bbde9065c89d41d21aa1df29d04b5892fc4af4e0
kate
  Wed Aug 24 10:24:57 2016 -0700
Update table names in doc. refs #17288

diff --git src/hg/near/makeNear.doc src/hg/near/makeNear.doc
index 6ba240b..c99333c 100644
--- src/hg/near/makeNear.doc
+++ src/hg/near/makeNear.doc
@@ -624,39 +624,50 @@
   > affyExonTissuesGs.ra
 grep -A5 affyExonTissuesAll ~/hg/makeDb/hgCgiData/Mouse/microarrayGroups.ra \
   | grep names | sed 's/^names //; s/,$//' | tr ',' '\n' \
   | awk 'BEGIN{OFS="\t"; id=0;}{ print id, $1, $1, "n/a", "n/a", "n/a", "3", "n/a,n/a,"$1","; id = id + 1;}' > all.expRecords
 hgLoadSqlTab mm8 affyExonTissuesGsExps expRecord.sql all.expRecords
 hgMedianMicroarray mm8 affyExonTissuesGs mm8.affyExonTissuesGsExps \
    affyExonTissuesGs.ra affyExonTissuesGsMedian mm8.affyExonTissuesGsMedianExps
 hgExpDistance mm8 affyExonTissuesGsMedian \
    affyExonTissuesGsMedianExps affyExonTissuesGsMedianDist
 
 ###############################################################
 ## GTEx
 ## (2016-08-16, kate)
 
 # Create a table that maps between known genes and GTEx (GENCODE V19) gene ids
-#hgMapToGene "-type=bed 12" hg19 gtexGeneModelV6 knownGene knownToGtexV6
+#hgMapToGene "-type=bed 12" hg19 gtexGeneModel knownGene knownToGtex
 cd /hive/data/genomes/hg19/bed/gtex
-hgMapToGene hg19 -type=genePred gtexGeneModelV6 knownGene knownToGtexV6
-hgMapToGene hg38 -type=genePred gtexGeneModelV6 knownGene knownToGtexV6
+#hgMapToGene hg19 -type=genePred gtexGeneModelV6 knownGene knownToGtex
+hgMapToGene hg19 -noLoad -all -type=genePred gtexGeneModelV6 knownGene knownToGtex.all
+hgMapToGene hg19 -all -type=genePred gtexGeneModelV6 knownGene knownToGtex
+
+#hgMapToGene hg38 -type=genePred gtexGeneModelV6 knownGene knownToGtex
+hgMapToGene hg38 -all -type=genePred gtexGeneModelV6 knownGene knownToGtex
 
 # Create expression distance table from median table.  This will take about an hour.
 #cd ~/src/hg/near/hgExpDistance
 # TODO: Consider adding weights file
 
-hgExpDistance hg19 -verbose=2 -lookup=knownToGtexV6 \
-        hgFixed.gtexTissueMedianV6 hgFixed.gtexTissue \
-                gtexDistanceV6 >&! distance.log &
+hgsql hgFixed -e select 1.0, id, name from gtexTissue > gtex.weights
+# edit to downweight brain (13 tissues total)
+
+hgExpDistance hg19 -verbose=2 -lookup=knownToGtex \
+        hgFixed.gtexTissueMedian hgFixed.gtexTissue \
+                gtexDistance >&! distance.log &
+
+hgExpDistance hg19 -verbose=2 -lookup=knownToGtex -weights=gtex.weights \
+        hgFixed.gtexTissueMedian hgFixed.gtexTissue \
+                gtexDistance2 >&! distance2.log &
 
 # Create ratio table.  
 # TODO: Consider adding -clump file, minAbsVal
-hgRatioMicroarray -database=hgFixed gtexTissueMedianV6 gtexTissueMedianRatioV6
+hgRatioMicroarray -database=hgFixed gtexTissueMedian gtexTissueMedianRatio
 
 # Get max scores for columnDb.ra
-hgMaxExp hgFixed gtexTissueMedianV6
+hgMaxExp hgFixed gtexTissueMedian
 # 219385.91
  
-hgMaxExp hgFixed gtexTissueMedianRatioV6
+hgMaxExp hgFixed gtexTissueMedianRatio
 # 12.53