[Bioperl-l] Downloading genbank (full) format
aleimba at gwdg.de
Wed Sep 23 08:08:06 UTC 2015
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.
Institut für Hygiene
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
> 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.
> Another possible but not yet confirmed issue:
> On Wed, Sep 23, 2015 at 5:57 AM, Cacau Centurion <cacaucenturion2 at gmail.com>
>> 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.
>> $seqin = Bio::SeqIO->new(-file => $out,
>> -format => $format,
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