[bedtools] For Gemini: Create a master ChromHMM track from the 9 distinct cell types.

.gitignore

*.txt
*.bedg

example01.sh

# icaoberg - this example is fork that uses a bedtools in a Singularity container
CONTAINER=../../singularity-bedtools.simg

echo "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmGm12878HMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmH1hescHMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmHepg2HMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmHmecHMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmHsmmHMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmHuvecHMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmK562HMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmNhekHMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmNhlfHMM.bed.gz" \
> chromhmm-files.txt

# download
for remote in `cat chromhmm-files.txt`
do
	wget $remote
done

# uncompress
for zip in `ls *.gz`
do
	gunzip -f $zip && rm -f $zip
done

# bed+ -> ~bedgraph
for bed in `ls *.bed`
do
	cut -f 1-4 $bed > $bed.bedg
done

# union of all intervals across all 9 cell types
if [ -f $CONTAINER ]; then
	singularity run --app bedtools $CONTAINER unionbedg -i *.bedg > master.chromhmm.bedg
fi
rm -f wg*