[65];
int start = cartInt(cart, "o");
int end = cartInt(cart, "t");
struct hashEl* hashItem;
struct hashCookie cookie;
struct trackDb *multizTrack;
struct sqlConnection *conn = hAllocConn(database);
cookie = hashFirst(trackHash);
hashItem = hashNext(&cookie);
while (hashItem != NULL)
{
memset(tableName, 0, 65);
strcpy(tableName, hashItem->name);
if (strstr(tableName, "multiz") != NULL)
break;
hashItem = hashNext(&cookie);
}
multizTrack = hashFindVal(trackHash, tableName);
winStart = start;
winEnd = end;
genericHeader(tdb, NULL);
if (tdb->html != NULL && tdb->html[0] != 0)
{
puts(tdb->html);
htmlHorizontalLine();
}
genericMafClick(conn, multizTrack, item, start);
printTrackHtml(multizTrack);
hFreeConn(&conn);
}
float computeMolecularWeight(char* dna, int length)
{
float weight = 0.0f;
int count[4] = {0,0,0,0};
int i = 0;
for (i = 0; i < length; i++)
{
if ((dna[i] == 'A') || (dna[i] == 'a'))
count[0]++;
else if ((dna[i] == 'C') || (dna[i] == 'c'))
count[1]++;
else if ((dna[i] == 'G') || (dna[i] == 'g'))
count[2]++;
else if ((dna[i] == 'T') || (dna[i] == 't'))
count[3]++;
}
weight = count[0] * 313.209 + count[1] * 289.184 + count[2] * 329.208 + count[3] * 304.196 - 63.980 + 2.016;
return weight;
}
float computeNMolePerOD(char* dna, int length)
{
int extCoeff = 0;
float nmolePerOD = 0.0f;
enum
{
baseA = 0,
baseC,
baseG,
baseT
};
int indExtCoeff[4] = {15400, 7400, 11500, 8700};
int neighborExtCoeff[4][4] = {
{27400, 21200, 25000, 22800},
{21200, 14600, 18000, 15200},
{25200, 17600, 21600, 20000},
{23400, 16200, 19000, 16800}};
int i = 0;
int *bases = malloc(sizeof(int) * length);
for (i = 0; i < length; i++)
{
if ((dna[i] == 'A') || (dna[i] == 'a'))
bases[i] = baseA;
else if ((dna[i] == 'C') || (dna[i] == 'c'))
bases[i] = baseC;
else if ((dna[i] == 'G') || (dna[i] == 'g'))
bases[i] = baseG;
else if ((dna[i] == 'T') || (dna[i] == 't'))
bases[i] = baseT;
}
for (i = 0; i < (length - 1); i++)
extCoeff += neighborExtCoeff[bases[i]][bases[i + 1]];
for (i = 1; i < (length - 1); i++)
extCoeff -= indExtCoeff[bases[i]];
nmolePerOD = pow(10, 6) / (float) extCoeff;
free(bases);
return nmolePerOD;
}
void doPrimers(struct trackDb *tdb, char *primerName)
/* Handle the array primer and GOLD primer tracks. */
{
struct bed *primer;
struct dnaSeq *sequence;
char query[512];
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr;
char *dupe, *words[16];
char **row;
int wordCount;
int rowOffset;
int bedSize = 0;
int pairCount = 0;
boolean forwardPrimer = TRUE;
genericHeader(tdb, primerName);
if (startsWith("Asn", primerName))
forwardPrimer = FALSE;
dupe = cloneString(tdb->type);
wordCount = chopLine(dupe, words);
if (wordCount > 1)
bedSize = atoi(words[1]);
if (bedSize < 3) bedSize = 3;
rowOffset = hOffsetPastBin(database, seqName, tdb->table);
sprintf(query, "select * from %s where name = '%s'", tdb->table, primerName);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
primer = bedLoadN(row+rowOffset, bedSize);
printf("Primer name: %s
\n",primerName);
printf("
Position: "
"",
hgTracksPathAndSettings(), database, primer->chrom, primer->chromStart + 1, primer->chromEnd);
printf("%s:%d-%d
\n", primer->chrom, primer->chromStart + 1, primer->chromEnd);
printf("Strand: %s
\n", primer->strand);
