Script for 2VEP DFI Analysis

gistfile1.txt

#!/bin/bash                                                                                                                                                                                                          

for d in $(ls -F | grep "^[a-z].*/$");
do
echo $d;
printf "=========================\n";
printf "Find covariance matrices\n";
nm=$(echo $d | cut -d/ -f1)
fdfi=$(grep -E "^${nm}:" catalytic_residues.txt | awk -F: '{print $2}');
cd $d;
#get covariance matrices                                                                                                                                                                                             
pdbfiles=$(ls *.pdb | grep -v "-");
echo $pdbfiles
pdbprefix=$(echo $pdbfiles | cut -d. -f1)
covarmat=$(ls *_mwcovarmat.dat);
echo $covarmat;
for mat in ${covarmat}
do
    echo $mat
    prefix=$(echo $mat | sed "s/_mwcovarmat.dat//g");
    echo $prefix
    echo $pdbprefix
    ~/dfi/dfi.py --pdb ${pdbfiles} --hess ${mat} --fdfi ${fdfi}
    mv -v ${pdbprefix}-dfianalysis.csv ${prefix}-dfianalysis.csv
done
echo "-------------------------";
sleep 1;
cd ..

done