Grammars and biological data formats

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

[perl6/specs] 2338ed: Attempt at clarification 1st parameter to .bless

Branch: refs/heads/master Home: https://github.com/perl6/specs Commit: 2338ed17f5a4e62deab184a0029dd3d044e63fac https://github.com/perl6/specs/commit/2338ed17f5a4e62deab184a0029dd3d044e63fac Author: Elizabeth Mattijsen l...@dijkmat.nl Date: 2014-08-11 (Mon, 11 Aug 2014)

[perl6/specs] 43ff89: [S99] Add emptyish lambda and pointy block

Branch: refs/heads/master Home: https://github.com/perl6/specs Commit: 43ff895139def4868861ccae1ce2a1f07d71f7a9 https://github.com/perl6/specs/commit/43ff895139def4868861ccae1ce2a1f07d71f7a9 Author: Jonathan Scott Duff d...@pobox.com Date: 2014-08-11 (Mon, 11 Aug 2014)

[perl6/specs] 56c571: Get rid of DESTROY fossils

Branch: refs/heads/master Home: https://github.com/perl6/specs Commit: 56c5710c527cf6a0e9df71f9ed06930e594ea453 https://github.com/perl6/specs/commit/56c5710c527cf6a0e9df71f9ed06930e594ea453 Author: Elizabeth Mattijsen l...@dijkmat.nl Date: 2014-08-11 (Mon, 11 Aug 2014)

[perl6/specs] aa6f24: Unprecomposed graphemes are 0, not 0x10ffff

Branch: refs/heads/master Home: https://github.com/perl6/specs Commit: aa6f2438d0002d2820425623de6a4938ec454e30 https://github.com/perl6/specs/commit/aa6f2438d0002d2820425623de6a4938ec454e30 Author: Elizabeth Mattijsen l...@dijkmat.nl Date: 2014-08-11 (Mon, 11 Aug 2014)

[perl6/specs] 34a30e: Make sure we expand TABs to spaces

Branch: refs/heads/master Home: https://github.com/perl6/specs Commit: 34a30e748abd2b50bba8ab7b718dbc6c6f21eb9b https://github.com/perl6/specs/commit/34a30e748abd2b50bba8ab7b718dbc6c6f21eb9b Author: Elizabeth Mattijsen l...@dijkmat.nl Date: 2014-08-12 (Tue, 12 Aug 2014)

[perl6/specs] 8b6d0b: Elaborate a bit on exit, END blocks and threads

Branch: refs/heads/master Home: https://github.com/perl6/specs Commit: 8b6d0bb3fef29ad61540730c8ff99b5c69c99709 https://github.com/perl6/specs/commit/8b6d0bb3fef29ad61540730c8ff99b5c69c99709 Author: Elizabeth Mattijsen l...@dijkmat.nl Date: 2014-08-11 (Mon, 11 Aug 2014)

[perl6/specs] a80149: Hint a bit at is export for methods

Branch: refs/heads/master Home: https://github.com/perl6/specs Commit: a8014958d3f4ebb5c02cb4c840fea487ce788a0b https://github.com/perl6/specs/commit/a8014958d3f4ebb5c02cb4c840fea487ce788a0b Author: Elizabeth Mattijsen l...@dijkmat.nl Date: 2014-08-11 (Mon, 11 Aug 2014)

[perl6/specs] b3fceb: lock() is now Lock.new and its methods

Branch: refs/heads/master Home: https://github.com/perl6/specs Commit: b3fceb8cf355d008ef29df432c60438aee6bf3d6 https://github.com/perl6/specs/commit/b3fceb8cf355d008ef29df432c60438aee6bf3d6 Author: Elizabeth Mattijsen l...@dijkmat.nl Date: 2014-08-11 (Mon, 11 Aug 2014)

[perl6/specs] 134561: Add Set/Bag/Mix smartmatch candidates to table

Branch: refs/heads/master Home: https://github.com/perl6/specs Commit: 1345614cf61c30f9c9f0492ff89e1e25c60d1d6d https://github.com/perl6/specs/commit/1345614cf61c30f9c9f0492ff89e1e25c60d1d6d Author: Elizabeth Mattijsen l...@dijkmat.nl Date: 2014-08-12 (Tue, 12 Aug 2014)

[perl6/specs] 98a97b: De-TAB

Branch: refs/heads/master Home: https://github.com/perl6/specs Commit: 98a97ba05497c67f383870287220c2a156dff884 https://github.com/perl6/specs/commit/98a97ba05497c67f383870287220c2a156dff884 Author: Elizabeth Mattijsen l...@dijkmat.nl Date: 2014-08-12 (Tue, 12 Aug 2014)

[perl6/specs] 22d8cd: Generalize ~~ calls to be on Setty, Baggy, Mixy

Branch: refs/heads/master Home: https://github.com/perl6/specs Commit: 22d8cd42ba02f242489a466d8e2377974cbb1cb5 https://github.com/perl6/specs/commit/22d8cd42ba02f242489a466d8e2377974cbb1cb5 Author: Mouq alexmoq...@gmail.com Date: 2014-08-13 (Wed, 13 Aug 2014) Changed

Re: Grammars and biological data formats

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

Re: Grammars and biological data formats

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:

Re: Grammars and biological data formats

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

[perl6/specs] b99ecf: whack down the smartmatch table

Branch: refs/heads/master Home: https://github.com/perl6/specs Commit: b99ecf40b7cd8197086a07ee857c5f1f91fad489 https://github.com/perl6/specs/commit/b99ecf40b7cd8197086a07ee857c5f1f91fad489 Author: TimToady la...@wall.org Date: 2014-08-13 (Wed, 13 Aug 2014) Changed paths:

[perl6/specs] e6fda2: Alas, mutable Set/Bag/Mix follow different rules

Branch: refs/heads/master Home: https://github.com/perl6/specs Commit: e6fda2fe3d62bd72c78a452c2c0b39c12e90279a https://github.com/perl6/specs/commit/e6fda2fe3d62bd72c78a452c2c0b39c12e90279a Author: Elizabeth Mattijsen l...@dijkmat.nl Date: 2014-08-13 (Wed, 13 Aug 2014)

[perl6/specs] 629dbe: hash smartmatching just shouldn't try to guess

Branch: refs/heads/master Home: https://github.com/perl6/specs Commit: 629dbe9af6832f0919c05116d1ca02974c51d991 https://github.com/perl6/specs/commit/629dbe9af6832f0919c05116d1ca02974c51d991 Author: TimToady la...@wall.org Date: 2014-08-13 (Wed, 13 Aug 2014) Changed paths:

[perl6/specs] 5c8641: Hopefully correctly map Setty/Baggy/Mixy in ~~

Branch: refs/heads/master Home: https://github.com/perl6/specs Commit: 5c864188247ffaa09797a68adf3c44ebf9b4f430 https://github.com/perl6/specs/commit/5c864188247ffaa09797a68adf3c44ebf9b4f430 Author: Elizabeth Mattijsen l...@dijkmat.nl Date: 2014-08-13 (Wed, 13 Aug 2014)

[perl6/specs] c58b91: put back non-slice hash item lookups

Branch: refs/heads/master Home: https://github.com/perl6/specs Commit: c58b91883af4147fea71f51719341efcaf7f1614 https://github.com/perl6/specs/commit/c58b91883af4147fea71f51719341efcaf7f1614 Author: TimToady la...@wall.org Date: 2014-08-13 (Wed, 13 Aug 2014) Changed paths: