From: cmzmasek <chris.zma@outlook.com>
Date: Tue, 21 Mar 2017 21:36:50 +0000 (-0700)
Subject: shell to run hmmscan
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a976c83f0ef715cb403b744479a42f3ecdb1ef3a;p=jalview.git

shell to run hmmscan
---

diff --git a/forester/sh/x_hmmscan.sh b/forester/sh/x_hmmscan.sh
new file mode 100644
index 0000000..bdd460b
--- /dev/null
+++ b/forester/sh/x_hmmscan.sh
@@ -0,0 +1,13 @@
+re="(.+)\.fasta"
+for i in * 
+do
+    if test -f "$i" 
+    then
+        if [[ $i =~ $re ]];
+        then
+            name=${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
+       fi
+    fi
+done
\ No newline at end of file