For the bioperl->MAGE bridge, I think what looking for is a
MicroarrayIO.pm subclass that delegates to the MAGE-Perl
reader/writer.
For the MAGE->bioperl bridge, we need to adapt the MicroarrayIO
subclasses (affymetrix, dchipxls, mas50txt) for use from MAGE-
Perl world. Having wrappers around these that generate and
handle SAX events, is I believe what Allen is referring to.
The bioperl blast parsers in Bio/SearchIO (in the bioperl-live CVS
module) does this sort of thing for the non-XML blast formats.
It's possible we could make use of some of these modules or
underlying strategies (e.g., SearchResultEventBuilder.pm).
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Hey Allen,
What are the relevant parts of BioPerl that overlap with
MAGE. Not that I'm skeptical, I'd just like to know where
the main focus lies.
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Jason,
Check out the bioperl-microarray cvs module:
http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-
microarray/Bio/Expression/?cvsroot=bioperl
For the bioperl->MAGE bridge, I think what looking for is a
MicroarrayIO.pm subclass that delegates to the MAGE-Perl
reader/writer.
For the MAGE->bioperl bridge, we need to adapt the MicroarrayIO
subclasses (affymetrix, dchipxls, mas50txt) for use from MAGE-
Perl world. Having wrappers around these that generate and
handle SAX events, is I believe what Allen is referring to.
The bioperl blast parsers in Bio/SearchIO (in the bioperl-live CVS
module) does this sort of thing for the non-XML blast formats.
It's possible we could make use of some of these modules or
underlying strategies (e.g., SearchResultEventBuilder.pm).