[Bioperl-l] Downloading genbank (full) format

[Peter Cock]

Hi Cacau,

It seems "gb" is just an alias for "genbank", but as you've
noticed some records are more like manifests for how to
build up the full record from its parts using a CONTIG
entry.

There is also "gbwithparts" which in the NCBI web interface
is "Genbank (full)", but there can be subtle errors with the
processing done at the NCBI end.

http://blastedbio.blogspot.co.uk/2012/03/missing-external-exons-in-genbank-with.html
http://blastedbio.blogspot.co.uk/2012/04/missing-feature-locations-in-genbank.html

Another possible but not yet confirmed issue:
http://lists.open-bio.org/pipermail/biopython/2015-September/015746.html

Peter

On Wed, Sep 23, 2015 at 5:57 AM, Cacau Centurion <cacaucenturion2 at gmail.com>
wrote:

> Hi,
>
> I would like to download sequences in genbank (full) format in batch. What
> should the format be (see the codes)?
>
> I tried 'gb' but got sequences in genbank format. Sometimes the full
> genome sequences might not be downloaded.
>
>
> #code
> $seqin = Bio::SeqIO->new(-file   => $out,
>                                 -format => $format,
>                                 );
>
>
> Yours,
> Cacau
>
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