From: cmzmasek <chris.zma@outlook.com>
Date: Thu, 13 Jul 2017 20:21:30 +0000 (-0700)
Subject: updated
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=707f5d436d3bf4790d5801c0d83106f6ce9b06f4;p=jalview.git

updated
---

diff --git a/forester/sh/x_dsx.sh b/forester/sh/x_dsx.sh
new file mode 100644
index 0000000..fa4987a
--- /dev/null
+++ b/forester/sh/x_dsx.sh
@@ -0,0 +1,18 @@
+re="(.+)_hmmscan$"
+for i in * 
+do
+    if test -f "$i" 
+    then
+        if [[ $i =~ $re ]]
+        then
+            name=${BASH_REMATCH[1]}
+            echo $name
+            ruby /home/zma/git/forester/forester/ruby/evoruby/exe/dsx.rb -d -e=1e-6 -l=50 ${name} ${name}_hmmscan
+            rc=$?
+            if [[ $rc != 0 ]]
+            then
+                exit $rc
+            fi
+        fi
+    fi
+done
\ No newline at end of file
diff --git a/forester/sh/x_hmmscan.sh b/forester/sh/x_hmmscan.sh
index 49657ab..ba0c04c 100644
--- a/forester/sh/x_hmmscan.sh
+++ b/forester/sh/x_hmmscan.sh
@@ -1,4 +1,4 @@
-re="(.+)\.fasta"
+re="(.+)_ni\.fasta$"
 for i in * 
 do
     if test -f "$i" 
@@ -7,7 +7,7 @@ do
         then
             name=${BASH_REMATCH[1]}
             echo $name
-            /usr/local/bin/hmmscan --max --domtblout ${name}.hmmscan -E 20 --domE 20 --noali ~/DATA/PFAM/PFAM_30/Pfam-A.hmm ${name}.fasta
+            /usr/local/bin/hmmscan --max --domtblout ${name}_hmmscan -E 20 --domE 20 --noali ~/DATA/PFAM/PFAM_30/Pfam-A.hmm ${name}_ni.fasta
         fi
     fi
 done
\ No newline at end of file
diff --git a/forester/sh/x_hsp_d2f.sh b/forester/sh/x_hsp_d2f.sh
new file mode 100644
index 0000000..1d61af9
--- /dev/null
+++ b/forester/sh/x_hsp_d2f.sh
@@ -0,0 +1,24 @@
+re="(.+)_hmmscan$"
+for i in * 
+do
+    if test -f "$i" 
+    then
+        if [[ $i =~ $re ]]
+        then
+            name=${BASH_REMATCH[1]}
+            echo $name
+            ruby /home/zma/git/forester/forester/ruby/evoruby/exe/hsp.rb $i
+            rc=$?
+            if [[ $rc != 0 ]]
+            then
+                exit $rc
+            fi
+            ruby /home/zma/git/forester/forester/ruby/evoruby/exe/d2f.rb -o ${name}_hmmscan_domain_table
+            rc=$?
+            if [[ $rc != 0 ]]
+            then
+                exit $rc
+            fi
+        fi
+    fi
+done
diff --git a/forester/sh/x_mafft.sh b/forester/sh/x_mafft.sh
index e5ddb95..9b7e204 100644
--- a/forester/sh/x_mafft.sh
+++ b/forester/sh/x_mafft.sh
@@ -1,4 +1,5 @@
-re="(.+)_ni\.fasta"
+re="(.+)_ni\.fasta$"
+#re="(.+)\.fasta$"
 cutoff=3
 for i in * 
 do
@@ -12,7 +13,7 @@ do
             echo $count
             if [ $count -gt $cutoff ]
             then
-                /usr/local/bin/mafft --maxiterate 1000 --globalpair $i > ${name}_mafft_1000_g.aln
+                /usr/local/bin/mafft --maxiterate 1000 --localpair $i > ${name}_mafft_1000_l.fasta
                 rc=$?
                 if [[ $rc != 0 ]]
                 then
diff --git a/forester/sh/x_msa_pro.sh b/forester/sh/x_msa_pro.sh
index 57544c1..9bfc92c 100644
--- a/forester/sh/x_msa_pro.sh
+++ b/forester/sh/x_msa_pro.sh
@@ -1,4 +1,4 @@
-re="(.+)_mafft_1000_g\.aln"
+re="(.+)_mafft_1000_l\.fasta"
 for i in * 
 do
     if test -f "$i" 
@@ -7,7 +7,7 @@ do
         then
             name=${BASH_REMATCH[1]}
             echo $name
-            ruby /home/zma/git/forester/forester/ruby/evoruby/exe/msa_pro.rb -i=f -o=p -d -c -rr=0.5 -rsl=20 $i ${name}_mafft_1000_g_05_20
+            ruby /home/zma/git/forester/forester/ruby/evoruby/exe/msa_pro.rb -i=f -o=p -d -c -rr=0.5 -rsl=20 $i ${name}_mafft_1000_l_05_20
             rc=$?
             if [[ $rc != 0 ]]
             then
diff --git a/forester/sh/x_phylo_pl.sh b/forester/sh/x_phylo_pl.sh
index 9a04718..09ea8d4 100644
--- a/forester/sh/x_phylo_pl.sh
+++ b/forester/sh/x_phylo_pl.sh
@@ -1,4 +1,4 @@
-re="(.+)_mafft_1000_g_05_20"
+re="(.+)_mafft_1000_l_05_20"
 for i in * 
 do
     if test -f "$i" 
diff --git a/forester/sh/x_tap.sh b/forester/sh/x_tap.sh
index aeec299..edad3ea 100644
--- a/forester/sh/x_tap.sh
+++ b/forester/sh/x_tap.sh
@@ -1,4 +1,4 @@
-re="(.+)\.fasta"
+re="(.+)\.fasta$"
 for i in * 
 do
     if test -f "$i"