Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

diff alignment/prank.pl @ 0:5b9a38ec4a39 draft default tip

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author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/alignment/prank.pl	Tue Mar 11 12:19:13 2014 -0700
@@ -0,0 +1,15 @@
+#!/usr/bin/perl
+
+my $input = $ARGV[0];
+my $format = $ARGV[1];
+my $missing = $ARGV[2];
+my $output = "output";
+my $fparam;
+
+if($missing eq 'yes'){
+	$fparam = "-F";
+}else{
+	$fparam = "";
+}
+my $run = qx/prank -d=$input -o=$output -f=$format $fparam/;
+print $run;