Dear All;
I tried a Clustw Alignment script as shown below, ClustAln.pl. It runs
successfully under MS-Dos command line (perl ClustAln.pl), while when I tried to run
it through the CGI approach (http://localhost/cgi-bin/ClustAln.pl)
, I get this error message:
**************************************************************************************
Error in tempdir() using \\\\XXXXXXXXXX: Could not create directory \\\\zsClfr1b9g:
Invalid argument at C:/Perl/site/lib/Bio/Root/IO.pm line 677.
**************************************************************************************
;;;;;;ClustAln.pl;;;;;;;;
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
#!C:\Perl\bin\perl.exe
use lib "C:\Perl\lib";
use FileIO;
use SeqFileIO;
use IO::String;
use CGI qw/:standard/;
use Bio::Perl;
use Bio::Tools::Run::Alignment::Clustalw;
use Bio::SimpleAlign;
use Bio::AlignIO;
use strict;
use warnings;
my @params = ('ktuple' => 2, 'matrix' => 'BLOSUM');
my $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
my $ktuple = 3;
$factory->ktuple($ktuple); # change the parameter before executing
my $str = Bio::SeqIO->new(-file=> 'Clustseq.fa',
'-format' => 'Fasta');
my @seq_array =();
while ( my $seq = $str->next_seq() ) {push (@seq_array, $seq) ;}
my $seq_array_ref = [EMAIL PROTECTED];
# where @seq_array is an array of Bio::Seq objects
my $aln = $factory->align($seq_array_ref);
my $out = Bio::AlignIO->new(-file => ">alout.aln",
-format => 'clustalw',
-flush => 0);
$out->write_aln($aln);
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
Could anybody point me what the problem here?
Thanks in advance
Jane
--
To unsubscribe, e-mail: [EMAIL PROTECTED]
For additional commands, e-mail: [EMAIL PROTECTED]
<http://learn.perl.org/> <http://learn.perl.org/first-response>
