X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fplot_matches;h=59148d7688b70b6befc33d2e6c9db37b2bac55b1;hb=5de6112b70b59420b245ce636a8b2e3c90acbe00;hp=9bdb0874693885ffb9ce5bdadfeb991c42ab5ec2;hpb=66938be910a5642b50ddf28991649858b5c36580;p=biopieces.git

diff --git a/bp_bin/plot_matches b/bp_bin/plot_matches
index 9bdb087..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(
     [
@@ -78,8 +79,6 @@ print $fh "$_\n" foreach @{ $result };
 
 close $fh;
 
-Maasha::Filesys::dir_remove( $tmp_dir );
-
 Maasha::Biopieces::close_stream( $in );
 Maasha::Biopieces::close_stream( $out );
 
@@ -114,7 +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";
@@ -137,7 +136,7 @@ sub dotplot_matches
     close $fh_forward;
     close $fh_backward;
 
-    $cmd  = "gnuplot";
+    $cmd  = "gnuplot -persist";
 
     $pid = open2( $fh_out, $fh_in, $cmd );