X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fplot_matches;h=59148d7688b70b6befc33d2e6c9db37b2bac55b1;hb=c96d5bccecf2141a208af8f58df1bcb2d007edfa;hp=cc6a345ef45e41ed0154fd6e2a74b68344401379;hpb=bb8bde10a78fa8fe9a2ce5620788beb3ee5226f0;p=biopieces.git

diff --git a/bp_bin/plot_matches b/bp_bin/plot_matches
index cc6a345..59148d7 100755
--- a/bp_bin/plot_matches
+++ b/bp_bin/plot_matches
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl -w
+#!/usr/bin/env perl
 
 # Copyright (C) 2007-2009 Martin A. Hansen.
 
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Plot;
@@ -39,7 +40,7 @@ use IPC::Open2;
 my ( $options, $in, $out, $default, $terminals, $record, @data, $fh, $result, %data_hash, $tmp_dir );
 
 $default   = "plot_matches";
-$terminals = "dumb,x11,aqua,post,svg";
+$terminals = "dumb,x11,aqua,post,svg,png";
 
 $options = Maasha::Biopieces::parse_options(
     [
@@ -112,7 +113,7 @@ sub dotplot_matches
 
     foreach $match ( @{ $matches } )
     {
-        if ( $match->{ "DIR" } =~ /^f/ )
+        if ( ($match->{ "DIR" } and $match->{ "DIR" } =~ /^f/) or ($match->{ "STRAND" } and $match->{ "STRAND" } eq '+') )
         {
             print $fh_forward join( "\t", $match->{ "Q_BEG" } + 1, $match->{ "S_BEG" } + 1 ), "\n";
             print $fh_forward join( "\t", $match->{ "Q_END" } + 1, $match->{ "S_END" } + 1 ), "\n";
@@ -135,7 +136,7 @@ sub dotplot_matches
     close $fh_forward;
     close $fh_backward;
 
-    $cmd  = "gnuplot";
+    $cmd  = "gnuplot -persist";
 
     $pid = open2( $fh_out, $fh_in, $cmd );