From d5b4cbe96883e41b093080a1d9d1235341cd9df4 Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Wed, 14 Sep 2011 12:07:28 +0100
Subject: [PATCH] JAL-931 (related) - utility to split an alignment database
 in stockholm format into individual alignment files

---
 utils/splitstockholm.pl |   30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 utils/splitstockholm.pl

diff --git a/utils/splitstockholm.pl b/utils/splitstockholm.pl
new file mode 100644
index 0000000..5a31679
--- /dev/null
+++ b/utils/splitstockholm.pl
@@ -0,0 +1,30 @@
+#!/usr/bin/perl
+# Splits a concatenated set of Stockholm Files into several individual files.
+
+use strict;
+use FileHandle;
+my $ac;
+my $lns="";
+my $fh;
+while (<>) {
+    if ($_=~m!^//!) {
+	$fh->print("//\n");
+	$fh->close();
+	$ac = undef;
+	$lns = "";
+    } else {
+	if ($_=~/GF\s+AC\s+([0-9.RPF]+)/) { 
+	    $ac=$1; 
+	    ($fh=new FileHandle)->open(">$ac.stk") or die("Couldn't open file '$ac.stk'"); 
+	    $lns=~/^. STOCKHOLM 1.0/ or $fh->print("# STOCKHOLM 1.0\n");
+	};
+	if (defined($fh)) {
+	    if (defined $lns) { 
+		$fh->print($lns); $lns=undef; }
+	    
+	    $fh->print($_);
+	} else {
+	    $lns .= $_;
+	}
+    }
+}
-- 
1.7.10.2