forester/sh/x_mafft.sh

   1 re="(.+)_ni\.fasta$"
   2 #re="(.+)\.fasta$"
   3 cutoff=3
   4 for i in *
   5 do
   6     if test -f "$i"
   7     then
   8         if [[ $i =~ $re ]]
   9         then
  10             name=${BASH_REMATCH[1]}
  11             echo $name
  12             count=$(grep -c '>' $i)
  13             echo $count
  14             if [ $count -gt $cutoff ]
  15             then
  16                 /usr/local/bin/mafft --maxiterate 1000 --localpair $i > ${name}_mafft_1000_l.fasta
  17                 rc=$?
  18                 if [[ $rc != 0 ]]
  19                 then
  20                     exit $rc
  21                 fi
  22             fi
  23         fi
  24     fi
  25 done