Parsing a GenBank file

[Rob2012]

Hi,

I would be happy if someone could help me get the following code to output the sequences (including the ids) of all records in the input file (http://biopython.org/DIST/docs/tutor...s_orchid.gbk):

 use Bio::SeqIO;
    use Bio::Seq;
    use Bio::DB::GenBank;

    $seq_obj = Bio::SeqIO->new(-file => "ls_orchid.gbk" , '-format' => 'genbank');
    $seqio_obj2 = Bio::SeqIO->new(-file => '>sequence.fasta', -format => 'genbank' );

    while ( my $seq = $seq_obj->next_seq() ) {
    print "Sequence ",$seq->id ($seq_obj)"\n";
    #print $seq_obj->seq,"\n";
    $seqio_obj2->write_seq($seq_obj);
    }

I would like to see an output consisting of purely sequences (preferably with headers) as follows:

seq1:
    ATTCGCTGCATGACAT..........
    Seq2:
    ACTGCGATGGATGGAT..

Thank you

[rhinoceros]

You could try biopieces read_genbank

[dpryan]

For those getting here later via google, the solution was posted on biostars.

[Rob2012]

Thanks Rhinoceros.