printf("Genomic size: %d nt
\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("Sequence: 5' %s 3'
\n", sequence->dna);
printf("GC content: %0.2f%%
\n", computeGCContent(sequence->dna, sequence->size));
printf("Molecular weight: %0.1f g/mol
\n", computeMolecularWeight(sequence->dna, sequence->size));
printf("nmole/OD260: %0.3f
\n", computeNMolePerOD(sequence->dna, sequence->size));
printf("ug/OD260: %0.3f
\n", computeNMolePerOD(sequence->dna, sequence->size) *
computeMolecularWeight(sequence->dna, sequence->size) * pow(10,-3));
}
if (primer->next != NULL)
printf("
\n");
}
sqlFreeResult(&sr);
printf("
Primer pairing
\n");
/* Print table */
printf("", HG_COL_BORDER);
printf("\n");
- printf("\n", HG_COL_INSIDE);
+ printf("\n", HG_COL_INSIDE);
printf("\n");
/* Print table column heading */
printf("\n");
printf("| Primer Name | \n");
printf("Primer Type | \n");
printf("Primer Sequence | \n");
printf("PCR Region | \n");
printf("PCR Length (bp) | \n");
printf("PCR Region
GC Content (%%) | \n");
printf(" \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("\n");
printf("| "
"",
hgTracksPathAndSettings(), database, row[1], atoi(row[2]) + 1, atoi(row[3]));
printf("%s | \n", row[4]);
printf("%s | \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("5' %s 3' | \n", sequence->dna);
}
else
printf("N/A | \n");
if (strcmp(primer->strand, "+") == 0)
{
sequence = hDnaFromSeq(database, primer->chrom, primer->chromStart, atoi(row[3]), dnaUpper);
printf(""
"",
hgTracksPathAndSettings(), database, primer->chrom, primer->chromStart + 1, atoi(row[3]));
printf("%s:%d-%d | \n", primer->chrom, primer->chromStart + 1, atoi(row[3]));
}
else
{
sequence = hDnaFromSeq(database, primer->chrom, atoi(row[2]), primer->chromEnd, dnaUpper);
printf(""
"",
hgTracksPathAndSettings(), database, primer->chrom, atoi(row[2]) + 1, primer->chromEnd);
printf("%s:%d-%d | \n", primer->chrom, atoi(row[2])+ 1, primer->chromEnd);
}
if (sequence != NULL)
{
printf("%d | \n", sequence->size);
printf("%0.2f | \n", computeGCContent(sequence->dna, sequence->size));
}
else
{
printf("N/A | \n");
printf("N/A | \n");
}
printf(" \n");
pairCount++;
}
}
sqlFreeResult(&sr);
/* Close table */
printf("\n");
printf(" \n");
printf("\n");
printf(" \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("");
if(startsWith("Make", itemName))
{
strand[0] = itemName[strlen(itemName)-1];
strand[1] = 0;
printf("", database, seqName, winStart, winEnd, strand);
}
else
{
printf("", database, seqName, itemName);
}
printf("");
}
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("Hybridization Site:
");
/* print hybridization site */
printf("");
printf("Pattern 5%s3
", rnaHyb->patternSeq);
printf(" ");
for(i=0;imatchLength;i++)
printf("|");
printf("
");
printf("Target 3%s5", rnaHyb->targetSeq);
printf("
");
printf("
Genomic size: %d nt
\n",rnaHyb->matchLength);
printf("Percentage G-C base-pairs: %d
", (int)(rnaHyb->gcContent * 100));
printf("Position: "
"",
hgTracksPathAndSettings(), database, rnaHyb->chrom, rnaHyb->chromStart+1, rnaHyb->chromEnd);
printf("%s:%d-%d
\n", rnaHyb->chrom, rnaHyb->chromStart+1, rnaHyb->chromEnd);
printf("Strand: %s
\n", rnaHyb->strand);
printf("Target Position: "
"",
hgTracksPathAndSettings(), database, rnaHyb->chromTarget, rnaHyb->chromStartTarget+1, rnaHyb->chromEndTarget+1);
