Bioperl: Interface to Wise2 programs

[Ewan Birney]

On Thu, 8 Jun 100, Robert E. Bruccoleri wrote:

> Dear All,
> 	Is anyone aware of an open source Perl module for running the
> Wise2 programs and parsing the output into convenient entities
> analogous to the very nice blast modules in Bioperl. The Wise2 API is
> difficult for me to work with. Thanks.

<sigh>

You don't like the Wise2 API (I can hear people agreeing with you around
the world). It is a very *complete* API...

Honestly - the API was dreadful. It was my first API I wrote in a complete
manner and is just not good. Apologies. (it does *work* which is pretty
cool...)



I guess... so ... I know of no modules to do this, despite being both the
author of Wise2 and the coordinator to bioperl.

I would suggest - for gene predictions - using the -genes output and
parsing it (it is easy to parse). Do not use the -gff output as it is
wrong.

For the alignments, take a look at the -alb output. Quite parsable and
very complete.




> 
> Sincerely,
> Bob
> 
> +----------------------------------+------------------------------------+
> | Robert E. Bruccoleri, Ph.D.      | Phone: 609 737 6383                |
> | President, Congenomics, Inc.     | Fax:   609 737 7528                |
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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