src/hg/makeDb/doc/hg18.txt 1.348

Index: src/hg/makeDb/doc/hg18.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg18.txt,v
retrieving revision 1.347
retrieving revision 1.348
diff -b -B -U 4 -r1.347 -r1.348
--- src/hg/makeDb/doc/hg18.txt	21 Feb 2009 00:55:16 -0000	1.347
+++ src/hg/makeDb/doc/hg18.txt	23 Feb 2009 18:42:27 -0000	1.348
@@ -26665,12 +26665,25 @@
 # add additional entries that related to "NR_...." RefSeqs
 
 hgGetNrOmimGene hg18 j.tmp 
 sort -u j.tmp > omimGeneNR.bed
+hgLoadBed hg18 omimGeneNR omimGeneNR.bed
 
 cat omimGene.bed omimGeneNR.bed |sort -u >omimGeneAll.bed
 hgLoadBed hg18 omimGene omimGeneAll.bed
 
+hgsql hg18 -N -e 'select * from omimToKnownCanonical' |sort -u >j.tmp
+hgsql hg18 -N -e \
+'select n.name, i.transcript from  omimGeneNR n, knownCanonical c,
+knownToRefSeq r, refLink l, knownIsoforms i where l.mrnaAcc=r.value and
+binary(n.name)=l.omimId and c.transcript=r.name and c.clusterId=i.clusterId
+and omimId <>0 '\
+|sort -u >omimToKnownGeneNR.tab
+cat j.tmp omimToKnownGeneNR.tab |sort -u >omimToKnownCanonicalNew.tab
+
+hgLoadSqlTab hg18 omimToKnownCanonical  \
+~/src/hg/lib/omimToKnownCanonical.sql omimToKnownCanonicalNew.tab
+
 #############################################################################
 # fox2ClipSeq from Gene Yeo (DONE - 2009-01-08 - Hiram)
     mkdir /hive/data/genomes/hg18/bed/fox2ClipSeq
     cd /hive/data/genomes/hg18/bed/fox2ClipSeq