[BioRuby] concatenate two EMBL sequence files

[Toshiaki Katayama]

Hello,

For your purpose, using BioPerl would be straight forward.

BioRuby doesn't have feature re-location mechanism and
no one is working on writing out in EMBL format for now.

I might consider to do the similar job by converting both
sequence to GFF.
By the way, having Bio::Locations#shift(slide_length) method
would be helpful.

Regards,
Toshiaki Katayama

On 2006/01/16, at 22:46, jan aerts (RI) wrote:

> Hello all,
>
> I'm trying to concatenate two EMBL files (_with_ features) into one larger sequence. Of course, positions of features of the second sequence have to recalculated in the new sequence.
> e.g.:
>   sequence 1 = 100 bp
>     feature A: 5..10
>   sequence 2 = 200 bp
>     feature B: 15..20
>   => concatenated sequence 3 = 300 bp
>        feature A: 5..10
>        feature B: 115..120
>
> I'd like to write out the new sequence as an EMBL file.
>
> Can anyone point me in the right direction? Many thanks.
>
> A possible perl-convert,
> Jan Aerts, PhD
> Bioinformatics Group
> Roslin Institute
> Roslin
> Scotland, UK
>
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