[Bioperl-l] Downloading genbank (full) format

[Andreas Leimbach]

Hi Cacau, Peter,

your code doesn't specify how you're downloading your sequences from
NCBI. Thus, this issue might be related if you're using Eutils.

Cheers,
Andreas

--
Andreas Leimbach
Universität Münster
Institut für Hygiene
Mendelstr. 7
D-48149 Münster
Germany

Tel.: +49 (0)551 39 33843
E-Mail: aleimba at gwdg.de

On 23.09.2015 09:36, Peter Cock wrote:
> 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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>>
> 
> 
> 
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