[Bioperl-l] get_Seq_by_id: CONTIG found

melody xyuany at mail2.sysu.edu.cn
Wed Jul 30 02:47:31 EDT 2008


I'm trying to download a bunch of sequences from GenBank using the gi ,when
I run the code,I got The message like this :
<BEGIN MESSAGE>
-------------------- WARNING ---------------------
MSG: CONTIG found. GenBank get_Stream_by_acc about to run.
---------------------------------------------------
Warning: unable to close filehandle FETCH properly.
<END MESSAGE>
What can I do if I want this code work.
Thanks a lot,
Melody xiong
 
<BEGIN EXAMPLE CODE>
use Bio::DB::GenBank;
my $db_obj = new Bio::DB::GenBank;
$db_obj->proxy(['http','ftp'],'http://proxy2.sysu.edu.cn:3128/');
        my $seq_obj=$db_obj->get_Seq_by_gi("42537818");
        my $seqio_obj=Bio::SeqIO->new(-file => ">temp2.txt", -format =>
"fasta" );
        $seqio_obj->write_seq($seq_obj);
        <END EXAMPLE CODE>
 

 



More information about the Bioperl-l mailing list