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debug message now uses the debug method

svn path=/bioperl-run/trunk/; revision=13005
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commit edf5b71f7f1b3df7da34e8a52411cf8ea373c164 1 parent f5abc36
@hyphaltip hyphaltip authored
Showing with 7 additions and 6 deletions.
  1. +7 −6 Bio/Tools/Run/Alignment/Clustalw.pm
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13 Bio/Tools/Run/Alignment/Clustalw.pm
@@ -310,7 +310,7 @@ methods. Internal methods are usually preceded with a _
package Bio::Tools::Run::Alignment::Clustalw;
-use vars qw($AUTOLOAD @ISA $DEBUG $PROGRAM $PROGRAMDIR
+use vars qw($AUTOLOAD @ISA $PROGRAM $PROGRAMDIR
$TMPDIR $TMPOUTFILE @CLUSTALW_SWITCHES @CLUSTALW_PARAMS
@OTHER_SWITCHES %OK_FIELD);
use strict;
@@ -535,14 +535,15 @@ sub _run {
chmod 0777, $infile1,$infile2;
$command = '-profile';
}
+
my $commandstring = $PROGRAM." $command"." $instring".
" -output=gcg". " $param_string";
-# next line is for debugging purposes
- if( $DEBUG ) {
- print "clustal command = $commandstring \n";
- }
- my $status = system($commandstring);
+
+ $self->debug( "clustal command = $commandstring");
+
+ my $status = system($commandstring);
$self->throw( "Clustalw call crashed: $? \n") unless $status==0;
+
my $outfile = $self->outfile() || $TMPOUTFILE ;
# retrieve alignment (Note: MSF format for AlignIO = GCG format of clustalw)
my $in = Bio::AlignIO->new(-file => $outfile, '-format' => 'MSF');
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