From 0c9e441a735b6be310bf9a3e1a3608d8595e0d4b Mon Sep 17 00:00:00 2001 From: cmzmasek Date: Fri, 9 Jun 2017 14:58:48 -0700 Subject: [PATCH] pplacer --- forester/sh/x_mpp.sh | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 forester/sh/x_mpp.sh diff --git a/forester/sh/x_mpp.sh b/forester/sh/x_mpp.sh new file mode 100644 index 0000000..24af780 --- /dev/null +++ b/forester/sh/x_mpp.sh @@ -0,0 +1,33 @@ +re="Q_(.+)\.fasta" + +for i in * +do + if test -f "$i" + then + if [[ $i =~ $re ]] + then + name=${BASH_REMATCH[1]} + echo $name + /usr/local/bin/mafft --keeplength --add $i CDS_aligned_partials_MAFFT_merged_ni.fasta > REF_PLUS_Q_${name}.fasta + rc=$? + if [[ $rc != 0 ]] + then + exit $rc + fi + + /home/zma/SOFTWARE/PHYLO/PPLACER/PPLACER11ALPHA19/pplacer-Linux-v1.1.alpha19/pplacer -m GTR -t RAxML_bestTree.CDS_aligned_partials_MAFFT_merged_GTR -s RAxML_info.CDS_aligned_partials_MAFFT_merged_GTR REF_PLUS_Q_${name}.fasta -o PP_Q_${name}.json + rc=$? + if [[ $rc != 0 ]] + then + exit $rc + fi + + /home/zma/SOFTWARE/PHYLO/PPLACER/PPLACER11ALPHA19/pplacer-Linux-v1.1.alpha19/guppy sing PP_Q_${name}.json + rc=$? + if [[ $rc != 0 ]] + then + exit $rc + fi + fi + fi +done \ No newline at end of file -- 1.7.10.2