21a6584e8ecdbba6d802ab30f3ec564c08b7dcc3 galt Sat Jun 29 02:11:16 2013 -0700 fixing callers of sqlGetField to use sqlSafeFrag diff --git src/hg/dnaGene/dnaGene.c src/hg/dnaGene/dnaGene.c index ae040a1..7d79622 100644 --- src/hg/dnaGene/dnaGene.c +++ src/hg/dnaGene/dnaGene.c @@ -1,269 +1,269 @@ /* dnaGene - collect DNA based RefSeq genes. To be used by Known Genes track */ #include "common.h" #include "hCommon.h" #include "hdb.h" void usage() /* Explain usage and exit. */ { errAbort( "dnaGene - collect DNA based RefSeq genes. To be used by Known Genes track.\n" "usage:\n" " dnaGene xxxx yyyy\n" " xxxx is the genome database name\n" " yyyy is the protein database name\n" "example: dnaGene hg15 proteins0405\n"); } char *dbName; char *genomeReadOnly; char tempDbName[40]; /* check if a locusID points to a KG mRNA */ boolean checkMrna(char *locusID) { struct sqlConnection *conn, *conn2; char query2[256]; struct sqlResult *sr2; char **row2; boolean result; char cond_str[256]; char *chp; char *gbAC; char *gbID; char *knownGeneID; conn = hAllocConn(); conn2 = hAllocConn(); result = FALSE; sqlSafef(query2, sizeof query2, "select gbAC from %s.locus2Acc0 where locusID=%s and seqType='m';", tempDbName, locusID); sr2 = sqlMustGetResult(conn2, query2); row2 = sqlNextRow(sr2); while (row2 != NULL) { gbAC = row2[0]; gbID = strdup(gbAC); chp = strstr(gbID, "."); if (chp != NULL) *chp = '\0'; - sprintf(cond_str, "name = '%s';", gbID); + sqlSafefFrag(cond_str, sizeof cond_str, "name = '%s';", gbID); knownGeneID = sqlGetField(dbName, "knownGene", "name", cond_str); if (knownGeneID != NULL) { result=TRUE; break; } row2 = sqlNextRow(sr2); } hFreeConn(&conn); hFreeConn(&conn2); sqlFreeResult(&sr2); return(result); } int main(int argc, char *argv[]) { struct sqlConnection *conn, *conn2, *conn3, *conn5; char query2[256], query3[256], query5[256]; struct sqlResult *sr2, *sr3, *sr5; char **row2, **row3, **row5; char cond_str[512]; char *chp; FILE *o1, *o2; boolean hasKGmRNA; char *proteinDisplayID; char *gbAC; char *locusID; /* LocusLink ID */ char *refAC; /* Refseq accession.version */ char *giNCBI2; /* NCBI gi for the protein record associated with the CDS */ char *revStatus; /* review status */ char *proteinAC2; /* protein accession.version */ char *taxID2; /* tax id */ char *protDbName; char *refSeq; char *name, *chrom, *strand, *txStart, *txEnd, *cdsStart, *cdsEnd, *exonCount, *exonStarts, *exonEnds; char *gseq, *hseq, *swissprot; int alignmentID=0; if (argc != 4) usage(); dbName = argv[1]; protDbName = argv[2]; genomeReadOnly = argv[3]; sprintf(tempDbName, "%sTemp", dbName); hSetDb(genomeReadOnly); conn = hAllocConn(); conn2= hAllocConn(); conn3= hAllocConn(); conn5= hAllocConn(); o1 = fopen("dnaGene.tab", "w"); o2 = fopen("j.dat", "w"); // scan all RefSeq entries sqlSafef(query2, sizeof query2, "select * from %s.locus2Ref0;", tempDbName); sr2 = sqlMustGetResult(conn2, query2); row2 = sqlNextRow(sr2); while (row2 != NULL) { locusID = row2[0]; refAC = row2[1]; giNCBI2 = row2[2]; revStatus = row2[3]; proteinAC2 = row2[4]; taxID2 = row2[5]; refSeq = strdup(refAC); chp = strstr(refAC, "."); if (chp != NULL) *chp = '\0'; proteinDisplayID = NULL; /* check if the locusID