[Bioperl-l] dbEST read pb

[Gilles Parmentier]

Hello all,

I tried the followin code to read a dbEST file (ie dbestXX.gb.gz):

####

use Bio::SeqIO ;
use Bio::Annotation::Collection ;

#This scripts extracts all ESTs for a given species from a local dbEST copy.

$| = 1 ;

system "ls $ARGV[0]/*.gz > dbest.list" ;
open (dblist_hnd, "dbest.list") || die ("Cannot open dbest.list\n") ;
my @dbest_files = <dblist_hnd> ;
close dblist_hnd ;

#This should be repeated for each dbEST file:
#for (my $ind_dbfile = 0 ; $ind_dbfile <= $#dbest_files ; $ind_dbfile++)
for (my $ind_dbfile = 0 ; $ind_dbfile <= 1 ; $ind_dbfile++)
     {
      $dbest_files[$ind_dbfile] =~ s/\n// ;
      $dbest_files[$ind_dbfile] =~ s/\r// ;
      print "Working for $dbest_files[$ind_dbfile]\n" ;
      system "gunzip -c $dbest_files[$ind_dbfile] > dummy" ;
      #Forgot header:
      my $in = Bio::SeqIO->new (-file =>"tail -9 dummy |",
                                -format => 'Genbank') ;
     $in->_read_GenBank_References ;

      while (my $seq = $in->next_seq ())
            {
             if ($seq->species->binomial eq "$ARGV[1] $ARGV[2]")
                {
                 #...
                 }
             }
      }

####

I have this output:

Working for ../../../dbEST//gbest1.seq.gz          <------- my output
Can't use an undefined value as a SCALAR reference at 
/Library/Perl/5.8.4/Bio/SeqIO/genbank.pm line 929.   <---bioperl error msg

I tried this with linux/debian and macosx, and I got the same.

Do I miss something or is this a bug ?

Thanks in adavance

Gilles