forester/sh/x_mafft.sh

   1 re="(.+)_ni\.fasta"
   2 cutoff=3
   3 for i in *
   4 do
   5     if test -f "$i"
   6     then
   7         if [[ $i =~ $re ]]
   8         then
   9             name=${BASH_REMATCH[1]}
  10             echo $name
  11             count=$(grep -c '>' $i)
  12             echo $count
  13             if [ $count -gt $cutoff ]
  14             then
  15                 /usr/local/bin/mafft --maxiterate 1000 --globalpair $i > ${name}_mafft_1000_g.aln
  16                 rc=$?
  17                 if [[ $rc != 0 ]]
  18                 then
  19                     exit $rc
  20                 fi
  21             fi
  22         fi
  23     fi
  24 done