[Bioperl-l] problems with getgenbank script
Pedro A Reche Gallardo
reche@research.dfci.harvard.edu
Fri, 19 Apr 2002 09:13:32 -0400
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Hi, I was using the follwing script to retrive many proteins from the
genbank database at the same time and it was worfind with perl 5.05. My
version of bioperl is 0.7. This is the code:
#!/usr/sbin/perl -w
#
# How to retrieve GenBank entries over the Web
#
#
#
use Bio::DB::GenBank;
use Bio::SeqIO;
my $gb = new Bio::DB::GenBank;
my $seqout = new Bio::SeqIO(-fh => \*STDOUT, -format => 'fasta');
my $seqio = $gb->get_Stream_by_batch([ qw(
16041831 13994242 14009490 7230618 7108749 13605922 7230620 15341249
14009488 14009486 14762236 12861474 11321634 8131948 6753344
16172015 16172015 15302083 14009484)]);
while( defined ($seq = $seqio->next_seq )) {
$seqout->write_seq($seq);
}
However, recently I updated my perl to 5.6 and after reinstalling the
bioperl module the script does'nt longer work. This is the error I am
getting.
-------------------- EXCEPTION --------------------
MSG: WebDBSeqI Error - check query sequences!
STACK Bio::DB::WebDBSeqI::get_seq_stream
/usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/WebDBSeqI.pm:300
STACK Bio::DB::NCBIHelper::get_Stream_by_batch
/usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/NCBIHelper.pm:209
STACK toplevel /usr1/par/bin/getgenbank.pl:13
-------------------------------------------
Does anyone know what is going on? Thanks in advance for any help.
Cheers
*******************************************************************
PEDRO A. RECHE , pHD TL: 617 632 3824
Dana-Farber Cancer Institute, FX: 617 632 4569
Harvard Medical School, EM: reche@research.dfci.harvard.edu
44 Binney Street, D1510A, EM: reche@mifoundation.org
Boston, MA 02115 URL:
http://www.reche.org
*******************************************************************
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<tt>Hi, I was using the follwing script to retrive many proteins from the
genbank database at the same time and it was worfind with perl 5.05. My
version of bioperl is 0.7. This is the code:</tt>
<br><tt>#!/usr/sbin/perl -w</tt>
<br><tt>#</tt>
<br><tt># How to retrieve GenBank entries over the Web</tt>
<br><tt>#</tt>
<br><tt>#</tt>
<br><tt>#</tt>
<br><tt>use Bio::DB::GenBank;</tt>
<br><tt>use Bio::SeqIO;</tt>
<br><tt>my $gb = new Bio::DB::GenBank;</tt><tt></tt>
<p><tt>my $seqout = new Bio::SeqIO(-fh => \*STDOUT, -format => 'fasta');</tt><tt></tt>
<p><tt>my $seqio = $gb->get_Stream_by_batch([ qw(</tt>
<br><tt>16041831 13994242 14009490 7230618 7108749 13605922 7230620 15341249</tt>
<br><tt>14009488 14009486 14762236 12861474 11321634 8131948 6753344</tt>
<br><tt>16172015 16172015 15302083 14009484)]);</tt><tt></tt>
<p><tt>while( defined ($seq = $seqio->next_seq )) {</tt>
<br><tt> $seqout->write_seq($seq);</tt>
<br><tt>}</tt><tt></tt>
<p><tt>However, recently I updated my perl to 5.6 and after reinstalling
the bioperl module the script does'nt longer work. This is the error I
am getting.</tt><tt></tt>
<p><tt>-------------------- EXCEPTION --------------------</tt>
<br><tt>MSG: WebDBSeqI Error - check query sequences!</tt>
<br><tt></tt> <tt></tt>
<p><tt>STACK Bio::DB::WebDBSeqI::get_seq_stream /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/WebDBSeqI.pm:300</tt>
<br><tt>STACK Bio::DB::NCBIHelper::get_Stream_by_batch /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/NCBIHelper.pm:209</tt>
<br><tt>STACK toplevel /usr1/par/bin/getgenbank.pl:13</tt>
<br><tt>-------------------------------------------</tt>
<br><tt>Does anyone know what is going on? Thanks in advance for any help.</tt><tt></tt>
<p><tt>Cheers</tt><br>
<BR>
<br><tt>*******************************************************************<br>
PEDRO A. RECHE , pHD
TL: 617 632 3824<br>
Dana-Farber Cancer Institute, FX: 617 632 4569<br>
Harvard Medical School,
EM: reche@research.dfci.harvard.edu<br>
44 Binney Street, D1510A, EM: reche@mifoundation.org <br>
Boston, MA 02115
URL: <A HREF="http://www.reche.org">http://www.reche.org</A> <br>
*******************************************************************</tt>
<br><tt></tt> </html>
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