[Bioperl-l] get_Seq_by_id: CONTIG found
melody
xyuany at mail2.sysu.edu.cn
Wed Jul 30 06:47:31 UTC 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>
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