[Bioperl-l] Bio::DB::GenBank and large number of requests

snoze pa snoze.pa at gmail.com
Wed Jan 30 13:01:46 EST 2008


U can use LWP one line code to grab sequences..

On Jan 29, 2008 11:19 AM, Tristan Lefebure <tristan.lefebure at gmail.com>
wrote:

> Hello,
>
> I would like to download a large number of sequences from GenBank (122,146
> to be exact) following a list of accession numbers.
> I first investigated around Bio::DB::EUtilities, but got lost and finally
> used Bio::DB::GenBank.
> My script works well for short request, but it gives the following error
> with the long request:
>
>  ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: WebDBSeqI Request Error:
> 500 short write
> Content-Type: text/plain
> Client-Date: Tue, 29 Jan 2008 17:22:46 GMT
> Client-Warning: Internal response
>
> 500 short write
>
> STACK: Error::throw
> STACK: Bio::Root::Root::throw
> /usr/local/share/perl/5.8.8/Bio/Root/Root.pm:359
> STACK: Bio::DB::WebDBSeqI::_request
> /usr/local/share/perl/5.8.8/Bio/DB/WebDBSeqI.pm:685
> STACK: Bio::DB::WebDBSeqI::get_seq_stream
> /usr/local/share/perl/5.8.8/Bio/DB/WebDBSeqI.pm:472
> STACK: Bio::DB::NCBIHelper::get_Stream_by_acc
> /usr/local/share/perl/5.8.8/Bio/DB/NCBIHelper.pm:361
> STACK: ./fetch_from_genbank.pl:58
> ---------------------------------------------------------
>
> Does that mean that we can only fetch 500 sequences at a time?
> Should I split my list in 500 ids framents and submit them one after the
> other?
>
> Any suggestions very welcomed...
> Thanks,
> -Tristan
>
>
> Here is the script:
>
> ##################################
> use strict;
> use warnings;
> use Bio::DB::GenBank;
> # use Bio::DB::EUtilities;
> use Bio::SeqIO;
> use Getopt::Long;
>
> # 2008-01-22 T Lefebure
> # I tried to use Bio::DB::EUtilities without much succes and get back to
> Bio::DB::GenBank.
> # The following procedure is not really good as the stream is first copied
> to a temporary file,
> # and than re-used by BioPerl to generate the final file.
>
> my $db = 'nucleotide';
> my $format = 'genbank';
> my $help= '';
> my $dformat = 'gb';
>
> GetOptions(
>        'help|?' => \$help,
>        'format=s'  => \$format,
>        'database=s'    => \$db,
> );
>
>
> my $printhelp = "\nUsage: $0 [options] <list of ids or acc> <output>
>
> Will download the corresponding data from GenBank. BioPerl is required.
>
> Options:
>        -h
>                print this help
>        -format: genbank|fasta|...
>                give output format (default=genbank)
>        -database: nucleotide|genome|protein|...
>                define the database to search in (default=nucleotide)
>
> The full description of the options can be find at
> http://www.ncbi.nlm.nih.gov/entrez/query/static/efetchseq_help.html\n<http://www.ncbi.nlm.nih.gov/entrez/query/static/efetchseq_help.html%5Cn>
> ";
>
> if ($#ARGV<1) {
>        print $printhelp;
>        exit;
> }
>
> open LIST, $ARGV[0];
> my @list = <LIST>;
>
> if ($format eq 'fasta') { $dformat = 'fasta' }
>
> my $gb = new Bio::DB::GenBank(  -retrievaltype => 'tempfile',
>                                -format => $dformat,
>                                -db => $db,
>                        );
> my $seqio = $gb->get_Stream_by_acc(\@list);
>
> my $seqout = Bio::SeqIO->new( -file => ">$ARGV[1]",
>                                -format => $format,
>                        );
> while (my $seqo = $seqio->next_seq ) {
>        print $seqo->id, "\n";
>        $seqout->write_seq($seqo);
> }
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