[Bioperl-l] LiveSeq

Heikki Lehvaslaiho heikki@ebi.ac.uk
Tue, 12 Dec 2000 10:11:28 +0000

Ewan Birney wrote:
> Joseph -
> Thanks for your commits.
> I think it would be nice Joseph to talk through your objects first on the
> list and get feedback, in particular for the naming of your objects. Once
> commited we can't do a great deal about changing their names.
> This is partly my and partly heikki's fault for not making sure that you
> talked things through on the list first. Don't lose sleep over it, but be
> aware that you are now working in a collaborative enviroment, and you
> should post to the list before making large commits.
> I think a nice post about what LiveSeq is and what it does to the list
> would be a good thing as well.

My apologies for not announcing this to the mailing list beforehand. I
had to be away yesterday and I had been putting pressure on Joseph to
commit his code for so long that he very dutifully did it on first
possible occasion after getting his login.

LiveSeq has actually been announced but so long ago that no one can
remember (see below for the text). Now that the files are in the
repository, we'll start cleaning the code and adding tests.

Any suggestions on naming and improving the code are welcome,


Subject: [Bioperl-l] Bio::Variation committed [Project: Computational  
         Mutation Expression Toolkit]
Date:    Wed, 19 Jul 2000 14:35:46 +0100
From:    Heikki Lehvaslaiho <heikki@ebi.ac.uk>


I just committed Bio::Variation files to bioperl-live. All in all 10
classes and 185 tests in seven t files. 'cvs update -d' and you can
see them all. Easiest way of getting grips with what these classes can
do is to have a look at test input files, e.g. t/mutation.dat.

You'll need Bio::LiveSeq to actually generate the information from
sequences, but those files are not committed, yet.


Heikki Lehvaslaiho wrote:
> Dear Bioperlers,
> We'd like to announce a project to add classes into Bioperl to handle
> sequence variations.
> The Computational Mutation Expression Toolkit project consists of two
> sets of Bioperl classes:
> Bio::LiveSeq
> Bio::LiveSeq name space contains a set of modules to read in (EMBL
> formatted) sequences and create a data structure (double linked list)
> to represent the DNA sequence. A model of an eucaryotic gene is built
> by creating virtual exon, transcript and translation objects which are
> dependant on the DNA sequence object. This novel strategy allows us to
> handle biological sequences in a way that makes it extremely easy to
> deal with sequence variations and coordinate system changes. The
> results can be written out as Bio::Variation objects.
> Bio::Variation
> Bio::Variation name space contains modules to store sequence variation
> information as differences between the reference sequence and changed
> sequences. Also included are classes to write out and recrete objects
> from EMBL-like flat files and XML. Lastly, there are simple classes to
> create some sequence change objects. At the moment, we do not have
> methods to create bioperl sequence objects from diffs but they should
> be easy to add.
> We've set up web pages with more information about the project:
>         http://www.ebi.ac.uk/mutations/toolkit/
> We'll start committing code to CVS shortly (or after summer holidays).
>     Heikki Lehvaslaiho & Joseph Insana
>      heikki@ebi.ac.uk    insana@ebi.ac.uk