printf("%s:%d-%d
\n", rnaHyb->chromTarget, rnaHyb->chromStartTarget+1, rnaHyb->chromEndTarget+1);
printf("Target Strand: %s
\n", rnaHyb->strandTarget);
printf("
");
if(strlen(rnaHyb->refSeqTarget) > 0)
{
printf("Additional information for target
");
printf("
");
doRefSeq(tdb, rnaHyb->refSeqTarget,"gbProtCodePep","gbProtCodeXra");
}
if(strlen(rnaHyb->JGITarget) > 0)
{
saveTableName = tdb->table;
tdb->table = jgiTable;
printf("Additional information for target
");
printf("
");
doJgiGene(tdb, rnaHyb->JGITarget);
tdb->table = saveTableName;
}
if(strlen(rnaHyb->trnaTarget) > 0)
{
saveTableName = tdb->table;
tdb->table = tRNATable;
printf("Additional information for target
");
printf("
");
doTrnaGenes(tdb, rnaHyb->trnaTarget);
tdb->table = saveTableName;
}
freeMem(rnaHyb);
}
sqlFreeResult(&sr);
}
hFreeConn(&conn);
}
void doarCOGs(struct trackDb *tdb, char *itemName)
{
char query[512];
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr;
char *dupe, *words[16];
char **row;
int wordCount;
int rowOffset;
struct arCOGs *infoload;
int start = cartInt(cart, "o");
int end = cartInt(cart, "t");
sprintf(query, "select * from mgCommonDb.arcogdesc where name = '%s'", itemName);
//sprintf(query, "select * from %s where query = '%s'", blastpHitsTable, queryName);
struct sqlResult *srarcogdesc = sqlGetResult(conn, query);
struct arcogdesc *description = NULL;
while ((row = sqlNextRow(srarcogdesc)) != NULL)
{
struct arcogdesc *element;
element = arcogdescLoad(row);
slAddTail(&description, element);
}
sqlFreeResult(&srarcogdesc);
genericHeader(tdb,itemName);
dupe = cloneString(tdb->type);
wordCount = chopLine(dupe, words);
rowOffset = hOffsetPastBin(database,seqName, tdb->table);
sprintf(query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d and chromEnd = '%d';", tdb->table, itemName,seqName,start, end);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
infoload = arCOGsLoad(row+rowOffset);
printf("Name: %s
\n", infoload->name);
printf("Description: %s
\n", description->description);
printf("Code: %s
\n", description->code);
printf("Gene: %s
\n", infoload->gene);
printf("Position: "
"",
hgTracksPathAndSettings(), database, infoload->chrom, infoload->chromStart + 1, infoload->chromEnd);
printf("%s:%d-%d
\n", infoload->chrom, infoload->chromStart + 1, infoload->chromEnd);
printf("Strand: %s
\n", infoload->strand);
printf("Genomic size: %d nt
\n", (infoload->chromEnd - infoload->chromStart));
if (infoload->next != NULL)
printf("
\n");
}
sqlFreeResult(&sr);
hFreeConn(&conn);
arCOGsFree(&infoload);
printTrackHtml(tdb);
}
void doloweOrthologs(struct trackDb *tdb, char *itemName)
{
char query[512];
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr;
char *dupe, *words[16];
char **row;
int wordCount;
int rowOffset;
struct bed *infoload;
int bedSize = 0;
int start = cartInt(cart, "o");
int end = cartInt(cart, "t");
dupe = cloneString(tdb->type);
wordCount = chopLine(dupe, words);
if (wordCount > 1)
bedSize = atoi(words[1]);
if (bedSize < 3) bedSize = 3;
genericHeader(tdb,itemName);
dupe = cloneString(tdb->type);
wordCount = chopLine(dupe, words);
rowOffset = hOffsetPastBin(database,seqName, tdb->table);
