[Biophp-dev] Updates

Nico Stuurman biophp-dev@bioinformatics.org
Tue, 3 Jun 2003 09:31:15 -0700

Hi Sean,

> The updates to esearch, esummary, and the generic xml parser should all
> be on CVS tomorrow morning (US West Coast time) along with HOPEFULLY a
> functioning NCBI BLAST set of code.

I'll try them out.  It might be a good idea to include some 'test' 
scripts`, as a demonstration/test of the functionality of the library 
and as a starting point for people to write their own scripts.

> Nico - can you give me some hints as to your planned structure for 
> filetype
> modules in the seqIOWrite section?  One of the things I can work on 
> while on
> the road are output modules for Phylip and Clustal (for example).  I'd 
> also
> like to work up a simplistic "compare the quality of the match between 
> two
> aligned sequences" algorithm, just for quick automated "throw out bad 
> matches"
> sort of applications.

Actually, if you want to try to have a go at the basis of the 
seqIOWrite section, that would be great.  I am very busy doing real 
biology right now, and I doubt I will get started soon on that part..