src/hg/protein/kgAliasM/kgAliasM.c 1.9

Index: src/hg/protein/kgAliasM/kgAliasM.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/protein/kgAliasM/kgAliasM.c,v
retrieving revision 1.8
retrieving revision 1.9
diff -b -B -U 1000000 -r1.8 -r1.9
--- src/hg/protein/kgAliasM/kgAliasM.c	3 Sep 2008 19:20:56 -0000	1.8
+++ src/hg/protein/kgAliasM/kgAliasM.c	23 Sep 2009 18:42:23 -0000	1.9
@@ -1,148 +1,148 @@
 /* kgAliasM - generate alias list table (the mRNA part, there is another protein part) */
 #include "common.h"
 #include "hCommon.h"
 #include "hdb.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "kgAliasM - create gene alias (mRNA part) .tab files "
   "usage:\n"
   "   kgAliasM xxxx yyyy\n"
   "            xxxx is genome  database name\n"
   "            yyyy is protein database name \n"
   "example: kgAliasM hg15 proteins0405\n");
 }
 
 int main(int argc, char *argv[])
 {
 struct sqlConnection *conn, *conn2;
 
 char query2[256];
 struct sqlResult *sr2;
 char **row2;
     
 char *chp0, *chp;
 char *kgID;
 FILE *o1, *o2;
 char cond_str[256];
 char *database;
 char *proteinDB;
 boolean doingAlias, bothDone;
 
 char *answer;
 char *symbol, *alias, *aliases;
 
 if (argc != 3) usage();
 database  = cloneString(argv[1]);
 proteinDB = cloneString(argv[2]);
 
 conn = hAllocConn(database);
 conn2= hAllocConn(database);
 o1 = fopen("j.dat", "w");
 o2 = fopen("jj.dat", "w");
 
 doingAlias = TRUE;
 bothDone   = FALSE;
 
 while (!bothDone)
     {
     if (doingAlias)
 	{
     	sprintf(query2,"select symbol, aliases from %s.hgnc;", proteinDB);
 	}
     else
 	{
         sprintf(query2,"select symbol, prvSymbols from %s.hgnc;", proteinDB);
     	}
     
     sr2 = sqlMustGetResult(conn2, query2);
     row2 = sqlNextRow(sr2);
     while (row2 != NULL)
 	{
 	symbol		= row2[0];
 	aliases		= row2[1];
 
 	if ( (symbol  != NULL) && (strlen(symbol) != 0) )
 	    {
             sprintf(cond_str, "geneSymbol = '%s'", symbol);
             answer = sqlGetField(database, "kgXref", "kgID", cond_str);
 	    if (answer != NULL)
 		{
 		kgID = strdup(answer);
 		fprintf(o2, "%s\t%s\n", kgID, symbol);
 		}
 	    if ( (aliases  != NULL) && (strlen(aliases) != 0) && (answer != NULL) )
 		{
 		kgID = strdup(answer);
     
 		chp0 = aliases; 
 	    	while (chp0 != NULL)
 		    {
 		    while (*chp0 == ' ') chp0++;
 		    chp = strstr(chp0, ",");
 		    if (chp == NULL)
 			{
 			alias = strdup(chp0);
 			
 			/* get rid of quote character in some aliases */
 			if (*alias == '"') 
 			    {
 			    *(alias + strlen(alias) - 1) = '\0';
 			    alias++;
 			    printf("%s\n", alias);fflush(stdout);
 			    }
 			chp0 = NULL;
 			}
 		    else
 			{
 			*chp = '\0';
 			
 			/* get rid of quote character in some aliases */
 			if (*chp0 == '"') 
 			    {
 			    *(chp0 + strlen(chp0) - 1) = '\0';
 			    chp0++;
 			    printf("%s\n", chp0);fflush(stdout);
 			    }
 			alias = strdup(chp0);
 			chp0 = chp+1;
 			}
 		    if (kgID != NULL)
 			{
 			fprintf(o1, "%s\t%s\t%s\n", kgID, symbol, alias);
 			fprintf(o2, "%s\t%s\n", kgID, alias);
 			}
 		    }
 		}
 	    }
 	row2 = sqlNextRow(sr2);
 	}
     sqlFreeResult(&sr2);
 
     if (doingAlias) 
 	{
 	doingAlias = FALSE;
 	}
     else
 	{
 	bothDone = TRUE;
 	}
     }
 fclose(o1);
 fclose(o2);
 
 /* geneAlias.tab has 3 columns, the 2nd is HUGO.symbol 
    and 3rd contains aliases and withdraws */
 
-system("cat  j.dat|sort|uniq  >geneAlias.tab");
+mustSystem("cat  j.dat|sort|uniq  >geneAlias.tab");
 
 /*  kgAliasM.tab has 2 columns, all entries from HUGO.symbol, HUGO.aliass, 
     and HUGO.withdraws are listed in the 2nd column. */
-system("cat jj.dat|sort|uniq  >kgAliasM.tab");
-system("rm j.dat");
-system("rm jj.dat");
+mustSystem("cat jj.dat|sort|uniq  >kgAliasM.tab");
+mustSystem("rm j.dat");
+mustSystem("rm jj.dat");
     
 return(0);
 }