src/hg/makeDb/doc/hg19.txt 1.66

Index: src/hg/makeDb/doc/hg19.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg19.txt,v
retrieving revision 1.65
retrieving revision 1.66
diff -b -B -U 4 -r1.65 -r1.66
--- src/hg/makeDb/doc/hg19.txt	2 Dec 2009 19:43:20 -0000	1.65
+++ src/hg/makeDb/doc/hg19.txt	7 Dec 2009 17:42:13 -0000	1.66
@@ -5773,8 +5773,14 @@
     time nice -n +19 hgLoadWiggle -pathPrefix=/gbdb/hg19/multiz46way hg19 \
 	phastCons46way phastCons46way.wig
     #	real    1m45.381s
 
+    wigTableStats.sh hg19 phastCons46way
+# db.table      min max mean count sumData
+# hg19.phastCons46way     0 1 0.103653 2845303719 2.94924e+08
+#	stdDev viewLimits
+#	0.230184 viewLimits=0:1
+
     #  Create histogram to get an overview of all the data
     ssh hgwdev
     cd /hive/data/genomes/hg19/bed/multiz46way/cons/all
     time nice -n +19 hgWiggle -doHistogram -db=hg19 \
@@ -5923,8 +5929,14 @@
 	/gbdb/hg19/multiz46way/phastCons46wayPrimates.wib
     time nice -n +19 hgLoadWiggle -pathPrefix=/gbdb/hg19/multiz46way hg19 \
 	phastCons46wayPrimates phastCons46wayPrimates.wig
 
+    wigTableStats.sh hg19 phastCons46wayPrimates
+# db.table      min max mean count sumData
+hg19.phastCons46wayPrimates     0 1 0.128883 2845303719 3.66712e+08
+#	stdDev viewLimits
+#	0.214067 viewLimits=0:1
+
     #  Create histogram to get an overview of all the data
     time nice -n +19 hgWiggle -doHistogram \
 	-hBinSize=0.001 -hBinCount=1000 -hMinVal=0.0 -verbose=2 \
 	    -db=hg19 phastCons46wayPrimates  > histogram.data 2>&1
@@ -6067,10 +6079,13 @@
 	/gbdb/hg19/multiz46way/phastCons46wayPlacental.wib
     time nice -n +19 hgLoadWiggle -pathPrefix=/gbdb/hg19/multiz46way hg19 \
 	phastCons46wayPlacental phastCons46wayPlacental.wig
 
-    #	Instead, temporary load into a table so we can do the histogram
-    hgLoadWiggle hg19 pc46 phastCons46wayPlacental.wig
+    wigTableStats.sh hg19 phastCons46wayPlacental
+# db.table      min max mean count sumData
+hg19.phastCons46wayPlacental    0 1 0.0885757 2845303719 2.52025e+08
+#	stdDev viewLimits
+#	0.210242 viewLimits=0:1
 
     #  Create histogram to get an overview of all the data
     time nice -n +19 hgWiggle -doHistogram \
 	-hBinSize=0.001 -hBinCount=1000 -hMinVal=0.0 -verbose=2 \
@@ -7540,8 +7555,30 @@
 # irows on
     #	appears to work OK
 
 #############################################################################
+## create upstream refGene maf files
+    cd /hive/data/genomes/hg19/bed/multiz46way/downloads/maf
+    # bash script
+#!/bin/sh
+for S in 1000 2000 5000
+do
+    echo "making upstream${S}.maf"
+    featureBits hg19 refGene:upstream:${S} -fa=/dev/null -bed=stdout \
+        | perl -wpe 's/_up[^\t]+/\t0/' | sort -k1,1 -k2,2n \
+        | /cluster/bin/$MACHTYPE/mafFrags hg19 multiz46way \
+                stdin stdout \
+                -orgs=/hive/data/genomes/hg19/bed/multiz46way/species.list \
+        | gzip -c > upstream${S}.maf.gz
+    echo "done upstream${S}.maf.gz"
+done
+
+    cd /usr/local/apache/htdocs/goldenPath/hg19/multiz46way/maf
+    ln -s /hive/data/genomes/hg19/bed/multiz46way/downloads/maf/up*.gz .
+    md5sum up*.gz >> md5sum.txt
+
+
+#############################################################################
 # AFFY U133AB (Done - 2009-09-30 - Jim)
     # Align probes 
     ssh swarm
     cd /cluster/data/hg19/bed