[Bioperl-l] Question about using XML::Parser::PerlSAX for sequence
Donald G. Jackson
donald.jackson at bms.com
Tue Jan 27 15:28:11 EST 2004
I'm working on a SeqIO adapter for the NCBI TinySeq XML format and have
a question about XML::Parser::PerlSAX.
Currently, my parser goes through the whole XML file and stores the
results in a stack. My next_seq() method pulls the next element off the
stack, converts it to a Bio::Seq object, and returns it. This works,
but I'd rather be able to step through the input XML one sequence at a
time. I thought bioperl selected PerlSAX because it could do that, but
I'm having trouble figuring out how. I looked at Bio::SeqIO::game, but
that also loads all of the parsed data into memory.
I'd like to implement something analagous to how Bio::SeqIO::fasta steps
through an input file, though without having to get to such low-level
methods. If anyone on the list has any suggestions, I'd be grateful!
PS - I'm putting together a test suite and hope to have the preliminary
version of Bio::SeqIO::tinyseq checked into the cvs repository in the
next day or so.
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