sprintf(query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d and chromEnd = '%d';", tdb->table, itemName,seqName,start, end);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
infoload = bedLoadN(row+rowOffset, bedSize);
printf("Name: %s\n", infoload->name);
printf(" List of Orthologs
",database,infoload->name);
printf("Position: "
"",
hgTracksPathAndSettings(), database, infoload->chrom, infoload->chromStart + 1, infoload->chromEnd);
printf("%s:%d-%d
\n", infoload->chrom, infoload->chromStart + 1, infoload->chromEnd);
printf("Strand: %s
\n", infoload->strand);
printf("Genomic size: %d nt
\n", (infoload->chromEnd - infoload->chromStart));
if (infoload->next != NULL)
printf("
\n");
}
sqlFreeResult(&sr);
hFreeConn(&conn);
printTrackHtml(tdb);
}
void doCddInfo(struct trackDb *tdb, char *itemName)
{
char query[512];
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr;
char *dupe, *words[16];
char **row;
int wordCount;
int rowOffset;
struct cddInfo *infoload;
int bedSize = 0;
int start = cartInt(cart, "o");
int end = cartInt(cart, "t");
dupe = cloneString(tdb->type);
wordCount = chopLine(dupe, words);
if (wordCount > 1)
bedSize = atoi(words[1]);
if (bedSize < 3) bedSize = 3;
sprintf(query, "select * from mgCommonDb.cddDesc where accession = '%s'", itemName);
//sprintf(query, "select * from %s where query = '%s'", blastpHitsTable, queryName);
struct sqlResult *srCddDesc = sqlGetResult(conn, query);
struct cddDesc *description = NULL;
while ((row = sqlNextRow(srCddDesc)) != NULL)
{
struct cddDesc *element;
element = cddDescLoad(row);
slAddTail(&description, element);
}
sqlFreeResult(&srCddDesc);
genericHeader(tdb,itemName);
dupe = cloneString(tdb->type);
wordCount = chopLine(dupe, words);
rowOffset = hOffsetPastBin(database,seqName, tdb->table);
sprintf(query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d and chromEnd = '%d';", tdb->table, itemName,seqName,start, end);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
infoload = cddInfoLoad(row+rowOffset);
printf("Name: %s
\n", infoload->fullname);
printf("Accession: %s",
infoload->name, infoload->NCBInum);
printf(" Link to NCBI Site
\n");
printf("E-value: %0.0e
\n", infoload->evalue);
printf("Description: %s
\n", description->name);
printf("Protein Identity: %u%%
\n", infoload->percentident);
printf("Percent Length: %u%%
\n", infoload->percentlength);
printf("Position: "
"",
hgTracksPathAndSettings(), database, infoload->chrom, infoload->chromStart + 1, infoload->chromEnd);
printf("%s:%d-%d
\n", infoload->chrom, infoload->chromStart + 1, infoload->chromEnd);
printf("Strand: %s
\n", infoload->strand);
printf("Genomic size: %d nt
\n", (infoload->chromEnd - infoload->chromStart));
if (infoload->next != NULL)
printf("
\n");
}
sqlFreeResult(&sr);
hFreeConn(&conn);
cddInfoFree(&infoload);
printTrackHtml(tdb);
}
void domegablastInfo(struct trackDb *tdb, char *itemName)
{
char query[512];
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr;
char *dupe, *words[16];
char **row;
int wordCount;
int rowOffset;
struct megablastInfo *infoload;
int start = cartInt(cart, "o");
int end = cartInt(cart, "t");
genericHeader(tdb,itemName);
dupe = cloneString(tdb->type);
wordCount = chopLine(dupe, words);
rowOffset = hOffsetPastBin(database,seqName, tdb->table);
