\n");
/* cog description */
itemCount = 0;
if (hTableExists(database, "COG"))
{
- sprintf(query, "select * from COG where name = '%s'", item);
+ sqlSafef(query, sizeof 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; xCOG: "
"%s "
"Code %s \n",
COGXra->name, COGXra->name, COG->code,COG->code);
printf(" %s
\n", COGXra->info);
itemCount++;
}
sqlFreeResult(&sr2);
@@ -634,76 +634,76 @@
}
}
sqlFreeResult(&sr);
//hFreeConn(&conn2);
}
/*
if (hTableExists(database, "arCOGs"))
{
struct arCOGs *infoload = NULL;
struct arcogdesc *description = NULL;
int rowOffset = hOffsetPastBin(database, seqName, "arCOGs");
//infoload = arCOGsLoad(row);
row = NULL;
- sprintf(query, "select * from arCOGs where gene = '%s'", item);
+ sqlSafef(query, sizeof query, "select * from arCOGs where gene = '%s'", item);
sr = sqlGetResult(conn, query);
conn2 = hAllocConn(database);
while ((row = sqlNextRow(sr)) != NULL)
{
infoload = arCOGsLoad(row+rowOffset);
if(infoload!=NULL)
{
- sprintf(query2, "select * from mgCommonDb.arcogdesc where name = '%s'",infoload->name );
+ sqlSafef(query2, sizeof query2, "select * from mgCommonDb.arcogdesc where name = '%s'",infoload->name );
sr2 = sqlGetResult(conn2, query2);
while ((row2 = sqlNextRow(sr2)) != NULL)
{
description=arcogdescLoad(row2);
if(description!=NULL)
{
printf("arCOG: %s Code %s",infoload->name, description->code);
printf(" %s
\n", description->description);
itemCount++;
}
}
sqlFreeResult(&sr2);
hFreeConn(&conn2);
}
}
}
*/
arcogCount = 0;
hasArCOG = FALSE;
row = NULL;
-sprintf(query, "show databases like 'arCogsDb'");
+sqlSafef(query, sizeof query, "show databases like 'arCogsDb'");
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
{
hasArCOG = TRUE;
}
sqlFreeResult(&sr);
if (hasArCOG)
{
/* Get species info */
memset(genome, 0, 50);
memset(clade, 0, 50);
getGenomeClade(conn, database, genome, clade);
- sprintf(query, "select distinct a.arcog_id, a.anntation, c.class_id from arCogsDb.arcogDef a, arCogsDb.arcog b, arCogsDb.arcogFun c where a.arcog_id = b.arcog_id and a.arcog_id = c.arcog_id and db_name = '%s' and name = '%s'",
+ sqlSafef(query, sizeof query, "select distinct a.arcog_id, a.anntation, c.class_id from arCogsDb.arcogDef a, arCogsDb.arcog b, arCogsDb.arcogFun c where a.arcog_id = b.arcog_id and a.arcog_id = c.arcog_id and db_name = '%s' and name = '%s'",
database, item);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
printf("arCOG: %s Code %s ",
row[0], row[0], genome, row[2], row[2]);
printf(" %s
\n", row[1]);
arcogCount++;
itemCount++;
}
sqlFreeResult(&sr);
if (arcogCount > 0)
printf("arCOG Gene Annotation
", genome, item);
}
@@ -724,105 +724,105 @@
printf("\n");
printf("\n");
printf("Protein Domain and Structure Information
| \n");
printf("\n");
/* interpro domains */
list = spExtDbAcc1List(spConn, spAcc, "InterPro");
if (list != NULL)
{
char query[256], **row, **row2;
struct sqlResult *sr, *sr2;
printf("InterPro Domains: ");
printf("",
spAcc);
printf("Graphical view of domain structure
");
- safef(query, sizeof(query),
+ sqlSafef(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];
safef(interPro, 128, "%s.interProXref", pdb);
if (hTableExists(database, interPro))
{
- safef(query, sizeof(query),
+ sqlSafef(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("", row[0]);
printf("%s - %s
\n", row[0], row2[0]);
}
sqlFreeResult(&sr2);
}
else
{
printf("", row[0]);
printf("%s - %s
\n", row[0], row[1]);
}
}
printf("
\n");
slFreeList(&list);
}
/* pfam domains */
list = spExtDbAcc1List(spConn, spAcc, "Pfam");
if (list != NULL)
{
printf("Pfam Domains:
");
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);
+ sqlSafef(query, sizeof(query), "select description from proteome.pfamDesc where pfamAC='%s'", el->name);
description = sqlQuickString(spConn, query);
if (description == NULL)
{
- safef(query, sizeof(query),
+ sqlSafef(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("",
el->name);
printf("%s - %s
\n", el->name, description);
freez(&description);
}
slFreeList(&list);
printf("
\n");
}
list = spExtDbAcc1List(spConn, spAcc, "PDB");
if (list != NULL)
{
char query[256], **row;
struct sqlResult *sr;
int column = 0, maxColumn=4, rowCount=0;
printf("Protein Data Bank (PDB) 3-D Structure
");
- safef(query, sizeof(query),
+ sqlSafef(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("\n");
while ((row = sqlNextRow(sr)) != NULL)
