61309f7c6fb5fb1d582fde243fbfa83559c1da21
chmalee
  Tue Oct 5 16:26:13 2021 -0700
Fix float parsing bug in gtex transcript expression track on hg19 and hg38, refs #28280

diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt
index 4813f45..517fb52 100644
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@ -31893,47 +31893,48 @@
 python download.py
 python filterPages.py > goodPages.txt
 python makeBed.py
 hgLoadBed hg19 snpedia snpedia.bed
 hgLoadSqlTab hg19 snpediaHtml snpediaHtml.sql snpedia.htmlTab
 ##############################################################################
 # Gtex transcript track hg38->hg19 coordinate conversion (DONE - 2017-07-27 - Chris)
 mkdir /hive/data/outside/gtex/barChartTrack/hg19backLift
 cd /hive/data/outside/gtex/barChartTrack/hg19backLift
 
 hgsql hg19 -e "select * from wgEncodeGencodeCompV24lift37" | awk '{print $2"\t"$5"\t"$6}' > foo
 cut -f 1 foo | cut -f 1 -d "." > foo2
 cut -f 2,3,4 foo > foo3
 paste foo2 foo3 > foo4
 
-cp ../sortedGtexTransExp.bed .
-cut -f 1,2,3 sortedGtexTransExp.bed > foo5
-cut -f 4 sortedGtexTransExp.bed > foo6
-cut -f 5- sortedGtexTransExp.bed > foo7
-paste foo6 foo5 > foo8
-paste foo8 foo7 > foo9
+# NOTE: CHRISL10-05-2021 - Re-run to fix float parse bug:
+cp ../sortedGtexTransExp.bed sortedGtexTransExpFixed.bed
+cut -f 1,2,3 sortedGtexTransExpFixed.bed > foo5Fixed
+cut -f 4 sortedGtexTransExpFixed.bed > foo6Fixed
+cut -f 5- sortedGtexTransExpFixed.bed > foo7Fixed
+paste foo6Fixed foo5Fixed > foo8Fixed
+paste foo8Fixed foo7Fixed > foo9Fixed
 
+join <(sort foo4) <(sort foo9Fixed) > foo10Fixed
 
-join <(sort foo4) <(sort foo9) > foo10
-
-cat foo10 | awk '{print $4"\t"$2"\t"$3"\t"$1"\t"$8"\t"$9"\t"$10"\t"$11"\t"$12"\t"$13"\t"$14}' > foo11
-
-# Copy over the header line from sortedGtexTransExp.bed
+cat foo10Fixed | awk '{print $4"\t"$2"\t"$3"\t"$1"\t"$8"\t"$9"\t"$10"\t"$11"\t"$12"\t"$13"\t"$14}' > foo11Fixed
 
 # Sort and convert into a bigBed file.
-sort -k1,1 -k2,2n foo11 > sortedGtexTransExpHg19.bed
-bedToBigBed -as=$HOME/kent/src/hg/lib/barChartTranscExp.as -type=bed6+5 sortedGtexTransExpHg19.bed /hive/data/genomes/hg19/chrom.sizes gtexTranscExprHg19.bb
+sort -k1,1 -k2,2n foo11Fixed > sortedGtexTransExpHg19Fixed.bed
+# remove final line with header info:
+vim sortedGtexTransExpHg19Fixed.bed
+bedToBigBed -as=$HOME/kent/src/hg/lib/barChartBed.as -type=bed6+5 sortedGtexTransExpHg19Fixed.bed /hive/data/genomes/hg19/chrom.sizes gtexTranscExprHg19.bb
+# END NOTE: CHRISL10-05-2021
 
 # Link the files into gbdb
 # <2007-0-30 kate)
 cd /gbdb/hg19/gtex
 ln -s /hive/data/outside/gtex/barChartTrack/hg19backLift/gtexTranscExprHg19.bb gtexTranscExpr.bb
 
 ##############################################################################
 # cosmicRegions (DONE - 2017-08-03 - Chris)
 # Make a new COSCMIC track for hg19 v82
 mkdir /hive/data/outside/cosmic/hg19/v82
 cd /hive/data/outside/cosmic/hg19/v82
 
 # Get the new data
 sftp ceisenha@ucsc.edu@sftp-cancer.sanger.ac.uk
 # Login to SFTP server (make an account online) then run this command