##############################################################################
# GeneHancer tracks (hg19 and hg38)
#
# GeneHancer: database of human enhancers and their inferred target genes
# This is a component of GeneCards, Weizmann Institute
# Collaborators:  GeneHancer lead, Simon Fishilevich (simon.fishilevich@weizmann.ac.il), with
# support from GeneCards lead Marilyn Safran (Marilyn.Safran@weizmann.ac.il)

# Publication: Database (Oxford). 2017; 2017: bax028.
# Published online 2017 Apr 17. doi: 10.1093/database/bax028
# GeneHancer: genome-wide integration of enhancers and target genes in GeneCards

##############################################################################
# RM #22048: GeneHancer (2018-09-10 kate)

# Files obtained from development hub prepared by Simon F:
# https://genecards.weizmann.ac.il/geneloc/gh_hub_interactions/hub.txt  

mkdir /hive/data/outside/geneHancer/lab
cd /hive/data/outside/geneHancer/lab


wget -r https://genecards.weizmann.ac.il/geneloc/gh_hub_interactions
# sloppy command above -- whack extras after getting files needed
mv genecards.weizmann.ac.il/geneloc/gh_hub_interactions/*/*.bb .

// rename to UCSC conventions
cd ..
mv GeneHancer_hg19.bb lab/geneHancerRegElementsAll.hg19.bb
mv GCs_genes_tss_hg19.bb lab/geneHancerGenesTssAll.hg19.bb
mv GH_interactions1_all_hg19.bb lab/geneHancerInteractionsAll.hg19.bb
mv GeneHancer_double_elite_hg19.bb lab/geneHancerRegElementsDoubleElite.hg19.bb
mv GCs_genes_tss_double_elite_hg19.bb lab/geneHancerGenesTssDoubleElite.hg19.bb
mv GH_interactions1_doubleElite_hg19.bb lab/geneHancerInteractionsDoubleElite.hg19.bb

mv GeneHancer.bb lab/geneHancerRegElementsAll.hg38.bb
mv GCs_genes_tss.bb lab/geneHancerGenesTssAll.hg38.bb
mv GH_interactions1_all.bb lab/geneHancerInteractionsAll.hg38.bb
mv GeneHancer_double_elite.bb lab/geneHancerRegElementsDoubleElite.hg38.bb
mv GCs_genes_tss_double_elite.bb lab/geneHancerGenesTssDoubleElite.hg38.bb
mv GH_interactions1_doubleElite.bb lab/geneHancerInteractionsDoubleElite.hg38.bb


# make trackDb

cd gh_hub_interactions
cp trackDb.txt ~/kent/src/hg/makeDb/trackDb/human/hg19/trackDb.geneHancer.ra
# merge with composite versionin UCSC development hub
cd ~/kent/src/hg/makeDb/trackDb/human/hg19
cat ~/public_html/hubs/geneHancer/hg38/trackDb.txt >> trackDb.geneHancer.ra
# edit

# track description
cp hg38/GeneHancer.html ~/kent/src/hg/makeDb/trackDb/human/hg19/geneHancer.html

# fix .as file for interactions tracks
bigBedInfo -as geneHancerInteractionsDoubleElite.hg38.bb > geneHancer.as
# edit to remove non-as stuff, remove extraneous eol chars, fix case to GB standard, also spelling
sed 's/\r//' geneHancer.as  > geneHancerGb.as

# correct interaction files chromStart, chromEnd (must be full extent of source and target regions)
# and replace : in name with more cosmetic / 
# (can now use new $<fieldName> to construct URL, instead of name field)

mkdir fixed gbdb
cat > make.csh << 'EOF'
cd lab
foreach v (All.hg19 All.hg38 DoubleElite.hg19 DoubleElite.hg38)
  set db = $v:e
  set f = geneHancerInteractions$v
  echo $f
  set sizes = /hive/data/genomes/$db/chrom.sizes
    
  bigBedToBed $f.bb $f.bed
  sed 's/:/\//' $f.bed | interactFixRanges stdin stdout | \
        bedSort stdin ../fixed/$f.bed
  bedToBigBed -type=bed5+3 -as=../geneHancerGb.as ../fixed/$f.bed $sizes ../gbdb/$f.bb
end
'EOF'