{
if (++column > maxColumn)
{
printf(" ");
column = 1;
if (rowCount == 0)
{
printf("| To conserve bandwidth, only the images from the first %d structures are shown.", maxColumn);
@@ -999,42 +999,42 @@
char **row;
char tempstring[255]="";
int flag, z, dashes, wordCount, rowOffset;
int start = cartInt(cart, "o"), num = 0, flag2=0;
float sequenceLength, dashlength=60;
genericHeader(tdb,trnaName);
dupe = cloneString(tdb->type);
wordCount = chopLine(dupe, words);
if (wordCount > 1)
num = atoi(words[1]);
if (num < 3) num = 3;
genericBedClick(conn, tdb, trnaName, start, num);
rowOffset = hOffsetPastBin(database, seqName, tdb->table);
-sprintf(query, "select * from %s where name = '%s'", tdb->table, trnaName);
+sqlSafef(query, sizeof query, "select * from %s where name = '%s'", tdb->table, trnaName);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
cb=bedLoadN(row+1, 6);
sequenceLength=(cb->chromEnd - cb->chromStart);
if(sequenceLength<0){ sequenceLength=sequenceLength*-1;}
sequenceLength=sequenceLength/3;
dashlength=sequenceLength/60;
/*Query the database for the extrainfo file for sargassoSea*/
conn=hAllocConn(database);/*sqlConnect(dupe);*/
-safef(tempstring, sizeof(tempstring),"select * from sargassoSeaXra where qname = '%s'", trnaName);
+sqlSafef(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(" \n |
\n
");
@@ -1206,31 +1206,31 @@
char query[512];
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr;
char *dupe, *words[16];
char **row;
int wordCount;
int rowOffset;
char* chrom = cartString(cart, "c");
genericHeader(tdb,trnaName);
dupe = cloneString(tdb->type);
wordCount = chopLine(dupe, words);
rowOffset = hOffsetPastBin(database, seqName, tdb->table);
-sprintf(query, "select * from %s where chrom = '%s' and name = '%s'", tdb->table, chrom, trnaName);
+sqlSafef(query, sizeof query, "select * from %s where chrom = '%s' and name = '%s'", tdb->table, chrom, trnaName);
sr = sqlGetResult(conn, query);
printf("\n");
while ((row = sqlNextRow(sr)) != NULL)
{
printf("\n");
printf("\n");
trna = tRNAsLoad(row+rowOffset);
printf("tRNA name: %s
\n",trna->name);
printf("tRNA Isotype: %s
\n",trna->aa);
printf("tRNA anticodon: %s
\n",trna->ac);
printf("tRNAscan-SE score: %.2f
\n",trna->trnaScore);
printf("Intron(s): %s
\n",trna->intron);
printf("Genomic size: %d nt
\n",trna->chromEnd-trna->chromStart);
printf("Position: "
@@ -1272,31 +1272,31 @@
{
struct snoRNAs *snorna;
char query[512];
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr;
char *dupe, *words[16];
char **row;
int wordCount;
int rowOffset;
genericHeader(tdb,snornaName);
dupe = cloneString(tdb->type);
wordCount = chopLine(dupe, words);
rowOffset = hOffsetPastBin(database, seqName, tdb->table);
-sprintf(query, "select * from %s where name = '%s'", tdb->table, snornaName);
+sqlSafef(query, sizeof query, "select * from %s where name = '%s'", tdb->table, snornaName);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
snorna = snoRNAsLoad(row+rowOffset);
printf("sRNA name: %s
\n",snorna->name);
printf("Snoscan score: %.2f
\n",snorna->snoScore);
printf("HMM snoRNA score: %.2f
\n",snorna->hmmScore);
printf("Predicted targets: %s
\n",snorna->targetList);
printf("Predicted guide interactions:%s \n",snorna->guideStr);
printf("Possible sRNA homolog(s): %s
\n",snorna->orthologs);
printf("
Genomic size: %d nt
\n",snorna->chromEnd-snorna->chromStart);
printf("Position: "
"",
@@ -1318,31 +1318,31 @@
struct gbRNAs *gbRna;
char query[512];
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr;
char *dupe, *words[16];
char **row;
int wordCount;
int rowOffset;
genericHeader(tdb,gbRnaName);
dupe = cloneString(tdb->type);
wordCount = chopLine(dupe, words);
rowOffset = hOffsetPastBin(database, seqName, tdb->table);
-sprintf(query, "select * from %s where name = '%s'", tdb->table, gbRnaName);
+sqlSafef(query, sizeof query, "select * from %s where name = '%s'", tdb->table, gbRnaName);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
gbRna = gbRNAsLoad(row+rowOffset);
printf("Genbank ncRNA name: %s
\n",gbRna->name);
printf("Product Description/Note: %s
\n",gbRna->product);
printf ("Intron(s): %s
\n",gbRna->intron);
printf("
Genomic size: %d nt
\n",gbRna->chromEnd-gbRna->chromStart);
printf("Position: "
"",
@@ -1360,31 +1360,31 @@
gbRNAsFree(&gbRna);
}
void doEasyGenes(struct trackDb *tdb, char *egName)
