Yeah, I'm thinking of a Cat-like class that would chunkify the data and check for matches.
The main reason I would like to stick with a consistent grammar-based approach is I have seen many instances in BioPerl where a parser is essentially rewritten based on its purpose (full parsing, lazy parsing, indexing of flat files, adding to a persistent data store, etc). Having a way to both parse a full grammar but also subparse for a specific token/rule is very handy, and when Cat comes around even more so. Chris Sent from my iPad > On Aug 14, 2014, at 6:40 AM, "Carl Mäsak" <cma...@gmail.com> wrote: > > I was going to pipe in and say that I wouldn't wait around for Cat, > I'd write something that reads chunks and then parses that. It'll be a > bit more code, but it'll work today. But I see you reached that > conclusion already. :) > > Lately I've found myself writing more and more grammars that parse > just one line of some input. Provided that the same action object gets > attached to the parse each time, that's an excellent place to store > information that you want to persist between lines. Actually, action > objects started to make a whole lot more sense to me after I found > that use case, because it takes on the role of a session/lifetime > object for the parse process itself. > > // Carl > > On Wed, Aug 13, 2014 at 3:19 PM, Fields, Christopher J > <cjfie...@illinois.edu> wrote: >> 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 >>
