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>