src/hg/protein/kgPepMrna/kgPepMrna.c 1.5

Index: src/hg/protein/kgPepMrna/kgPepMrna.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/protein/kgPepMrna/kgPepMrna.c,v
retrieving revision 1.4
retrieving revision 1.5
diff -b -B -U 1000000 -r1.4 -r1.5
--- src/hg/protein/kgPepMrna/kgPepMrna.c	3 Sep 2008 19:20:57 -0000	1.4
+++ src/hg/protein/kgPepMrna/kgPepMrna.c	23 Sep 2009 18:42:24 -0000	1.5
@@ -1,125 +1,125 @@
 /* kgPepMrna generates new .tab files with unused mRNA and protein sequences from known genes db tables removed. */
 
 #include "common.h"
 #include "hCommon.h"
 #include "hdb.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "kgPepMrna - generate new .tab files with unused mRNA and protein sequences from known genes db tables removed."
   "usage:\n"
   "   kgPepMrna tempKgDb roDb YYMMDD\n"
   "      tempKGDb is the temp KG build database name\n"
   "      roDb is the read only genome database name\n"
   "      YYMMDD is the release date of the UniProt and proteins DBs\n"
   "example: kgPepMrna kgHg17FTemp hg17 0405\n");
 }
 
 int main(int argc, char *argv[])
 {
 struct sqlConnection *conn, *conn2;
 char query2[256];
 struct sqlResult *sr2;
 char **row2;
 
 char cond_str[256];
 char *kgID;
 char *proteinID;
 char *protAcc;
 char *seq;
  
 char *tempKgDb; 
 char *roDbName;
 char *protDbDate;
 
 char proteinsDbName[100];
 char spDbName[100];
 
 FILE *o1, *o2;
 
 struct dnaSeq *kgSeq;
     
 if (argc != 4) usage();
 
 o1 = fopen("j.dat",  "w");
 o2 = fopen("jj.dat", "w");
     
 tempKgDb   = argv[1];
 roDbName  = argv[2];
 protDbDate = argv[3];
 
 sprintf(proteinsDbName, "proteins%s", protDbDate);
 sprintf(spDbName,   "sp%s", protDbDate);
 
 conn= hAllocConn(roDbName);
 conn2= hAllocConn(roDbName);
 sprintf(query2,"select name, proteinID from %s.knownGene;", roDbName);
 sr2 = sqlMustGetResult(conn2, query2);
 row2 = sqlNextRow(sr2);
 while (row2 != NULL)
     {
     kgID      = row2[0];
     proteinID = row2[1];
     
     sprintf(cond_str, "val = '%s';", proteinID);
     protAcc = sqlGetField(spDbName, "displayId", "acc", cond_str);
     if (protAcc != NULL)
     	{
     	sprintf(cond_str, "acc = '%s';", protAcc);
     	seq = sqlGetField(spDbName, "protein", "val", cond_str);
 	}
     else
     	{
     	sprintf(cond_str, "acc = '%s';", proteinID);
     	seq = sqlGetField(spDbName, "varProtein", "val", cond_str);
     	if (seq == NULL)
     	    {
 	    fprintf(stderr, 
 	    "%s does not have a AA sequence in either protein or varProtein table.\n", proteinID);
 	    exit(1);
 	    }
 	}
         
     fprintf(o1, "%s\t%s\n", kgID, seq);fflush(o1);
 
     sprintf(cond_str, "name = '%s';", kgID);
         
     seq = sqlGetField(tempKgDb, "mrnaSeq", "seq", cond_str);
     if (seq != NULL)
     	{
         fprintf(o2, "%s\t%s\n", kgID, seq);fflush(o1);
         }
     else
         {
 	kgSeq = hGenBankGetMrna(roDbName, kgID, NULL);
 	   
 	if (kgSeq != NULL)
 	    {
             fprintf(o2, "%s\t%s\n", kgID, kgSeq->dna);fflush(o1);
             }
 	else
 	    {
 	    fprintf(stderr, "No mRNA seq for %s\n", kgID);fflush(stderr);
 	    }
 	}
     row2 = sqlNextRow(sr2);
     }
 
 sqlFreeResult(&sr2);
 hFreeConn(&conn);
 hFreeConn(&conn2);
 
 fclose(o1);
 fclose(o2);
     
-system("cat j.dat |sort|uniq > knownGenePep.tab");
-system("cat jj.dat|sort|uniq > knownGeneMrna.tab");
-system("rm j.dat");
-system("rm jj.dat");
+mustSystem("cat j.dat |sort|uniq > knownGenePep.tab");
+mustSystem("cat jj.dat|sort|uniq > knownGeneMrna.tab");
+mustSystem("rm j.dat");
+mustSystem("rm jj.dat");
 
 return(0);
 }