{
struct easyGene *egList = NULL, *eg;
char query[512];
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr;
char **row;
int rowOffset;
genericHeader(tdb,egName);
rowOffset = hOffsetPastBin(database, seqName, tdb->table);
-sprintf(query, "select * from %s where name = '%s'", tdb->table, egName);
+sqlSafef(query, sizeof query, "select * from %s where name = '%s'", tdb->table, egName);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
slAddTail(&egList,easyGeneLoad(row+rowOffset));
slReverse(&egList);
sqlFreeResult(&sr);
hFreeConn(&conn);
for (eg = egList; eg != NULL; eg = eg->next)
{
if (eg->genbank[0] == 'Y')
printf("\n");
else
printf("\n");
printf("Item: %s
\n",eg->name);
printf("Feature identifier: %s
\n",eg->feat);
printf("Start codon: %s
\n",eg->startCodon);
@@ -1418,54 +1418,54 @@
char **row;
char tempstring[255]="";
int flag, z, dashes, wordCount, rowOffset, currentGI=0;
int start = cartInt(cart, "o"), num = 0, flag2=0;
float sequenceLength, dashlength=60;
genericHeader(tdb,trnaName);
dupe = cloneString(tdb->type);
wordCount = chopLine(dupe, words);
if (wordCount > 1)
num = atoi(words[1]);
if (num < 3) num = 3;
genericBedClick(conn, tdb, trnaName, start, num);
rowOffset = hOffsetPastBin(database, seqName, tdb->table);
-sprintf(query, "select * from %s where name = '%s'", tdb->table, trnaName);
+sqlSafef(query, sizeof query, "select * from %s where name = '%s'", tdb->table, trnaName);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
cb=codeBlastLoad(row);
}
sequenceLength=(cb->chromEnd - cb->chromStart);
if(sequenceLength<0){ sequenceLength=sequenceLength*-1;}
sequenceLength=sequenceLength/3;
dashlength=sequenceLength/60;
conn=hAllocConn(database);/*sqlConnect(dupe);*/
-sprintf(query, "select * from gbProtCodePep where name = '%s'", trnaName);
+sqlSafef(query, sizeof 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);
+sqlSafef(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(
"
Query NCBI Blast",pp->seq);
/*Print out table with Blast information*/
@@ -1754,68 +1754,68 @@
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'",
+ sqlSafef(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
\n");
}
sqlFreeResult(&sr);
}
if (extraTable != NULL && hTableExists(database, extraTable))
{
conn = hAllocConn(database);
- sprintf(query, "select * from %s where name = '%s'", extraTable, item);
+ sqlSafef(query, sizeof query, "select * from %s where name = '%s'", extraTable, item);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
minGeneInfoStaticLoad(row, &ginfo);
printf("Product: %s
\n", ginfo.product);
printf("Note: %s
\n", ginfo.note);
}
sqlFreeResult(&sr);
}
if (hTableExists(database, "COG"))
{
conn = hAllocConn(database);
- sprintf(query, "select * from COG where name = '%s'", item);
+ sqlSafef(query, sizeof 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; xCOG: %s INFO: %s
\n", COGXra->name, COGXra->info);
}
sqlFreeResult(&sr2);
hFreeConn(&conn2);
}
}
}
}
printTrackHtml(tdb);
hFreeConn(&conn);
@@ -1828,31 +1828,31 @@
char query[512];
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr;
char *dupe, *words[16];
char **row;
int wordCount;
int start = cartInt(cart, "o"), num = 0;
genericHeader(tdb,opName);
dupe = cloneString(tdb->type);
wordCount = chopLine(dupe, words);
if (wordCount > 1)
num = atoi(words[1]);
if (num < 3) num = 3;
genericBedClick(conn, tdb, opName, start, num);
-sprintf(query, "select * from %sInfo where name = '%s'", tdb->table, opName);
+sqlSafef(query, sizeof query, "select * from %sInfo where name = '%s'", tdb->table, opName);
sr = sqlGetResult(conn, query);*/
/* Make the operon table like on the TIGR web page. */
/*if ((row = sqlNextRow(sr)) != NULL)
{
int i,j;
char *infos[30];
op = tigrOperonLoad(row);
chopCommas(op->info,infos);
printf("\n \n");
for (i = 0; i <= op->size; i++)
{
printf(" ");
for (j = 0; j <= op->size; j++)
{
printf("");
@@ -1891,31 +1891,31 @@
struct tigrCmrGene *tigr;
char query[512];
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr;
char *dupe, *words[16];
char **row;
int wordCount;
int rowOffset;
/* int start = cartInt(cart, "o"), num = 0; */
genericHeader(tdb,tigrName);
dupe = cloneString(tdb->type);
wordCount = chopLine(dupe, words);
rowOffset = hOffsetPastBin(database, seqName, tdb->table);
- sprintf(query, "select * from %s where name = '%s'", tdb->table, tigrName);
