[Bioperl-l] Isn't there Bio::Tools::Run for Phred

[Robson Francisco de Souza]

	Hi,

On Thu, 10 Apr 2003, Chad Matsalla wrote:
> > I would like to get consensus sequences from a lot of EST sequences.
> > For this, I will use phred. By the way, Is there Bio::Tools::Run
> > object for Phred?
> 
> Do you mean phrap?
> 
> If so, you can use Robson's Bio::Assembly::IO::phrap.

	Unfortunately, my modules do not include routines to run phrap or
phred programs. They are just parsers for the output files. But you could
easily run the programs by direct system calls and parse the results
latter.
	Bio::Tools::Run modules are being planned.

> My systems are still using Bio::Tools::Alignment::Consed to parse
> acefiles generated by phrap but I have the feeling that Robson's stuff
> is more tied into the bioperl ways of doing things.

	Hope so :).
	Chad, do you keep using your modules because of the doublet
methods? I think that having a single set of modules for each tool would
avoid confusion. What do you think about merging them?
	Cheers,
			Robson


> Hope that helps,
> 
> Chad Matsalla
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