of this RefSeq points to a KG mRNA */ hasKGmRNA = checkMrna(locusID); /* check if this RefSeq has 'g' type sequence(s) referenced */ - sprintf(cond_str, "locusID=%s and seqType='g';", locusID); + sqlSafefFrag(cond_str, sizeof cond_str, "locusID=%s and seqType='g';", locusID); gseq = sqlGetField(tempDbName, "locus2Acc0", "gbac", cond_str); /* process only 'g' type record which does not have corresponding KG entry */ if ((!hasKGmRNA) && (gseq != NULL)) { - sprintf(cond_str, "name='%s'", refAC); + sqlSafefFrag(cond_str, sizeof cond_str, "name='%s'", refAC); hseq = sqlGetField(genomeReadOnly, "refGene", "name", cond_str); if (hseq != NULL) { - sprintf(cond_str, "refseq='%s';", refAC); + sqlSafefFrag(cond_str, sizeof cond_str, "refseq='%s';", refAC); swissprot = sqlGetField(protDbName, "hugo", "swissprot", cond_str); if (swissprot != NULL) { if (strlen(swissprot) >0) { // HUGO has an entry with swissprot ID, get display ID - sprintf(cond_str, "accession='%s';", swissprot); + sqlSafefFrag(cond_str, sizeof cond_str, "accession='%s';", swissprot); proteinDisplayID = sqlGetField(protDbName, "spXref2", "displayID", cond_str); if (proteinDisplayID == NULL) { fprintf(stderr, "%s: a HUGO.swissprot, ", swissprot); fprintf(stderr, "but not a SP Primary AC.\n"); fflush(stdout); } } else { //printf("HGNC has a non-NULL but empty swissprot field "); //printf("for %s\n", refAC);fflush(stdout); } } // not finding it in HUGO does not mean not a valid one for sure if (proteinDisplayID == NULL) { // get gbAC and check if spXref2 actually has it sqlSafef(query3, sizeof query3, "select gbAC from %s.locus2Acc0 where locusID=%s;", tempDbName, locusID); sr3 = sqlMustGetResult(conn3, query3); row3 = sqlNextRow(sr3); while (row3 != NULL) { gbAC = row3[0]; chp = strstr(gbAC, "."); if (chp != NULL) *chp = '\0'; - sprintf(cond_str, "extAC='%s'", gbAC); + sqlSafefFrag(cond_str, sizeof cond_str, "extAC='%s'", gbAC); proteinDisplayID = sqlGetField(protDbName, "spXref2", "displayID", cond_str); if (proteinDisplayID == NULL) { //printf("%s %s is in refGene, but has no SWISS-PROT.\n", // locusID, refAC); //fflush(stdout); } else { //printf("%s %s got 2nd chance.\n", refAC, gbAC);fflush(stdout); break; } row3 = sqlNextRow(sr3); } sqlFreeResult(&sr3); } if (proteinDisplayID != NULL) { // generate KG entry sqlSafef(query5, sizeof query5, "select * from %s.refGene where name='%s';", genomeReadOnly, refAC); sr5 = sqlMustGetResult(conn5, query5); row5 = sqlNextRow(sr5); while (row5 != NULL) { name = row5[0]; chrom = row5[1]; strand = row5[2]; txStart = row5[3]; txEnd = row5[4]; cdsStart = row5[5]; cdsEnd = row5[6]; exonCount = row5[7]; exonStarts = row5[8]; exonEnds = row5[9]; fprintf(o1, "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\tdna%d\n", name, chrom, strand, txStart, txEnd, cdsStart, cdsEnd, exonCount, exonStarts, exonEnds, proteinDisplayID, alignmentID); alignmentID++; fprintf(o2, "%s\t%c\t%s\n", name, 'g', proteinAC2); row5 = sqlNextRow(sr5); } sqlFreeResult(&sr5); } } } row2 = sqlNextRow(sr2); } fclose(o1); fclose(o2); sqlFreeResult(&sr2); hFreeConn(&conn); hFreeConn(&conn2); hFreeConn(&conn5); system("sort j.dat|uniq >dnaLink.tab"); system("rm j.dat"); return(0); }