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

[Chad Matsalla]

On Thu, 10 Apr 2003, Robson Francisco de Souza 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.

>From my experience I believe that making these Run modules is
fraught with peril. Different operating systems, different path
delimeters, testing problems, packaging... the list goes on and on. I
would use them... maybe... but in the end I would likely run the program
with a perl program and parse the results using bioperl.

> > 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?

I, and a number of collegues out there, have systems tied into that
system and as much as I would like to merge them I cannot. I don't plan
to do any more work in this area other then maintenance so I don't think
that rewrites are a good use of time.

But I must say I am very pleased to hear that someone is fixing my
primer3 runner. That was next on my list. Ha!

Chad Matsalla