From: Tim Reddy Tim <treddy@hudsonalpha.org>
Date: Mon, 12 Jan 2009 22:47:46 +0000 (+0000)
Subject: Added file to flatten fasta as prep for bioprospector
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=cee84746af512a847a96a2b9b2ec55992b08b154

Added file to flatten fasta as prep for bioprospector
---

diff --git a/htswanalysis/scripts/flatten_fasta.pm b/htswanalysis/scripts/flatten_fasta.pm
new file mode 100755
index 0000000..adb6adf
--- /dev/null
+++ b/htswanalysis/scripts/flatten_fasta.pm
@@ -0,0 +1,14 @@
+#!/usr/bin/perl -w
+
+my $started = 0;
+while( my $line = <>) {
+  if($line =~ /^>/) { 
+    if(!$started) { $started = 1; } else { print "\n"; }
+    print $line; 
+  }
+  else {
+    chomp $line;
+    print $line;
+  }
+}
+print "\n";