[BioPython] Biopython projects for students

[Andrew Nunberg]

I can come up with some ideas..
1) a seq object that contains quaity data from phred and a seq object that
can have both sequence and quality data
2) a gff class that handles gff versions 1,2,3
    I see there is a gff class but seems to be tied to the Bio::DB class in
bioperl.  I would like to see a generic gff class that you can just build
your own gff objects(if this can be done currently, please excuse my
ignorance)
3) add parsing and manipulation of ace files(from phrap) as is done in
bioperl's Bio::Assembly
4)extend biopython's seqio to include other file formats: genbank,phd, scf,
etc...(as far as I could tell fasta is only supported, but I could be wrong)


Just some things off the top of my head
-- 
Andrew Nunberg
Bioinformagician
Orion Genomics
(314)-615-6989
www.oriongenomics.com


> From: James Cussens <jc at cs.york.ac.uk>
> Date: Wed, 21 Jan 2004 10:52:40 +0000
> To: biopython at biopython.org
> Subject: [BioPython] Biopython projects for students
> 
> I'm trying to come up with Biopython projects for final year students in
> my dept. Problem is: I have to define the projects now, but the students
> don't start on them until October! I'm worried that a project which says
> "add support for x to BioPython" might be superceded by the time October
> comes around. If anyone can think of something useful, but which is
> unlikely to be done that soon, I would appreciate your thoughts.
> 
> The students are CS students, not specifically bioinformaticians - and
> the projects last from October to mid-March.
> 
> James
> 
> -- 
> James Cussens                                        jc at cs.york.ac.uk
> Department of Computer Science                Tel  +44 (0)1904 434732
> University of York                            Fax  +44 (0)1904 432767
> Heslington, York YO10 5DD, UK            http://www.cs.york.ac.uk/~jc
> 
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