src/hg/instinct/bioInt2/bioPathwayLevelUsingEM.c 1.3

Index: src/hg/instinct/bioInt2/bioPathwayLevelUsingEM.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/instinct/bioInt2/bioPathwayLevelUsingEM.c,v
retrieving revision 1.2
retrieving revision 1.3
diff -b -B -U 4 -r1.2 -r1.3
--- src/hg/instinct/bioInt2/bioPathwayLevelUsingEM.c	5 Sep 2009 01:12:01 -0000	1.2
+++ src/hg/instinct/bioInt2/bioPathwayLevelUsingEM.c	21 Sep 2009 16:57:04 -0000	1.3
@@ -77,10 +77,10 @@
 
 //fprintf(f, "inference [pathway_match=_pid_66_,method=BP,updates=SEQFIX,tol=1e-9,maxiter=10000,logdomain=0]\n");
 //fprintf(f, "inference [pathway_match=_pid_48_,method=BP,updates=SEQFIX,tol=1e-9,maxiter=10000,logdomain=0]\n");
 fprintf(f, "inference [method=JTREE,updates=HUGIN,verbose=1]\n");
-fprintf(f, "evidence [suffix=_genome.tab,node=genome,disc=-0.451727;0.467580,epsilon=0.01,epsilon0=0.2]\n");
-fprintf(f, "evidence [suffix=_mRNA.tab,node=mRNA,disc=-0.1817733;0.1824913,epsilon=0.01,epsilon0=0.2]\n");
+fprintf(f, "evidence [suffix=_genome.tab,node=genome,disc=-1.3;1.3,epsilon=0.01,epsilon0=0.2]\n");
+fprintf(f, "evidence [suffix=_mRNA.tab,node=mRNA,disc=-1.3;1.3,epsilon=0.01,epsilon0=0.2]\n");
 fprintf(f, "em_step [_mRNA.tab=-obs>,_genome.tab=-obs>]\n");
 fprintf(f, "em [max_iters=30,log_z_tol=0.001]\n");
 
 return carefulCloseWarn(&f);
@@ -290,16 +290,20 @@
 	datasetsFreeList(&currDS);
 }
 
 // run EM step
+if (!sqlTableExists(biConn, EM_TABLE))
+    createPathwayEMValsTable(biConn, EM_TABLE);
+
 for (pa = spPathways; pa; pa = pa->next)
     {
     struct pathwayData *pd = pa->val;
     int feature_id = pd->id;
     count++;
 
 	// skip these pathways cause EM is expensive on them
-	if(feature_id == 66 || feature_id == 48 || feature_id == 3 || feature_id == 9)
+	if(feature_id == 8 || feature_id == 20 || feature_id == 27 || feature_id == 28 || feature_id == 29 || feature_id == 30 || feature_id == 32 || feature_id == 40 || feature_id == 42 || feature_id == 55  || feature_id == 56 || feature_id == 58 || feature_id == 59 || feature_id == 72 || feature_id == 74 || feature_id == 92 || feature_id == 99 || feature_id == 104 || feature_id == 106 || feature_id == 112 || feature_id == 121 || feature_id == 132 || feature_id == 135
+	   )
 		{
 		fprintf(stderr, "Skipping pathway %d because EM is too expensive.\n",count);
 		continue;
 		}