[BioPython] Biopython projects for students

[Frank Kauff]

Hi,

we are working with phred and phrap a lot and wrote a phd and an ace
parser. The phd should be ready for release soon, the ace parserjust 
needs support for some of the ace commands I have ignored so far because
I didn't need them...

Frank

On Wed, 2004-01-21 at 13:14, Andrew Nunberg wrote:
> 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
-- 
Frank Kauff
Dept. of Biology
Duke University
Box 90338
Durham, NC 27708
USA

Phone 919-660-7382
Fax 919-660-7293