[Bioperl-l] Bio::Tools::AnalysisResult

Hilmar Lapp hlapp@gmx.net
Wed, 13 Sep 2000 12:06:22 +0200

I've committed an initial draft version of a base class for parsers of
analysis tools results. Please check it out and comment. I'm not sure
whether it accomplishes what you expected it to accomplish. (At least, it
saves me some code duplications.)

Quoted from the doc:

The AnalysisResult module is supposed to be the base class for modules
encapsulating parsers and interpreters for the result of a analysis that
carried out with a query sequence.

The notion of an analysis represented by this base class is that of a
unary or
binary operator, taking either one query or a query and a subject and
a result. The query is e.g. a sequence, and a subject is either a
too, or a database of sequences. 

This module also implements the Bio::SeqAnalysisParserI interface, and
can be used wherever such an object fits. See L<Bio::SeqAnalysisParserI>.
Developers will find a ready-to-use L<parse>() method, but need to
next_feature() in an inheriting class. Support for initialization with
file names and reading from streams is also ready to use.

Note that this module does not provide support for B<running> an
Rather, it is positioned in the subsequent parsing step (concerned with
turning raw results into BioPerl objects).

	- adapt Genscan.pm and MZEF.pm to inherit from this module (me)
	- adapt BPLite to use it (i.e., inherit from it) (Lorenz, me)
	- adapt HMMER to use it (Ewan?)
	- adapt other parsers to use it (who?)
	- adapt Blast.pm to use it (long-term, if ever)

All the adaptations will hopefully bring the base module closer to being
useful :)


Hilmar Lapp                                email: hlapp@gmx.net
NFI Vienna, IFD/Bioinformatics             phone: +43 1 86634 631
A-1235 Vienna                                fax: +43 1 86634 727