[Bioperl-l] concatenate two embl sequence files
heikki at sanbi.ac.za
Wed Jan 18 02:11:20 EST 2006
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?
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
_/_/_/_/_/ Associate Professor skype: heikki_lehvaslaiho
_/ _/ _/ SANBI, South African National Bioinformatics Institute
_/ _/ _/ University of Western Cape, South Africa
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