cjfields at illinois.edu
Fri Apr 9 16:06:47 EDT 2010
Is it the same as regular ol' eutils?
Note the rettype = gbc|gpc, but retmode = text, not xml. This worked
my @ids = @ARGV;
my $eutil = Bio::DB::EUtilities->new(-eutil => 'efetch',
-db => 'nuccore',
-id => \@ids,
-rettype => 'gbc',
-retmode => 'text');
On Thu, 2010-04-08 at 20:15 +0000, Mark A. Jensen wrote:
> FWIW -In my SoapE investigations I found NCBI-hosted XML schema for insdc, but didn't ever run across a format descriptor that gets return data in that format-- MAJ
> >-----Original Message-----
> >From: Chris Fields [mailto:cjfields at illinois.edu]
> >Sent: Thursday, April 8, 2010 04:09 PM
> >To: 'Dave Messina'
> >Cc: 'bioperl-l', 'Wayne Davis'
> >Subject: Re: [Bioperl-l] Bio::SeqIO::genbank
> >On Thu, 2010-04-08 at 21:39 +0200, Dave Messina wrote:
> >> Hi Wayne,
> >> > if $mol is not in the fixed list of genbank molecule types it should
> >> > be set to the default value of 'DNA', or some other smarter way of
> >> > forcing the molecule type into the fixed vocabulary would be a help.
> >> Sounds good to me. Did you modify your local copy of Bio::SeqIO::genbank and try it out?
> >> I will say, though, that Genbank is a tricky format, both to read and to write. Even if BioPerl would write Genbank records that are fully compliant with the spec, I'm pretty sure they would not be round-trippable*. That is, if you read a Genbank record into BioPerl and then wrote it back out, the output wouldn't exactly match the input.
> >This is true. Jason and I talked about this recently and arrived pretty
> >much at the same conclusion. We're mainly interested in parsing data
> >into a usable framework for manipulation. Recreating data isn't our top
> >> I think that NCBI is trying to nudge people toward their XML format. I know it won't help this particular situation, but it might be an option to consider for the future.
> >The only problem I had with the XML spit out from eutils has been it was
> >an on-the-fly conversion of the ASN.1. Not sure what the status of it
> >is now.
> >What's going on with the INSDC XML format? That was supposed to be an
> >international standard and appeared more lightweight (if such a thing
> >can be said about XML).
> >> Speaking of which, what is the current status of the BioPerl Genbank XML parser? Jay, did you ever release that?
> >> Dave
> >> * not that they were designed to be: http://www.bioperl.org/wiki/HOWTO:SeqIO#Caveats
> >I think it was in a branch, can't recall.
> >Bioperl-l mailing list
> >Bioperl-l at lists.open-bio.org
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