(accidentally sent to perl6-lang, apologies for cross-posting but this seems more appropriate)
I have a fairly simple question regarding the feasibility of using grammars with commonly used biological data formats. My main question: if I wanted to parse() or subparse() vary large files (not unheard of to have FASTA/FASTQ or other similar data files exceed 100’s of GB) would a grammar be the best solution? For instance, based on what I am reading the semantics appear to be greedy; for instance: Grammar.parsefile($file) appears to be a convenient shorthand for: Grammar.parse($file.slurp) since Grammar.parse() works on a Str, not a IO::Handle or Buf. Or am I misunderstanding how this could be accomplished? (just to point out, I know I can subparse() as well but that also appears to act on a string…) As an example, I have a simple grammar for parsing FASTA, which a (deceptively) simple format for storing sequence data: http://en.wikipedia.org/wiki/FASTA_format I have a simple grammar here: https://github.com/cjfields/bioperl6/blob/master/lib/Bio/Grammar/Fasta.pm6 and tests here: https://github.com/cjfields/bioperl6/blob/master/t/Grammar/fasta.t Tests pass with the latest Rakudo just fine. chris
