src/hg/instinct/hgBed15ToArrayVal/hgBed15ToArrayVal.c 1.3

Index: src/hg/instinct/hgBed15ToArrayVal/hgBed15ToArrayVal.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/instinct/hgBed15ToArrayVal/hgBed15ToArrayVal.c,v
retrieving revision 1.2
retrieving revision 1.3
diff -b -B -U 1000000 -r1.2 -r1.3
--- src/hg/instinct/hgBed15ToArrayVal/hgBed15ToArrayVal.c	24 Sep 2008 00:02:54 -0000	1.2
+++ src/hg/instinct/hgBed15ToArrayVal/hgBed15ToArrayVal.c	10 Mar 2010 22:57:17 -0000	1.3
@@ -1,131 +1,133 @@
 /* hgBed15ToArrayVal - generate 3 cols tab separated file from a bed 15 table */
 #include "common.h"
 #include "hCommon.h"
 #include "hdb.h"
 
 #define MAXSAMPLE 5000
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "hgBed15ToArrayVal - generate 3 cols tab separated file from a bed 15 table.\n"
   "usage:\n"
   "   hgBed15ToArrayVal sampleDb sampleTable arrayDb bed15Table outFile\n"
   "      sampleDb datbase name \n"
   "      sampleTable table name \n"
   "      arrayDb datbase name of the source array data\n"
   "      bed15Table table name of the bed15 array data \n"
   "      outFile output file name\n"
   "example: hgBed15ToArrayVal vantVeer labTrack hg18 vantVeerExp vantVeerExpArrayVal.tab\n");
 
 }
 
+char localDb[128] = "localDb";
+
 int main(int argc, char *argv[])
 {
 struct sqlConnection *conn;
 
 int sampleCount = 0;
  
 char *sampleId[MAXSAMPLE];
 char query[256];
 struct sqlResult *sr;
 char **row;
 char expId1[255], measure[255];
  
 char *chp, *chp1, *chp2;
 
 /* a unique numerical value, representing NULL (to be set to NULL after loading) */
 char nullString[100] = {"-9999.8888"};
 
 char *probeName,  *expCount, *expIds, *expScores;
 boolean oneRecDone = FALSE;
 
 char *sampleDb, *sampleTable, *outFn;
 char *expDb, *expTable;
 FILE *outf;
 
 if (argc != 6) usage();
 
 sampleDb 	= argv[1];
 sampleTable	= argv[2];
 expDb 		= argv[3];
 expTable	= argv[4];
 outFn   	= argv[5];
 
 outf = mustOpen(outFn, "w");
-conn= hAllocConn(sampleDb);
+conn= hAllocConnProfile(localDb, sampleDb);
 
 sprintf(query,"select * from %s.%s", sampleDb, sampleTable);
 
 sr = sqlMustGetResult(conn, query);
 row = sqlNextRow(sr);
 sampleCount = 0;
 while (row != NULL)
     {
     sampleId[sampleCount] = strdup(row[1]);
     sampleCount++;
     row = sqlNextRow(sr);
     }
 sqlFreeResult(&sr);
 
 sprintf(query,"select name, expCount, expIds, expScores from %s.%s", expDb, expTable);
 
 sr = sqlMustGetResult(conn, query);
 row = sqlNextRow(sr);
 while (row != NULL)
     {
     probeName 	= row[0];
     expCount 	= row[1];
     expIds	= row[2];
     expScores	= row[3];
 
     chp1 = expIds;
     chp2 = expScores;
 
     oneRecDone = FALSE;
     while (!oneRecDone)
     	{
     	chp = chp1;
     	while (!((*chp == ',') || (*chp == '\0')))chp++;
     	if (*chp == '\0') oneRecDone = TRUE;
     	*chp = '\0';
     	safef(expId1, sizeof(expId1), "%s", chp1);
     	chp++;
     	chp1 = chp;
     
     	chp = chp2;
     	while (!((*chp == ',') || (*chp == '\0')))chp++;
     	*chp = '\0';
         if (strlen(chp2) != 0) 
 	    {    
     	    if (!sameWord(chp2, "NA"))
 		{
 	    	safef(measure, sizeof(measure), "%s", chp2);
 		}
 	    else
 	    	{
     	    	safef(measure, sizeof(measure), "%s", nullString);
     	    	}
     	    }
 	else
 	    {
     	    safef(measure, sizeof(measure), "%s", nullString);
     	    }
 
 	chp ++;
     	chp2 = chp;
     
     	if (!oneRecDone) 
 	    fprintf(outf, "%s\t%s\t%s\n", sampleId[atoi(expId1)], probeName, measure);
     	}
 
     row = sqlNextRow(sr);
     }
 sqlFreeResult(&sr);
 
 hFreeConn(&conn);
 fclose(outf);
     
 return(0);
 }