[Bioperl-l] Downloading genbank (full) format

[Carnë Draug]

On 22 September 2015 at 21:57, 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,
>                                 );
>

Take a look at the bp_genbank_ref_extractor for how to do it [1].
Alternatively, you can just use that program.  It batch downloads
all the results from a genbank search (see the examples from its
documentation [2]).


[1] https://github.com/bioperl/Bio-EUtilities/blob/master/bin/bp_genbank_ref_extractor
[2] https://github.com/bioperl/Bio-EUtilities/blob/master/bin/bp_genbank_ref_extractor#L249