sprintf(query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d and chromEnd = '%d';", tdb->table, itemName,seqName,start, end);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
infoload = megablastInfoLoad(row+rowOffset);
printf("Name: %s
\n", infoload->name);
printf("Accession: %s",
infoload->name, infoload->name);
printf(" Link to NCBI Site
\n");
printf("Description: %s
\n", infoload->fullname);
printf("E-value: %0.0e", infoload->evalue);
#ifdef LISTUI
printf(" Sort by E-value",database);
#endif
printf("
\n");
printf("Protein Identity: %u%%\n", infoload->percentident);
#ifdef LISTUI
printf(" Sort by Percent Identity",database);
#endif
printf("
\n");
printf("Position: "
"",
hgTracksPathAndSettings(), database, infoload->chrom, infoload->chromStart + 1, infoload->chromEnd);
printf("%s:%d-%d
\n", infoload->chrom, infoload->chromStart + 1, infoload->chromEnd);
printf("Strand: %s
\n", infoload->strand);
printf("Genomic size: %d nt
\n", (infoload->chromEnd - infoload->chromStart));
if (infoload->next != NULL)
printf("
\n");
}
sqlFreeResult(&sr);
hFreeConn(&conn);
megablastInfoFree(&infoload);
printTrackHtml(tdb);
}
void doAlignInfo(struct trackDb *tdb, char *itemName)
{
char query[512];
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr;
char *dupe, *words[16];
char **row;
int wordCount;
int rowOffset;
struct alignInfo *infoload;
int bedSize = 0;
int start = cartInt(cart, "o");
dupe = cloneString(tdb->type);
wordCount = chopLine(dupe, words);
if (wordCount > 1)
bedSize = atoi(words[1]);
if (bedSize < 3) bedSize = 3;
genericHeader(tdb,itemName);
dupe = cloneString(tdb->type);
wordCount = chopLine(dupe, words);
rowOffset = hOffsetPastBin(database, seqName, tdb->table);
sprintf(query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d;", tdb->table, itemName,seqName,start);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
infoload = alignInfoLoad(row+rowOffset);
printf("Name: %s ", infoload->name);
linkToOtherBrowserTitle(infoload->orgn, infoload->alignChrom, infoload->alignChromStart + 1, infoload->alignChromEnd, "Aligned Feature");
//printf("",
//hgTracksPathAndSettings(), infoload->orgn, infoload->alignChrom, infoload->alignChromStart + 1, infoload->alignChromEnd);
printf("Link to Feature
\n" );
printf("Position: "
"",
hgTracksPathAndSettings(), database, infoload->chrom, infoload->chromStart + 1, infoload->chromEnd);
printf("%s:%d-%d
\n", infoload->chrom, infoload->chromStart + 1, infoload->chromEnd);
printf("Strand: %s
\n", infoload->strand);
printf("Genomic size: %d nt
\n", (infoload->chromEnd - infoload->chromStart));
if (infoload->next != NULL)
printf("
\n");
break;
}
sqlFreeResult(&sr);
hFreeConn(&conn);
alignInfoFree(&infoload);
printTrackHtml(tdb);
}
void doCRISPRs(struct trackDb *tdb, char *crisprName)
/* Handle the CRISPR array track. */
{
struct bed *crispr;
struct dnaSeq *sequence;
char tempSeq[512];
char query[512];
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr;
char *dupe, *words[16];
char **row;
int wordCount;
int rowOffset;
int bedSize = 0;
int pairCount = 0;
genericHeader(tdb, crisprName);
dupe = cloneString(tdb->type);
wordCount = chopLine(dupe, words);
if (wordCount > 1)
bedSize = atoi(words[1]);
if (bedSize < 3) bedSize = 3;
