From a9f59eb1c1ade542d1a8072b99d60b89715e450d Mon Sep 17 00:00:00 2001
From: jason <jason@bioperl.org>
Date: Mon, 18 Dec 2000 22:36:25 +0000
Subject: [PATCH] more intelligent detection of installed modules (File::Spec)
 and cleanup of .dnd files

svn path=/bioperl-run/trunk/; revision=12921
---
 Bio/Tools/Run/Alignment/Clustalw.pm |  8 ++++----
 Bio/Tools/Run/Alignment/TCoffee.pm  | 14 ++++++++++----
 2 files changed, 14 insertions(+), 8 deletions(-)

diff --git a/Bio/Tools/Run/Alignment/Clustalw.pm b/Bio/Tools/Run/Alignment/Clustalw.pm
index 3f9775f..4d367be 100644
--- a/Bio/Tools/Run/Alignment/Clustalw.pm
+++ b/Bio/Tools/Run/Alignment/Clustalw.pm
@@ -7,7 +7,6 @@
 # Copyright Peter Schattner
 #
 # You may distribute this module under the same terms as perl itself
-
 # POD documentation - main docs before the code
 
 =head1 NAME
@@ -451,9 +450,10 @@ sub _runclustalw {
 
     # Clean up the temporary files created along the way...
     # Replace file suffix with dnd to find name of dendrogram file(s) to delete
-    $infile1 =~ s/\.[^\.]*// ;
-    $infile2 =~ s/\.[^\.]*// ;
-    unlink ( "$infile1.dnd", "$infile2.dnd");
+    foreach my $f ( $infile1, $infile2 ) {
+	$f =~ s/\.[^\.]*$// ;   
+	unlink $f .'.dnd' if( $f ne '' );
+    } 
     return $aln;
 }
 
diff --git a/Bio/Tools/Run/Alignment/TCoffee.pm b/Bio/Tools/Run/Alignment/TCoffee.pm
index 69593ce..2dc9a0c 100644
--- a/Bio/Tools/Run/Alignment/TCoffee.pm
+++ b/Bio/Tools/Run/Alignment/TCoffee.pm
@@ -491,14 +491,14 @@ methods. Internal methods are usually preceded with a _
 
 package Bio::Tools::Run::Alignment::TCoffee;
 
-use vars qw($AUTOLOAD @ISA $TMPOUTFILE $DEBUG $PROGRAM $PROGRAMDIR);
+use vars qw($AUTOLOAD @ISA $TMPOUTFILE $DEBUG $PROGRAM $PROGRAMDIR $FILESPECLOADED);
 use strict;
 use Bio::Seq;
 use Bio::SeqIO;
 use Bio::SimpleAlign;
 use Bio::AlignIO;
 use Bio::Root::RootI;
-use File::Spec;
+eval { require 'File/Spec.pm'; $FILESPECLOADED = 0; };
 
 @ISA = qw(Bio::Root::RootI);
 
@@ -701,7 +701,7 @@ sub _run {
     }
     
     my $status = system($commandstring);
-    $self->throw( "TCoffee call crashed: $? \n") if(-z $TMPOUTFILE);
+    $self->throw( "TCoffee call crashed: $? \n") if( -z $TMPOUTFILE );
 
     my $outfile = $self->outfile() || $TMPOUTFILE;
 
@@ -714,9 +714,15 @@ sub _run {
     # Replace file suffix with dnd to find name of dendrogram file(s) to delete
     if( ! $self->keepdnd ) {
 	foreach my $f ( $infilename, $infile1, $infile2 ) {
+	    next if( !defined $f || $f eq '');
 	    $f =~ s/\.[^\.]*$// ;   
 	    # because TCoffee writes these files to the CWD
-	    (undef, undef, $f) = File::Spec->splitpath($f);    
+	    if( $FILESPECLOADED ) {
+		(undef, undef, $f) = File::Spec->splitpath($f);    
+	    } else { 		
+		my @line = split(/\//, $f);
+		$f = pop @line;	    
+	    }
 	    unlink $f .'.dnd' if( $f ne '' );
 	}
     }
-- 
2.11.4.GIT