src/hg/protein/spm3/spm3.c 1.5

Index: src/hg/protein/spm3/spm3.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/protein/spm3/spm3.c,v
retrieving revision 1.4
retrieving revision 1.5
diff -b -B -U 1000000 -r1.4 -r1.5
--- src/hg/protein/spm3/spm3.c	3 Sep 2008 19:21:03 -0000	1.4
+++ src/hg/protein/spm3/spm3.c	23 Sep 2009 18:42:25 -0000	1.5
@@ -1,116 +1,116 @@
 /* spm3 - from all mRNAs in a genome (e.g. rn3) referenced by SWISS-PROT 
           generate a list of proteins and a list of protein/mRNA pairs */
 #include "common.h"
 #include "hCommon.h"
 #include "hdb.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "spm3 - from all mRNAs in a genome (e.g. rn3) referenced by SWISS-PROT \n"
   "       generate a list of proteins and a list of protein/mRNA pairs.\n"
   "usage:\n"
   "   spm3 xxxx yyyy\n"
   "      xxxx is the release date of SWISS-PROT data\n"
   "      yyyy is the genome underconstructino\n"
   "example: spm3 070403 rn3\n");
 }
 
 int main(int argc, char *argv[])
 {
 struct sqlConnection *conn2, *conn3;
  
 char query2[256], query3[256];
 struct sqlResult *sr2, *sr3;
 char **row2, **row3;
 
 char *accession;
 char *displayID;
 char *division;
 char *extDB;
 char *extAC;
 
 char *proteinDataDate;
 char *genomeRelease;
  
 FILE   *o2, *o3;
 char *name, *chrom, *strand, *txStart, *txEnd, *cdsStart, *cdsEnd,
      *exonCount, *exonStarts, *exonEnds;
 
 char *bioDBID, *bioentryID;
 
 if (argc != 3) usage();
 proteinDataDate = argv[1];
 genomeRelease   = argv[2];
    
 o2 = fopen("jj.dat", "w");
 o3 = fopen("j.dat", "w");
 conn2= hAllocConn(hDefaultDb());
 conn3= hAllocConn(hDefaultDb());
 	
 sprintf(query2,"select * from %sTemp.refGene;", genomeRelease);
 sr2 = sqlMustGetResult(conn2, query2);
 row2 = sqlNextRow(sr2);
 while (row2 != NULL)
     {
     name 	= row2[0];
     chrom 	= row2[1];
     strand	= row2[2];
     txStart 	= row2[3];
     txEnd   	= row2[4];
     cdsStart	= row2[5]; 
     cdsEnd	= row2[6];
     exonCount = row2[7]; 
     exonStarts= row2[8]; 
     exonEnds  = row2[9];	
 
     sprintf(query3, "select * from proteins%s.spXref2 where extAC='%s' and extDB='EMBL';",
     	    proteinDataDate, name);
 
     sr3 = sqlMustGetResult(conn3, query3);
     row3 = sqlNextRow(sr3);
 	      
     while (row3 != NULL)
 	{
    	accession = row3[0];
        	displayID = row3[1];	 
         division  = row3[2];  
 	extDB	  = row3[3];     
 	extAC	  = row3[4];
 	bioentryID= row3[5];
 	bioDBID	  = row3[6];
 
 	if (! ( (strcmp(bioDBID, "1") == 0) || 
 		(strcmp(bioDBID, "2") == 0) || 
 		(strcmp(bioDBID, "3") == 0)
 	      )
 	   )
 	    {
 	    printf("non-recognized bioDB index %s encountered.\n", bioDBID);
 	    printf("displayId=%s bioDBID=%s\n", displayID, bioDBID);
 	    fflush(stdout);
 	    exit(1);
 	    }
 
 	fprintf(o2, "%s\n", displayID);
 	fprintf(o3, "%s\t%s\n", displayID, extAC);
 	row3 = sqlNextRow(sr3);
 	}
     sqlFreeResult(&sr3);
     row2 = sqlNextRow(sr2);
     }
 sqlFreeResult(&sr2);
 
 hFreeConn(&conn2);
 hFreeConn(&conn3);
 fclose(o2);
 fclose(o3);
     
-system("cat j.dat |sort|uniq >proteinMrna.tab");
-system("cat jj.dat|sort|uniq >protein.lis");
-system("rm j.dat");
-system("rm jj.dat");
+mustSystem("cat j.dat |sort|uniq >proteinMrna.tab");
+mustSystem("cat jj.dat|sort|uniq >protein.lis");
+mustSystem("rm j.dat");
+mustSystem("rm jj.dat");
 return(0);
 }