From: cmzmasek <chris.zma@outlook.com>
Date: Fri, 9 Jun 2017 21:58:48 +0000 (-0700)
Subject: pplacer
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=0c9e441a735b6be310bf9a3e1a3608d8595e0d4b;p=jalview.git

pplacer
---

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