# link into /gbdb

ln `pwd`/lab/*Tss*.bb gbdb
ln `pwd`/lab/*RegElements*.bb gbdb

cd /gbdb
mkdir {hg19,hg38}/geneHancer
ln -s /hive/data/outside/geneHancer/gbdb/*.hg19.bb hg19/geneHancer
ln -s /hive/data/outside/geneHancer/gbdb/*.hg38.bb hg38/geneHancer

# cleanup
rm -fr genecards.weizmann.ac.il

##############################################################################
# Data correction from Simon 12/31/18 
#
# (2019-01-02 kate)
 
"Unfortunately we discovered a bug with the data of the GeneHancer 
# native track (which belongs to the current version of GeneCards, V4.8)
# One field (`Experiment') is not populated properly in all 4 interaction bb files."
#
# The 'experiment' field in the GeneHancer hub is fixed (for GeneCards version 4.8, 
# used in the UCSC live main track).  We also fixed the issue with interaction interval.
#
# RM #22712

# retrieve corrected files from 'OwnCloud' platform:  GeneHancer_hub_V4_8_fix.zip 

cd /hive/data/outside/geneHancer
mkdir v2
cd v2
unzip GeneHancer_hub_V4_8_fix.zip
ls *.bb
#GH_interactions1_all.bb       GH_interactions1_doubleElite.bb
#GH_interactions1_all_hg19.bb  GH_interactions1_doubleElite_hg19.bb

# sanity check by converting a file to bigBed and comparing to previous version
# -> OK

ln -s `pwd`/v2/GH_interactions1_doubleElite_hg19.bb gbdb/geneHancerInteractionsDoubleElite.v2.hg19.bb
ln -s `pwd`/v2/GH_interactions1_all_hg19.bb gbdb/geneHancerInteractionsAll.v2.hg19.bb
ln -s `pwd`/v2/GH_interactions1_doubleElite.bb gbdb/geneHancerInteractionsDoubleElite.v2.hg38.bb
ln -s `pwd`/v2/GH_interactions1_all.bb gbdb/geneHancerInteractionsAll.v2.hg38.bb

cd /gbdb
ln -s /hive/data/outside/geneHancer/gbdb/*.v2.hg19.bb hg19/geneHancer
ln -s /hive/data/outside/geneHancer/gbdb/*.v2.hg38.bb hg38/geneHancer
#

# Minor changes for compatiility with previous version of track:
#       1. Separator in item label is slash not colon
#       2. GeneHancer* fields in .as should have initial char lower case (geneHancer*)
# (2019-01-15 kate)

cat > makeV2.csh << 'EOF'
mkdir -f v2.fixed
cd gbdb
foreach v (All.v2.hg19 All.v2.hg38 DoubleElite.v2.hg19 DoubleElite.v2.hg38)
  set db = $v:e
  set f = geneHancerInteractions$v
  echo $f
  set sizes = /hive/data/genomes/$db/chrom.sizes
  bigBedToBed $f.bb ../v2/$f.bed
  sed 's/:/\//' ../v2/$f.bed | interactFixRanges stdin stdout | \
        bedSort stdin ../v2.fixed/$f.bed
  bedToBigBed -type=bed5+3 -as=../geneHancerGb.as ../v2.fixed/$f.bed $sizes ../gbdb/$f.v2.fixed.bb
end
'EOF'

rm /gbdb/{hg19,hg38}/geneHancer/*.v2.*

set dir = /hive/data/outside/geneHancer/gbdb
ln -s $dir/geneHancerInteractionsAll.v2.hg19.v2.fixed.bb /gbdb/hg19/geneHancer/geneHancerInteractionsAll.v2.hg19.bb
ln -s $dir/geneHancerInteractionsDoubleElite.v2.hg19.v2.fixed.bb /gbdb/hg19/geneHancer/geneHancerInteractionsDoubleElite.v2.hg19.bb
ln -s $dir/geneHancerInteractionsAll.v2.hg38.v2.fixed.bb /gbdb/hg38/geneHancer/geneHancerInteractionsAll.v2.hg38.bb
ln -s $dir/geneHancerInteractionsDoubleElite.v2.hg38.v2.fixed.bb /gbdb/hg38/geneHancer/geneHancerInteractionsDoubleElite.v2.hg38.bb