[Bioperl-l] concatenate two embl sequence files

[Heikki Lehvaslaiho]

Jan, 

It would be easy if someone had written a function to do it. Even writing the 
function is not hard.  I do not think there is no other way than go through 
all features, though.

In my opinion this would be an excellent addition to Bio::Seq::Utilities.

E.g. cat($arrayrefofsequences, optional_seq_class_to_create)
     return a new seq, species and other info based on the first seq in array 

Could you  write it and post to bugzilla?

	-Heikki


On Tuesday 17 January 2006 11:54, jan aerts (RI) wrote:
> Hi all,
>
> Does anyone know of an easy way to concatenate two sequences, including
> recalculation of features positions of the second one? E.g.
>   seq 1 = 100 bp
>     feature A: 5..15
>   seq 2 = 200 bp
>     feature B: 20..30
>   => concatenated sequence 3 = 300 bp
>        feature A: 5..15
>        feature B: 120..130  <<<<<<<<<<<
>
> Annotations (features without range) should be transferred as well.
>
> Of course, it must be possible to create a blank sequence and work my
> way through all features, adding them to a new collection of features
> and stuff. But I was wondering if a simpler technique is possible.
>
> Many thanks,
> Jan Aerts
> Bioinformatics Department
> Roslin Institute
> Roslin, Scotland, UK
>
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     _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
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