+ sqlSafef(query, sizeof query, "select * from %s where name = '%s'", tdb->table, tigrName);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
tigr = tigrCmrGeneLoad(row);
if (tigr != NULL)
{
printf("TIGR locus name: %s
\n",tigrName);
printf("TIGR gene description: %s
\n",tigr->tigrCommon);
printf("Alternate TIGR gene name: ");
if (strlen(tigr->tigrGene) >0) {
printf("%s
\n",tigr->tigrGene);
}
else {
printf("None
");
}
@@ -1955,31 +1955,31 @@
{
struct jgiGene *jgi;
char query[512];
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr;
char *dupe, *words[16];
char **row;
int wordCount;
int rowOffset;
genericHeader(tdb,jgiName);
dupe = cloneString(tdb->type);
wordCount = chopLine(dupe, words);
rowOffset = hOffsetPastBin(database, seqName, tdb->table);
- sprintf(query, "select * from %s where name = '%s'", tdb->table, jgiName);
+ sqlSafef(query, sizeof query, "select * from %s where name = '%s'", tdb->table, jgiName);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
jgi = jgiGeneLoad(row+rowOffset);
printf("JGI locus name: %s
\n",jgiName);
printf("JGI gene symbol: %s
\n",jgi->jgiSymbol);
printf("JGI gene description: %s
\n",jgi->jgiDescription);
printf("JGI gene id: "
"",
jgi->jgiGeneId);
printf("%s
\n", jgi->jgiGeneId);
printf("GC content: %.0f %%
\n",jgi->jgiGc);
printf("
Position: "
"",
@@ -2006,41 +2006,41 @@
struct sqlResult *sr;
char *dupe, *words[16];
char **row;
int wordCount;
int rowOffset;
char *description;
int start = cartInt(cart, "o");
spConn = sqlConnect(UNIPROT_DB_NAME);
genericHeader(tdb,hitName);
dupe = cloneString(tdb->type);
wordCount = chopLine(dupe, words);
rowOffset = hOffsetPastBin(database, seqName, tdb->table);
- sprintf(query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", tdb->table, hitName,seqName,start);
+ sqlSafef(query, sizeof query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", tdb->table, hitName,seqName,start);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
pfamHit = lowelabPfamHitsLoad(row+rowOffset);
- safef(query, sizeof(query), "select description from proteome.pfamDesc where pfamAC='%s'", pfamHit->pfamAC);
+ sqlSafef(query, sizeof(query), "select description from proteome.pfamDesc where pfamAC='%s'", pfamHit->pfamAC);
if (!sqlTableExists(spConn,"proteome.pfamDesc"))
{
- safef(query, sizeof(query),
+ sqlSafef(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("",
pfamHit->pfamAC );
printf("%s - %s
\n", pfamHit->pfamAC, description);
freez(&description);
@@ -2083,31 +2083,31 @@
char *dupe, *words[16];
char **row;
int wordCount;
int rowOffset;
int bedSize = 0;
genericHeader(tdb, tigrOperonName);
dupe = cloneString(tdb->type);
wordCount = chopLine(dupe, words);
if (wordCount > 1)
bedSize = atoi(words[1]);
if (bedSize < 3) bedSize = 3;
rowOffset = hOffsetPastBin(database, seqName, tdb->table);
- sprintf(query, "select * from %s where name = '%s'", tdb->table, tigrOperonName);
+ sqlSafef(query, sizeof query, "select * from %s where name = '%s'", tdb->table, tigrOperonName);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
tigrOperon = bedLoadN(row+rowOffset, bedSize);
printf("Operon name: %s
\n",tigrOperonName);
printf("
Position: "
"",
hgTracksPathAndSettings(), database, tigrOperon->chrom, tigrOperon->chromStart + 1, tigrOperon->chromEnd);
printf("%s:%d-%d
\n", tigrOperon->chrom, tigrOperon->chromStart + 1, tigrOperon->chromEnd);
printf("Strand: %s
\n", tigrOperon->strand);
printf("Genomic size: %d nt
\n", (tigrOperon->chromEnd - tigrOperon->chromStart));
if (tigrOperon->next != NULL)
printf("
\n");
}
@@ -2118,31 +2118,31 @@
/* Print table */
printf("", HG_COL_BORDER);
printf("\n");
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);
+ sqlSafef(query, sizeof 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;
}
@@ -2176,31 +2176,31 @@
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);
+ sqlSafef(query, sizeof 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");
}
@@ -2211,31 +2211,31 @@
/* Print table */
printf("", HG_COL_BORDER);
printf("\n");
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);
+ sqlSafef(query, sizeof 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;
}
@@ -2270,31 +2270,31 @@
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",
+ sqlSafef(query, sizeof 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 */
{
@@ -2304,55 +2304,55 @@
