f38078ce59f74d48998cad7e5cfe810fa5c4c08a
kate
  Thu Aug 18 17:16:19 2016 -0700
Add GTEx to gene sorter. refs #17288

diff --git src/hg/near/makeNear.doc src/hg/near/makeNear.doc
index 78fb13e..6ba240b 100644
--- src/hg/near/makeNear.doc
+++ src/hg/near/makeNear.doc
@@ -618,15 +618,45 @@
    hgsql mm8 | tail -n+2 > expData.txt
 affyAllExonGSColumn expData.txt ids.txt column.txt
 hgLoadSqlTab mm8 affyExonTissuesGs expData.sql column.txt
 grep -A5 affyExonTissuesGroupByTissueMedian ~/hg/makeDb/hgCgiData/Mouse/microarrayGroups.ra \
   | grep names | sed 's/names //; s/,$//' | tr ',' '\n' \
   | awk 'BEGIN{OFS=" "; ix=0;}{print $1, $1, ix, ix+1, ix+2; ix = ix + 3;}' \
   > affyExonTissuesGs.ra
 grep -A5 affyExonTissuesAll ~/hg/makeDb/hgCgiData/Mouse/microarrayGroups.ra \
   | grep names | sed 's/^names //; s/,$//' | 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
+cd /hive/data/genomes/hg19/bed/gtex
+hgMapToGene hg19 -type=genePred gtexGeneModelV6 knownGene knownToGtexV6
+hgMapToGene hg38 -type=genePred gtexGeneModelV6 knownGene knownToGtexV6
+
+# 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 &
+
+# Create ratio table.  
+# TODO: Consider adding -clump file, minAbsVal
+hgRatioMicroarray -database=hgFixed gtexTissueMedianV6 gtexTissueMedianRatioV6
+
+# Get max scores for columnDb.ra
+hgMaxExp hgFixed gtexTissueMedianV6
+# 219385.91
+ 
+hgMaxExp hgFixed gtexTissueMedianRatioV6
+# 12.53
+