rowOffset = hOffsetPastBin(database, seqName, tdb->table);
safef(query, ArraySize(query), "select * from %s where name = '%s'", tdb->table, crisprName);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
crispr = bedLoadN(row+rowOffset, bedSize);
printf("Name: %s
\n", crisprName);
printf("Position: "
"",
hgTracksPathAndSettings(), database, crispr->chrom, crispr->chromStart + 1, crispr->chromEnd);
printf("%s:%d-%d
\n", crispr->chrom, crispr->chromStart + 1, crispr->chromEnd);
printf("Strand: %s
\n", crispr->strand);
printf("Genomic size: %d nt
\n", (crispr->chromEnd - crispr->chromStart));
printf("Number of spacers: %u
\n", crispr->blockCount - 1);
sequence = hDnaFromSeq(database, crispr->chrom, crispr->chromStart, crispr->chromEnd, dnaUpper);
if (sequence != NULL)
{
/* Print table */
printf("", HG_COL_BORDER);
printf("\n");
- printf("\n", HG_COL_INSIDE);
+ printf("\n", HG_COL_INSIDE);
printf("\n");
/* Print table column heading */
printf("\n");
printf("| Direct Repeat | \n");
printf("Spacer | \n");
printf(" \n");
printf("\n");
printf("| Start Pos | \n");
printf("Sequence | \n");
printf("Length | \n");
printf("Start Pos | \n");
printf("Sequence | \n");
printf("Length | \n");
printf(" \n");
if (strcmp(crispr->strand, "+") == 0)
{
for (pairCount = 0; pairCount < (int) crispr->blockCount; pairCount++)
{
printf("\n");
memset(tempSeq, '\0', sizeof(tempSeq));
memcpy(tempSeq, sequence->dna + crispr->chromStarts[pairCount], crispr->blockSizes[pairCount]);
printf("| %d | %s | %d | \n", crispr->chromStart + 1 + crispr->chromStarts[pairCount], tempSeq, crispr->blockSizes[pairCount]);
if (pairCount + 1 < crispr->blockCount)
{
memset(tempSeq, '\0', sizeof(tempSeq));
memcpy(tempSeq, sequence->dna + crispr->chromStarts[pairCount] + crispr->blockSizes[pairCount],
crispr->chromStarts[pairCount+1] - crispr->blockSizes[pairCount] - crispr->chromStarts[pairCount]);
printf("%d | %s | %d | \n", crispr->chromStart + 1 + crispr->chromStarts[pairCount] + crispr->blockSizes[pairCount], tempSeq,
crispr->chromStarts[pairCount+1] - crispr->blockSizes[pairCount] - crispr->chromStarts[pairCount]);
}
else
{
printf(" | | | \n");
}
printf(" \n");
}
}
else
{
for (pairCount = ((int)crispr->blockCount - 1); pairCount >= 0; pairCount--)
{
printf("\n");
memset(tempSeq, '\0', sizeof(tempSeq));
memcpy(tempSeq, sequence->dna + crispr->chromStarts[pairCount], crispr->blockSizes[pairCount]);
reverseComplement(tempSeq, strlen(tempSeq));
printf("| %d | %s | %d | \n", crispr->chromStart + crispr->chromStarts[pairCount] + crispr->blockSizes[pairCount], tempSeq, crispr->blockSizes[pairCount]);
if (pairCount - 1 >= 0)
{
memset(tempSeq, '\0', sizeof(tempSeq));
memcpy(tempSeq, sequence->dna + crispr->chromStarts[pairCount-1] + crispr->blockSizes[pairCount-1],
crispr->chromStarts[pairCount] - crispr->blockSizes[pairCount-1] - crispr->chromStarts[pairCount-1]);
reverseComplement(tempSeq, strlen(tempSeq));
printf("%d | %s | %d | \n", crispr->chromStart + crispr->chromStarts[pairCount], tempSeq,
crispr->chromStarts[pairCount] - crispr->blockSizes[pairCount-1] - crispr->chromStarts[pairCount-1]);
}
else
{
printf(" | | | \n");
}
printf(" \n");
}
}
/* Close table */
printf("\n");
printf(" \n");
printf("\n");
printf(" \n");
}
if (crispr->next != NULL)
