On Aug 13, 2014, at 8:11 AM, Christopher Fields <cjfie...@illinois.edu> wrote:
> On Aug 13, 2014, at 4:50 AM, Solomon Foster <colo...@gmail.com> wrote: > >> On Sat, Aug 9, 2014 at 7:26 PM, Fields, Christopher J >> <cjfie...@illinois.edu> wrote: >>> 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? >> >> My understanding is it is intended that parsing can work on Cats >> (hypothetical lazy strings) but this hasn't been implemented yet >> anywhere. >> >> -- >> Solomon Foster: colo...@gmail.com >> HarmonyWare, Inc: http://www.harmonyware.com > > Yeah, that’s what I recall as well. I see very little in the specs re: Cat > unfortunately. > > chris Ah, nevermind. I did a search of the IRC channel and found it’s considered to be a ‘6.1’ feature: http://irclog.perlgeek.de/perl6/2014-07-06#i_8978974 It is mentioned a few times in the specs, I’m guessing based on where it’s thought to fit in best. For the moment the proposal is to run grammar parsing on sized chunks of the input data, which might be how Cat would be implemented anyway. chris
