src/hg/protein/pbHgnc/pbHgnc.c 1.6

Index: src/hg/protein/pbHgnc/pbHgnc.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/protein/pbHgnc/pbHgnc.c,v
retrieving revision 1.5
retrieving revision 1.6
diff -b -B -U 1000000 -r1.5 -r1.6
--- src/hg/protein/pbHgnc/pbHgnc.c	3 Sep 2008 19:21:00 -0000	1.5
+++ src/hg/protein/pbHgnc/pbHgnc.c	23 Sep 2009 18:42:25 -0000	1.6
@@ -1,119 +1,119 @@
 /* pbHgnc - process HGNC data */
 #include "common.h"
 #include "hCommon.h"
 #include "hdb.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "pbHgnc - process HGNC data\n"
   "usage:\n"
   "   pbHgnc yymmdd\n"
   "      yymmdd is the release date of SWISS-PROT data\n"
   "example: pbHgnc 051015\n");
 }
 
 int main(int argc, char *argv[])
 {
 struct sqlConnection *conn2, *conn3;
   
 char query2[256];
 struct sqlResult *sr2;
 char **row2;
 
 char *proteinDataDate;
  
 FILE   *o2;
 char *entrez;
 
 char *chp;
 char *hgncId, *name, *symbol, *refSeqIds, *uniProt;
 int j;
 char *locusType;
 
 char *refseq;
 boolean gotRefseq;
 
 if (argc != 2) usage();
 proteinDataDate = argv[1];
    
 o2 = fopen("j.dat", "w");
 conn2= hAllocConn(hDefaultDb());
 conn3= hAllocConn(hDefaultDb());
 
 sprintf(query2,
 	"select hgncId, symbol, name, refSeqMapped, refSeqIds, uniProt, entrezMapped, locusType from proteins%s.hgnc where status not like '%cWithdrawn%c'", 
 	proteinDataDate, '%', '%');
 sr2 = sqlMustGetResult(conn2, query2);
 row2 = sqlNextRow(sr2);
 while (row2 != NULL)
     {
     j=0;
     hgncId 	= row2[j];j++;
     symbol 	= row2[j];j++;
     name	= row2[j];j++;
     refseq 	= row2[j];j++;
     refSeqIds 	= row2[j];j++;
     uniProt   	= row2[j];j++;
     entrez   	= row2[j];j++;
     locusType  	= row2[j];j++;
     
     chp = strstr(hgncId, "HGNC:");
     hgncId = chp+5;
 
     gotRefseq = FALSE;
 
     /* process refSeqMapped first */
 
     if (!sameWord(refseq, ""))
     	{
     	fprintf(o2, "%s\t%s\t%s\t%s\t%s\t%s\n", symbol, refseq, uniProt, hgncId, entrez, name);
 	gotRefseq = TRUE;
 	}
 
     /* process refSeqIds next */
 
     chp = strstr(refSeqIds, ",");
     if (chp != NULL) 
     	{
     	*chp = '\0';
         while (chp != NULL)
 	    {    
 	    fprintf(o2, "%s\t%s\t%s\t%s\t%s\t%s\n", symbol, refseq, uniProt, hgncId, entrez, name);
 	    chp++;
  	    while (*chp == ' ') chp++;
 	    refseq = chp;
             chp = strstr(refseq, ",");
 	    if (chp != NULL) *chp = '\0';
 	    }
 	fprintf(o2, "%s\t%s\t%s\t%s\t%s\t%s\n", symbol, refseq, uniProt, hgncId, entrez, name);
 	gotRefseq = TRUE;
 	}
     else
     	{
 	if (!sameWord(refseq,""))
 	    {
 	    fprintf(o2, "%s\t%s\t%s\t%s\t%s\t%s\n", symbol, refseq, uniProt, hgncId, entrez, name);
 	    }
 	else
 	    {
 	    /* output the record if no RefSeq in either refSeqIds or refSeqMapped */
 	    if (!gotRefseq)
 	    	{
 	    	fprintf(o2, 
 		"%s\t%s\t%s\t%s\t%s\t%s\n", symbol, refseq, uniProt, hgncId, entrez, name);
 		}
 	    }
 	}
     row2 = sqlNextRow(sr2);
     }
 sqlFreeResult(&sr2);
 
 hFreeConn(&conn2);
 fclose(o2);
     
-system("cat j.dat |sort -u >hgncXref.tab");
+mustSystem("cat j.dat |sort -u >hgncXref.tab");
 return(0);
 }