From a976c83f0ef715cb403b744479a42f3ecdb1ef3a Mon Sep 17 00:00:00 2001
From: cmzmasek <chris.zma@outlook.com>
Date: Tue, 21 Mar 2017 14:36:50 -0700
Subject: [PATCH] shell to run hmmscan

---
 forester/sh/x_hmmscan.sh |   13 +++++++++++++
 1 file changed, 13 insertions(+)
 create mode 100644 forester/sh/x_hmmscan.sh

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
-- 
1.7.10.2