[Bioperl-l] Downloading genbank (full) format

[Andreas Leimbach]

sorry, forgot to include the link:
https://github.com/bioperl/bioperl-live/issues/89

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 10:08, Andreas Leimbach wrote:
> 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
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at mailman.open-bio.org
>>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>>
>>
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