printf("
\n");
}
sqlFreeResult(&sr);
bedFree(&crispr);
hFreeConn(&conn);
printTrackHtml(tdb);
}
bool loweLabClick(char *track, char *item, struct trackDb *tdb)
/* check if we have one of the lowelab tracks */
{
if (sameWord(track, "gbProtCode"))
{
llDoCodingGenes(tdb, item,"gbProtCodePep","gbProtCodeXra");
}
else if (sameWord(track, "refSeq"))
{
doRefSeq(tdb, item,"gbProtCodePep","gbProtCodeXra");
}
else if (startsWith("annotRev", track))
{
doRefSeq(tdb, item,"Pep","Xra");
}
else if (sameWord(track, "sargassoSea"))
{
doSargassoSea(tdb, item);
}
else if (sameWord(track, "tigrCmrORFs"))
{
doTigrCmrGene(tdb,item);
}
else if (sameWord(track, "jgiGene"))
{
doJgiGene(tdb,item);
}
else if (sameWord(track, "lowelabPfamHits"))
{
doPfamHit(tdb,item);
}
/*else if (sameWord(track, "tigrOperons"))*/
else if (sameWord(track, "lowelabTIGROperons"))
{
doTigrOperons(tdb,item);
}
else if (sameWord(track, "lowelabArkinOperons"))
{
doArkinOperons(tdb,item);
}
else if (sameWord(track,"codeBlast"))
{
doCodeBlast(tdb, item);
}
else if (sameWord(track,"gbRNAs"))
{
doGbRnaGenes(tdb, item);
}
else if (sameWord(track,"tRNAs"))
{
doTrnaGenes(tdb, item);
}
else if (sameWord(track,"snoRNAs"))
{
doSnornaGenes(tdb, item);
}
else if (sameWord(track,"easyGene"))
{
doEasyGenes(tdb, item);
}
else if (startsWith("BlastP_", track)
&& differentWord(track, "BlastP_Crenarchaea") && differentWord(track, "BlastP_Nanoarch") && differentWord(track, "BlastP_Euryarch")
&& differentWord(track, "BlastP_Bacteria"))
{
doBlastP(tdb, item);
}
else if (startsWith("BlastX_", track)
&& differentWord(track, "BlastX_Crenarchaea") && differentWord(track, "BlastX_Nanoarch") && differentWord(track, "BlastX_Euryarch")
&& differentWord(track, "BlastX_Bacteria"))
{
doBlastX(tdb, item);
}
else if (sameWord(track,"ultraConserved"))
{
doUltraConserved(tdb, item);
}
else if (sameWord(track,"genomePcrPrimers") || sameWord(track,"goldRTPrimers"))
{
doPrimers(tdb, item);
}
else if (sameWord(track,"wiki") || sameWord(track,"wikibme"))
{
doWiki(track,tdb,item);
}
else if (sameWord(track,"rnaHybridization"))
{
doRNAHybridization(tdb, item);
}
else if (sameWord(track,"cddInfo"))
{
doCddInfo(tdb, item);
}
else if (sameWord(track,"alignInfo"))
{
doAlignInfo(tdb, item);
}
else if (sameWord(track,"arCOGs"))
{
doarCOGs(tdb, item);
}
else if (sameWord(track,"megablastInfo") || sameWord(track,"vecScreenInfo"))
{
domegablastInfo(tdb, item);
}
else if (sameWord(track,"loweOrthologs"))
{
doloweOrthologs(tdb, item);
}
else if (sameWord(track,"selfHomologs"))
{
doSelfHomologs(tdb, item);
}
else if (sameWord(track,"CRISPRs"))
{
doCRISPRs(tdb, item);
}
else
return FALSE;
return TRUE;
}
| | | | | |
![](\"http://www.rcsb.org/pdb/images/%s_bio_r_80.jpg\")
![](\"http://salilab.org/modbaseimages/image/modbase.jpg?database_id=%s\")
![](\"http://salilab.org/modbaseimages/image/modbase.jpg?database_id=%s&axis=x°ree=90\")
![](\"http://salilab.org/modbaseimages/image/modbase.jpg?database_id=%s&axis=y°ree=90\")
![tRNA secondary structure for %s](\"../RNA-img/%s/%s-%s.gif\")
\n",
database,database,trna->name,trna->name);
else
printf("![tRNA secondary structure for %s](\"../RNA-img/%s/%s-%s-%s.gif\")
\n",
database,database,trna->chrom,trna->name,trna->name);
printf("