[Bioperl-l] genpept/swiss
Andrew Dalke
dalke@acm.org
Mon, 4 Sep 2000 17:44:34 -0600
Kris Boulez <krbou@pgsgent.be>:
>While at that moment I want to
>be able to say that he can ignore the warning if (e.g.) he has read the
>sequence correctly.
With Martel it means making a new parser, but I've tried to make it
easy to describe new ones.
For example, to read only the sequence fields in EMBL
you might use the following, untested code:
not_sequence_header = Re("(?!ORIGIN).*)\n")
sequence_header = Str("ORIGIN\n")
sequence_line = Re(" *\d+ (?P<sequence>.*)\n")
record_end = Str("//\n")
record = Rep(not_sequence_header) + \
sequence_header + \
Group("sequence_block", Rep(sequence_line)) + \
record_end
parser = record.make_parser()
...
In other words, this reads lines until it finds the "ORIGIN" line, then
the next lines (up to the "//\n") are read in as sequence data.
Andrew
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Date: Fri, 1 Sep 2000 15:23:10 +0100 (BST)
From: James Gilbert <jgrg@sanger.ac.uk>
To: Bioperl <vsns-bcd-perl@lists.uni-bielefeld.de>
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Subject: [Bioperl-l] minor EMBL and GenBank fixes
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I've fixed SeqIO::embl and SeqIO::genbank, where
the accession_number method was returning
"unknown". This was becasue accession_number was
being added to the Bio::Seq object during the
header parsing loop. accession is actually stored
in the Bio::PrimarySeq object, but a new
Bio::PrimarySeq object was being made after the
sequence (unnecessary, because it is made along
with the new Bio::Seq object).
James
James G.R. Gilbert
The Sanger Centre
Wellcome Trust Genome Campus
Hinxton
Cambridge Tel: 01223 494906
CB10 1SA Fax: 01223 494919
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Date: Wed, 30 Aug 2000 23:58:41 -0700
From: "Mike Cariaso" <mcariaso@genelogic.com>
Organization: Gene Logic
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Subject: [Bioperl-l] Bio::DB::Genbank && Firewalls
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As reported Bio::DB::GenBank and Bio::DB::GenPept do not work through firewalls.
I've put together some code to make it work, but my code uses LWP::UserAgent
and HTTP::Request. Also I see (after this was done) that AJM has submitted a
non-LWP patch.
It doesn't yet have any error checking, and I'd eventually like to set it up so
that its only used if there is a firewall or a flag set, to avoid introducing
another external library dependency, but I was hoping others might look it over,
and perhaps explain the right way to prepare a patch. I'm familiar with diff
already, and I know there is lots of little things I could do to contribute, but
the first submission is a bit of a hurdle for me.
The fix is a drop in replacement for the subroutine _get_stream in
Bio::DB::GenBank.pm.
sub _get_stream {
my($self, $entrez) = @_;
my $ua = LWP::UserAgent->new();
$ua->env_proxy;
my $req = HTTP::Request->new(GET =>
'http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?'.$entrez);
my $res = $ua->request($req);
my $fh = IO::File->new_tmpfile();
my $content = $res->content;
$content =~ s/^.*?-----+\n//s;
$fh->print($content);
$fh->flush;
$fh->reset;
return Bio::SeqIO->new('-fh' => $fh, '-format' => 'Fasta');
}
You'll need to add
use LWP::UserAgent;
use HTTP::Request;
use IO::File;
somewhere near the other 'use' statements at the top.
The exact same code will also need to be dropped in for GenPept. Which shows a
strong need to move this into some base class or common lib, but that can wait
for now.
Lastly, the POD for UserAgent can explain how to use the firewall in more
detail, but all you have to do is
setenv http_proxy http://proxy.domain.com:/8080/
ow whatever is appropriate for your shell and network config.
--
mike cariaso ---------------- mcariaso@genelogic.com
ph:510-981-3156 ---------------------------- fax:510-649-3449
----------------- fear darkness, not fire -------------------