removed debug message

[biopieces.git] / bp_bin / plot_matches

diff --git a/bp_bin/plot_matches b/bp_bin/plot_matches
index a2d97cf76b02aead93c80caa1041a3e493a80676..59148d7688b70b6befc33d2e6c9db37b2bac55b1 100755 (executable)
--- 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;
@@ -36,10 +37,10 @@ use IPC::Open2;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $default, $terminals, $record, @data, $fh, $result, %data_hash, $tmp_dir );
+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(
     [
@@ -78,7 +79,8 @@ print $fh "$_\n" foreach @{ $result };
 
 close $fh;
 
-Maasha::Filesys::dir_remove( $tmp_dir );
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
 
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SUBROUTINES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
@@ -111,7 +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";
@@ -134,7 +136,7 @@ sub dotplot_matches
     close $fh_forward;
     close $fh_backward;
 
-    $cmd  = "gnuplot";
+    $cmd  = "gnuplot -persist";
 
     $pid = open2( $fh_out, $fh_in, $cmd );
     
@@ -189,20 +191,13 @@ sub dotplot_matches
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -210,4 +205,3 @@ END
 
 
 __END__
-