[Bioperl-l] Bio::SearchIO::sim4 parser

[Luc.Gauthier at aventis.com]

Hi everybody,

I am currently writing modules that find great benefit in using the
Bio::SearchIO system.

A couple of days ago, I found myself in front of a problem. I am using
BioPerl 1.2.2, which
does not contain a parser for sim4 output. So I started to use
Bio::Tools::Sim4::Result from
Ewan Birney and Hilmar Lapp. Great module! but it kind of "broke" the generic
way of coding
I was following with Bio::SearchIO.

Then I found out that a sim4 parser existed in the "live" version of BopPerl.
No problem for me,
I have control on the libraries I use, so I downloaded the code from CVS and
started using this
new version. Unfortunately, it again did not work as I was expecting. It
indeed seems to treat
hits as distinct results so it could not fit in the system I was developing.

So I wrote a new parser, based on that Bio::SearchIO::sim4 module and
Bio::Tools::Sim4::Result
too. Actually, I only modified some methods, mainly 'next_result'. In the
end, I get a parser that
works great for me. It can parse 0/1/3/4 outputs (like the existing modules)
and gets maximum data,
including sequences and homology string, along with gaps and everything.
Above all, each
alignment is now treated as a hit.

I would greatly appreciate contributing to the project, if it could be of
interest to anyone !
I must also admit that it would ease future maintenance for me if it became
part of the
standard distribution ! ;)

Well, would someone want to see the code?
How do you proceed when you want to contribute to BioPerl?

Thank you and have a good day !
Luc Gauthier