[Bioperl-l] error loading sequence

Munirul Islam ba6450 at wayne.edu
Tue Jul 24 17:16:54 EDT 2007


Hello everyone:

I am having problem loading a sequence file from within a directory.  

#############################################################
$dirname = "rundir";
opendir (DIR, $dirname) || die("can't open $dirname");
      
while (defined($file = readdir(DIR))) {
    next if $file =~ /^\.\.?$/;		# skip . and ..
    $abs_path = File::Spec->rel2abs( $file ) ;
    
    # gives a file not found exception for the following code
    my $alignio = Bio::AlignIO->new(-format => 'nexus',
				-file   => $abs_path);
    my $aln = $alignio->next_aln;
    @sequencenames -> $aln->_read_taxlabels;
	  		
    foreach $taxa (@sequencenames) {
	print $taxa . "\n";
    } 		
}        
#############################################################

Your suggestions please.

Regards,

Munirul Islam
PhD Student
Computer Science
Wayne State University
Detroit, Michigan, USA


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