#!/bin/bash

ln -s /projects/ps-renlab/yangli/projects/catlas/humanenhancer/data/HEA.full.taxonomyLable.tsv .
awk 'BEGIN{FS=OFS="\t"}{print $1,$3,$8,$5,$6,$7}' HEA.full.taxonomyLable.tsv | awk 'BEGIN{FS="\t"}{ printf "%s\t%s\t%s\t%d\t%.2f\t%d \n", $1,$2,$3,$4,$5,$6 }' | sed '1d' > cellnames.tsv

sed -e "s/\t/\",\"/g" cellnames.tsv |  sed -e "s/^/  [\"/g" | sed -e "s/ $/\"],/g" > cellnames.array.json
sed -i -e '1i {"data": [' cellnames.array.json
sed -i -e '$a]}' cellnames.array.json 

cd bw

SAVEIFS=$IFS
IFS=$(echo -en "\n\b")
for i in `cut -f 1 -d$'\t' ../cellnames.tsv`;
do echo $i;
ln -s /projects/ps-renlab/yangli/projects/catlas/humanenhancer/data/tracks/bw/${i}.bw ${i}.bw
done;
IFS=$SAVEIFS

cd cCREs
SAVEIFS=$IFS
IFS=$(echo -en "\n\b")
for i in `cut -f 1 -d$'\t' ../cellnames.tsv`
do echo $i;
ln -s /projects/ps-renlab/yangli/projects/catlas/humanenhancer/data/tracks/cCREs/${i}.cCRE.bed ${i}.cCRE.bed
done;
IFS=$SAVEIFS

SAVEIFS=$IFS
IFS=$(echo -en "\n\b")
for i in `cut -f 1 -d$'\t' cellnames.tsv`
do echo $i;
echo -e "<tr><td></td><td><input type=\"checkbox\" id=\"bn${i}\" value=\"bn${i}\"  onchange=\"onChecked(this);\"/>${i}</td></tr>" >> igv_tracks.tmp
done;
IFS=$SAVEIFS

SAVEIFS=$IFS
IFS=$(echo -en "\n\b")
for i in `cut -f 1 -d$'\t' cellnames.tsv`
do echo $i
c=`awk -v name="${i}" 'BEGIN{FS=OFS="\t"}($1==name){print $0}' HEA.full.taxonomyLable.tsv | cut -f 2`;
echo -e "\tType: '${i}', label: '${i}', name: '${i}', color: '${c}', min: "0", max: "50", demo: '0',
\tbw_url: base+'/bw/${i}.bw',
\tbed_url: base+'/cCREs/${i}.cCRE.bed'
\t}, {" >> catlas.igv_tracks.tmp
done;
IFS=$SAVEIFS

catlas.igv_tracks.tmp