To do list.

[Peter Rice]

David Martin wrote:

> Having just seen the 'to do' list on the web can I throw my spanner in..
> 
> Could the results output from a number of programs be modified in the
> following way:
> 
> A results object (in much the same way as a sequence object) is
> created. The program author doesn't have to worry about any formatting
> because the result object knows about it.
> New output styles get added at a library level, not an application level.

This is top of my list of things to do. My initial plan is to add a new output
type of 'report' which will use data stored internally as a feature table and
will generate various output formats. These will include the existing feature
formats (e.g. GFF and EMBL) but also include formats rather similar to the
results of 'restrict' 'antigenic' and other programs that effectively report
'features'.

The applications will need (often minor) changes to store results in a feature
table.

This works too for simple lists and the other output types you mentioned.

Default 'formats' can be included in the ACD file. An output type and a format
combination would work nicely (with the output type saying what the program
will pass, and the format available on the command line as an associated
qualifier).

New formats can be easily added (like sequence formats) by extending the
report generating code.

>In addition to this, a new database access format. Not sequences but codon
>usage. The codon usage tables distributed with emboss are positively
>fossilised (6 years old). An access method for reading a species from CUTG
>.spsum files would be great.

Something like an SRS query (possibly through a remote SRS web server)
perhaps?

Something could be defined as a database in emboss.defaults and used by the
codon usage table code.

It would create the need for a new standard for naming codon usage tables, and
a new name for it. Maybe ACA (A CUT above?) Or you could just ask for the code
and then look in (1) a codon usage file and (2) some standard database name

-- 
------------------------------------------------
Peter Rice, LION Bioscience Ltd, Cambridge, UK
peter.rice at uk.lionbioscience.com +44 1223 224723