[Bioperl-l] Bug - Bio::Tools::Run::Alignment::Clustalw - patch

[djibrilo]

Dear,

I have detected some problems on this module (Bio::Tools::Run::Alignment::Clustalw) when I use it from Windows. The executable crashed when there are some spaces on my path files because the system command crash on DOS.

To resolv this problem, you have to add double quote in the module around -outfile and -infile values. 

That is a patch to resolv it. I have tested and it is work well on WinXP, Win2000, Vista with Perl 5.8.

 

--- C:/Perl/site/lib/Bio/Tools/Run/Alignment/Clustalw.pm    Fri Oct  9 15:02:04 2009
+++ C:/Perl/site/lib/Bio/Tools/Run/Alignment/Clustalw_new.pm    Fri Oct  9 15:05:41 2009
@@ -592,7 +592,7 @@
         $instring =  "$infile1";
         $command = '';
     } else { 
-        $instring = " -infile=$infile1";
+        $instring = " -infile=". '"' . $infile1 . '"';
     }
     $param_string .= " $infile2";
 
@@ -775,7 +775,8 @@
     next unless (defined $value);
     my $attr_key = lc $attr; #put params in format expected by clustalw
     $attr_key = ' -'.$attr_key;
-    $param_string .= $attr_key.'='.$value;
+    $param_string .= $attr_key . '=' . '"' . $value . '"';
+    #$param_string .= $attr_key.'='.$value;
     }
 
     for  $attr ( @CLUSTALW_SWITCHES) {