forester/sh/x_hmmscan.sh

   1 re="(.+)\.fasta"
   2 for i in *
   3 do
   4     if test -f "$i"
   5     then
   6         if [[ $i =~ $re ]];
   7         then
   8             name=${BASH_REMATCH[1]}
   9             echo $name
  10             /usr/local/bin/hmmscan --max --domtblout ${name}.hmmscan -E 20 --domE 20 --noali ~/DATA/PFAM/PFAM_30/Pfam-A.hmm ${name}.fasta
  11        fi
  12     fi
  13 done