Re: Downloading genbank (full) format

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 <[email protected]>
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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>

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