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",
+ sqlSafef(query, sizeof 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",
+ sqlSafef(query, sizeof 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'",
+ sqlSafef(query, sizeof 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
@@ -2383,55 +2383,55 @@
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"));
+ sqlSafef(query, sizeof 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);
+ sqlSafef(query, sizeof 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 */
{
@@ -2500,82 +2500,82 @@
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]);
+ sqlSafef(query, sizeof 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'",
+ sqlSafef(query, sizeof 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]);
+ sqlSafef(query, sizeof 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]);
+ sqlSafef(query, sizeof 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
@@ -2616,31 +2616,31 @@
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'");
+ sqlSafef(query, sizeof 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);
@@ -2657,31 +2657,31 @@
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'");
+ sqlSafef(query, sizeof 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);
@@ -2699,55 +2699,55 @@
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",
+ sqlSafef(query, sizeof 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",
+ sqlSafef(query, sizeof 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'",
+ sqlSafef(query, sizeof 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
@@ -2788,42 +2788,42 @@
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);
+ sqlSafef(query, sizeof 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);
+ sqlSafef(query, sizeof 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)) ||
@@ -2905,31 +2905,31 @@
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'",
+ sqlSafef(query, sizeof 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);
}
@@ -3126,31 +3126,31 @@
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);
+ sqlSafef(query, sizeof 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)
@@ -3181,52 +3181,52 @@
/* 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);
+ sqlSafef(query, sizeof 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 = '-'",
+ sqlSafef(query, sizeof query, "%s union ", query);
+ sqlSafef(query, sizeof 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);
+ sqlSafef(query, sizeof 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);
+ sqlSafef(query, sizeof 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 = '+'",
+ sqlSafef(query, sizeof query, "%s union ", query);
+ sqlSafef(query, sizeof 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);
+ sqlSafef(query, sizeof 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);
@@ -3321,31 +3321,31 @@
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);
+ sqlSafef(query, sizeof 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("
");
@@ -3412,52 +3412,52 @@
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);
+ sqlSafef(query, sizeof query, "select * from mgCommonDb.arcogdesc where name = '%s'", itemName);
+ //sqlSafef(query, sizeof 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);
+ sqlSafef(query, sizeof 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));
@@ -3484,31 +3484,31 @@
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);
+ sqlSafef(query, sizeof 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");
@@ -3526,51 +3526,51 @@
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);
+ sqlSafef(query, sizeof query, "select * from mgCommonDb.cddDesc where accession = '%s'", itemName);
+ //sqlSafef(query, sizeof 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);
+ sqlSafef(query, sizeof 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);
@@ -3594,31 +3594,31 @@
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);
+ sqlSafef(query, sizeof 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);
@@ -3655,31 +3655,31 @@
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);
+ sqlSafef(query, sizeof 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);
@@ -3708,31 +3708,31 @@
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);
+ sqlSafef(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)
| | | | | |