| CC: | bug-bioperl-run [...] rt.cpan.org |
| Subject: | Bug - Bio::Tools::Run::Alignment::Clustalw - patch |
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) {
Best Regards,
Djibril