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# Done 07/17/2015 Chris Eisenhart (ceisenhart) 
mkdir /hive/data/genomes/hg38/bed/hg18MassiveLift/fosEndPairs
cd /hive/data/genomes/hg38/bed/hg18MassiveLift/fosEndPairs
hgsql hg18 -e "select * from fosEndPairs" | tail -n +2 | cut -f2- > hg18.fosEndPairs.fep.bed
hgsql hg18 -e "select * from all_fosends" | tail -n +2 | cut -f2- > hg18.all_fosends.psl
awk -f toBed12.awk hg18.fosEndPairs.fep.bed > hg18.fosEndPairs.bed12
liftOver -bedPlus=12 hg18.fosEndPairs.bed12 /gbdb/hg18/liftOver/hg18ToHg38.over.chain.gz hg38.fosEndPairs.{bed12,unmapped12}
liftOver -pslT hg18.all_fosends.psl /gbdb/hg18/liftOver/hg18ToHg38.over.chain.gz hg38.all_fosends.{psl,unmapped} 
cut -f14 hg38.fosEndPairs.bed12 | tr ',' '\n' | sort > hg38.fosEndPairs.names
cut -f10 hg38.all_fosends.psl | sort > hg38.all_fosends.names
grep -Fxv -f hg38.all_fosends.names hg38.fosEndPairs.names > bad.names
grep -Fv -f bad.names hg38.fosEndPairs.bed12 > hg38.fosEndPairs.good.bed12
wc -l hg38*.bed12
#  383587 hg38.fosEndPairs.bed12
#  #  382789 hg38.fosEndPairs.good.bed12
#  #    798 bad ones removed. Could have caused join errors if left in. 
#  # convert back to fosEndPairs bed6+
  awk -f toFosEndPairs.awk hg38.fosEndPairs.good.bed12 >
  hg38.fosEndPairs.fep.bed
  cp ~/kent/src/hg/lib/fosEndPairs.sql .
hgLoadBed -sqlTable=fosEndPairs.sql -notItemRgb hg38 fosEndPairs hg38.fosEndPairs.fep.bed
hgLoadPsl -table=all_fosends hg38 hg38.all_fosends.psl
#  386129 hg18.fosEndPairs.fep.bed
#  382789 hg38.fosEndPairs.fep.bed
#  99.135% lifted
# Now we need the sequences from all_fosends to be loaded into the seq table in hg38
mkdir /gbdb/hg19/fosends
ln -s /gbdb/hg18/fosends/fosEnds.fa /gbdb/hg38/fosEnds.fromHg18.fa
hgLoadSeq hg38 /gbdb/hg38/fosends/fosEnds.fromHg18.fa

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# Done fishClones Chris Eisenhart 07/20/2015

cd /hive/data/genomes/hg19/bed/hg18MassiveLift
mkdir fishClones
cd fishClones/
hgsql hg18 -e "select * from fishClones" | tail -n +2 > hg18.bed5p
liftOver -bedPlus=5 hg18.bed5p /gbdb/hg18/liftOver/hg18ToHg38.over.chain.gz hg38.bed5p hg38.unmapped
wc -l *.bed5p
#   9788 hg18.bed5p
#   9731 hg38.bed5p
grep -i split hg38.unmapped  | wc -l
# 54
grep -i partially  hg19.unmapped  | wc -l
# 3
cp ~/kent/src/hg/lib/fishClones.sql .
hgLoadBed -noBin -tab -sqlTable=fishClones.sql -notItemRgb hg38 fishClones hg38.bed5p
#Read 9731 elements of size 16 from hg38.bed5p
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