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edit_trackDb.sh
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edit_trackDb.sh
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trackDb="$1"
lib_assemblies="$2"
lib_assembly_array=()
## add the new data
while read assembly; do
echo $assembly
## ensure the assembly was not loaded before
if [ $(echo ${lib_assembly_array[@]} | grep -o $assembly | wc -l) -eq 0 ]; then
lib_assembly_array+=($assembly)
fi; done < $lib_assemblies
## restart the trackDb
> $trackDb
## edit the trackDb
priority=1
for assembly in ${lib_assembly_array[@]}; do
## create non-composite entry of the assembly
echo $assembly;
filename=$(basename $assembly)
echo "track $assembly" >> $trackDb
echo "bigDataUrl BigBed/$filename.BigBed" >> $trackDb
echo "shortLabel $assembly" >> $trackDb
echo "longLabel $assembly" >> $trackDb
echo "type bigBed 12" >> $trackDb
echo "colorByStrand 255,0,0 0,0,255" >> $trackDb
echo "visibility dense" >> $trackDb
echo "priority $priority" >> $trackDb
echo "html $filename" >> $trackDb
echo " " >> $trackDb
let "priority++"
done