Skip to content
Permalink
Branch: master
Find file Copy path
Find file Copy path
Fetching contributors…
Cannot retrieve contributors at this time
26 lines (20 sloc) 848 Bytes
#!/usr/bin/bash
if [ "$#" -lt 5 ]; then
echo ""
echo "USAGE: bash extract_TF.bsh species TF_name dTOX_reult out_file"
echo ""
echo "Species -- Currently only hg19 and mm10"
echo "TF_name -- TF Name, e.g. JUND, ELK1, MYC "
echo "dTOX_reult -- the result file generated by the 'run-dTOX' script. (Compressed bed file) "
echo "out_file -- the name of the output file. (Compressed bed file)"
exit 1
fi
pushd `dirname $0` > /dev/null
bsh_path=`pwd`
popd > /dev/null
species=$1
TF_name=$2
dTOX_reult=$3
out_file=$4
echo "Using: R --vanilla --slave --args $species $TF_name $dTOX_reult $out_file < $bsh_path/Rscript/extract-bound-TF.R > extract-bound-TF.log"
R --vanilla --slave --args $species $TF_name $dTOX_reult $out_file < $bsh_path/Rscript/extract-bound-TF.R > extract-bound-TF.log
You can’t perform that action at this time.