[Bioperl-l] game.pm filehandle/chunkable update

Bradley Marshall bradmars@yahoo.com
Mon, 11 Dec 2000 18:59:04 -0800 (PST)

I've updated the game.pm module to correctly (I think)
support filehandles.  You can now do:

$in = Bio::SeqIO::game->new(-file=>$file,


$in = Bio::SeqIO::game->new(-fh=>$file,

It also recognizes the top-level tag:


To qualify as being chunkable, a document must be laid
out as such:

<bx-seq:seq bx-seq:id='seq1'>

ALL bx-annotation, bx-feature and bx-computation
objects regarding seq1. 

<bx-seq:seq bx-seq:id='seq2'>

ALL bx-annotation, bx-feature and bx-computation
objects regarding seq2. 

NOTE:  You can have NON TOP LEVEL sequences and still
be "chunkable", only top-level sequences will be


<bx-seq:seq bx-seq:id='seq1'>
<bx-annotation:annotation seq=seq1>
	<bx-seq:seq id='seq2'>

counts as being chunkable, but seq2 will be ignored by

This revision is more memory intensive, since it loads
the data from <bx-seq:seq> to the next <bx-seq:seq>
into memory as a string and then parses that.

Non-chunkable documents are loaded into memory in
their entirety before being parsed.


- Allow people to use other parsers (ie ones that
don't need expat, which is non-CPAN).  These will have
to be detected at run-time.

That's all for now...

Happy parsing!

Do You Yahoo!?
Yahoo! Shopping - Thousands of Stores. Millions of Products.