src/hg/protein/kgProtAliasNCBI/kgProtAliasNCBI.c 1.7

1.7 2009/09/23 18:42:24 angie
Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
Index: src/hg/protein/kgProtAliasNCBI/kgProtAliasNCBI.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/protein/kgProtAliasNCBI/kgProtAliasNCBI.c,v
retrieving revision 1.6
retrieving revision 1.7
diff -b -B -U 1000000 -r1.6 -r1.7
--- src/hg/protein/kgProtAliasNCBI/kgProtAliasNCBI.c	3 Sep 2008 19:20:58 -0000	1.6
+++ src/hg/protein/kgProtAliasNCBI/kgProtAliasNCBI.c	23 Sep 2009 18:42:24 -0000	1.7
@@ -1,111 +1,111 @@
 /* kgProtAliasNCBI - generate alias list table for NCBI protein AC */
 #include "common.h"
 #include "hCommon.h"
 #include "hdb.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "kgProtAliasNCBI - create gene alias (mRNA part) .tab files "
   "usage:\n"
   "   kgProtAliasNCBI <DB> <RO_DB>\n"
   "            <DB> is knownGene DB under construction\n"
   "            <RO_DB> is read only target genome database\n"
   "example: kgProtAliasNCBI kgDB hg16\n");
 }
 
 int main(int argc, char *argv[])
 {
 struct sqlConnection *conn, *conn2;
 
 char query[256], query2[256];
 struct sqlResult *sr, *sr2;
 char **row, **row2;
  
 char *chp;
 char *kgID;
 FILE *o2;
 char cond_str[256];
 char *database;
 char *ro_db;
 
 char *proteinID;
 char *proteinAC;
 
 if (argc != 3) usage();
 database  = cloneString(argv[1]);
 ro_db  = cloneString(argv[2]);
 
 conn = hAllocConn(database);
 conn2= hAllocConn(database);
 o2 = fopen("jj.dat", "w");
 
 sprintf(query2,"select name, proteinID from %s.knownGene;", database);
 sr2 = sqlMustGetResult(conn2, query2);
 row2 = sqlNextRow(sr2);
 while (row2 != NULL)
     {
     kgID = row2[0];
     proteinID = row2[1];
 
     // get RefSeq protein AC numbers (NP_xxxxx) if they exist
     sprintf(cond_str, "kgID='%s'", kgID);
     proteinAC = sqlGetField(database, "kgXref", "protAcc", cond_str);
     if (proteinAC != NULL)
 	{
 	if (strlen(proteinAC) > 0)
 	    {
 	    fprintf(o2, "%s\t%s\t%s\n", kgID, proteinID, proteinAC);
 	    }
 	}
 
     // get Genbank protein accession numbers
     if (strstr(kgID, "NM_") != NULL)
 	{
 	sprintf(query,"select protAcc from %s.refLink where mrnaAcc = '%s';", ro_db, kgID);
 	sr = sqlMustGetResult(conn, query);
 	row = sqlNextRow(sr);
 	while (row != NULL)
     	    {
     	    proteinAC = row[0];
 	    fprintf(o2, "%s\t%s\t%s\n", kgID, proteinID, proteinAC);
 	    row = sqlNextRow(sr);
 	    }
     	sqlFreeResult(&sr);
 	}
     else
 	{
 	sprintf(query,"select proteinAC from %sTemp.locus2Acc0 where gbAC like '%s%c';", database, kgID, '%');
 	sr = sqlMustGetResult(conn, query);
 	row = sqlNextRow(sr);
 	while (row != NULL)
     	    {
     	    proteinAC = row[0];
 
 	    chp = strstr(proteinAC, ".");
 	    if (chp != NULL)
 		{
 		*chp = '\0';
 		}
 	    if (proteinAC[0] != '-')
 		{
 		fprintf(o2, "%s\t%s\t%s\n", kgID, proteinID, proteinAC);
 		}
 	    row = sqlNextRow(sr);
 	    }
     	sqlFreeResult(&sr);
 	}
     row2 = sqlNextRow(sr2);
     }
 sqlFreeResult(&sr2);
 fclose(o2);
 hFreeConn(&conn);
 hFreeConn(&conn2);
 
-system("cat jj.dat|sort|uniq  >kgProtAliasNCBI.tab");
-system("rm jj.dat");
+mustSystem("cat jj.dat|sort|uniq  >kgProtAliasNCBI.tab");
+mustSystem("rm jj.dat");
     
 return(0);
 }