forester/sh/x_mpp.sh

   1 re="Q_(.+)\.fasta"
   2
   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             /usr/local/bin/mafft --keeplength --add $i CDS_aligned_partials_MAFFT_merged_ni.fasta > REF_PLUS_Q_${name}.fasta
  12             rc=$?
  13             if [[ $rc != 0 ]]
  14             then
  15                 exit $rc
  16             fi
  17
  18            /home/zma/SOFTWARE/PHYLO/PPLACER/PPLACER11ALPHA19/pplacer-Linux-v1.1.alpha19/pplacer -m GTR -t RAxML_bestTree.CDS_aligned_partials_MAFFT_merged_GTR -s RAxML_info.CDS_aligned_partials_MAFFT_merged_GTR REF_PLUS_Q_${name}.fasta -o PP_Q_${name}.json
  19            rc=$?
  20            if [[ $rc != 0 ]]
  21            then
  22                exit $rc
  23            fi
  24
  25            /home/zma/SOFTWARE/PHYLO/PPLACER/PPLACER11ALPHA19/pplacer-Linux-v1.1.alpha19/guppy sing PP_Q_${name}.json
  26            rc=$?
  27            if [[ $rc != 0 ]]
  28            then
  29                exit $rc
  30            fi
  31         fi
  32     fi
  33 done