[Bioperl-l] Consed.pm

[Ewan Birney]

On Fri, 15 Jun 2001, Chad Matsalla wrote:

> 
> Hello all,
> 
> I have created a module I use to categorise and parse acefiles and assorted cling-on files created by phrap, capN (where for me N is 3 or 4), and other programs.
> 
> The module contains objects used to:
> 1) classify contigs based on how many sequences are contained within it
> 2) return a contig's members, consensus sequence, and consensus quality
> 3) return a contig's putative name (depending on the names of its members)
> 4) return the quality of arbitrary sequences in the project
> 
> Would this be of any use to people? I am just cleaning up the code and it is basically ready for release if anybody is interested. It has been extensively tested in our sequencing pipeline and has proven to be reliable and predictable.

Sounds great!

I guess this is not using a Bioperl framework? (that's ok - we can port it
into a bioperl framework if you are cool with that - or you are welcome to
do so).

Can you describe the objects in a little more detail - perhaps the
synopsis style of how to use them so we could get an idea of where they
fit into the system?


> 
> Chad S. Matsalla
> Bioinformatics Programmer/Analyst
> Agriculture & Agri-Food Canda
> 
> 
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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