1 files changed, 0 insertions, 59 deletions
diff --git a/sci-biology/repbase/files/clean b/sci-biology/repbase/files/clean
deleted file mode 100755
index 37ee59c..0000000
--- a/sci-biology/repbase/files/clean
+++ /dev/null
@@ -1,59 +0,0 @@
-#!/usr/bin/perl -w 
-
-use strict;
-
-my $name="";
-my $sequence="";
-my $infile  = $ARGV[0];
-my $outfile = $ARGV[1];
-
-open(LIB, $infile);
-
-open(CLIB, ">", $outfile);
-
-while (<LIB>)
-{
-    if (m/^>/)
-    {
-	if (not $name eq "")
-	{
-	    if ($sequence eq "")
-	    {
-		print "---------------------------------------------------------------------------------------\n";
-		print "Empty sequence: " . $name . "\n";
-	    } 
-	    else
-	    {
-		if ($sequence =~ m/^[ACGTNWSYRMHKXDVB]*$/)
-		{
-		    $sequence =~ s/[WSYRMHKXDVB]/N/g;
-		    if (not $sequence =~ m/NNNN/)
-		    {
-			print CLIB $name;
-			print CLIB $sequence . "\n";
-		    }
-		    else
-		    {
-			print "---------------------------------------------------------------------------------------\n";
-			print "Too many N's:  " . $name;
-		    }
-		}
-		else
-		{
-		    print "---------------------------------------------------------------------------------------\n";
-		    print "Invalid entry: " . $name;
-		    $sequence =~ s/[ACGTN]//g;
-		    print "Reduced sequence:\n";
-		    print $sequence . "\n";
-		}
-		$sequence = "";
-	    }
-	}
-	$name = $_;
-    }
-    else
-    {
-	$sequence .= uc($_);
-	$sequence =~ s/\n//g;
-    }
-}