1 files changed, 59 insertions, 0 deletions
diff --git a/sci-biology/repbase/files/clean b/sci-biology/repbase/files/clean
new file mode 100755
index 0000000..37ee59c
--- /dev/null
+++ b/sci-biology/repbase/files/clean
@@ -0,0 +1,59 @@
+#!/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;
+    }
+}