Camelia, the Perl 6 bug

IRC log for #bioperl, 2011-02-11

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All times shown according to UTC.

Time Nick Message
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01:22 CIA-67 bioperl-live: Jonathan "Duke" Leto topic/tree_api_refresh * r8bd382a / (3 files in 2 dirs): Add warnings to some StandAloneBlast files - http://bit.ly/e6wlf5
01:22 CIA-67 bioperl-live: Greg Jordan topic/tree_api_refresh * r57857c8 / (24 files in 18 dirs): Fix merge conflicts. - http://bit.ly/gI8DBc
01:22 CIA-67 bioperl-live: Greg Jordan topic/tree_api_refresh * ra13b385 / (3 files in 2 dirs): Merge branch 'master' of github.com:bioperl/bioperl-live into topic/tree_api_refresh - http://bit.ly/fJ4hqE
01:22 CIA-67 bioperl-live: Greg Jordan topic/tree_api_refresh * rad9cb74 / (4 files in 2 dirs): Small updates to tree modules. - http://bit.ly/dExbqK
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18:35 rbuels pyrimidine: i want to push out a CPAN module that has low-level, stupid functions for parsing the various parts of gff3 lines.  functions like $hashref = gff3_parse_attributes_column( $string ).
18:35 rbuels pyrimidine: because i find myself needed low-level things like this all the time
18:36 rbuels pyrimidine: in the course of tweaking various parts of the tomato genome annotation
18:36 rbuels pyrimidine: i was thinking of calling it Bio::GFF3::LowLevel, does that sound reasonable?
18:38 perl_splut maybe Bio::GFF::Detailed?
18:46 rbuels well, all methods of parsing are detailed, right?
18:47 perl_splut was thinking of Detailed due to wanting more methods of control in the parsing
18:49 * rbuels nods
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20:08 pyrimidine rbuels: sounds like a good idea.  Actually was thinking it might be a good idea to package up various functions like that and release them as (non-bioperl-tied) CPAN modules
20:11 pyrimidine actually, I have been tossing around the idea of a releasing low-level generic parsers for a while now (where one could utilize them for both parsing and indexing)
20:11 pyrimidine sort of implemented this in various ways but I think I've settled on one specific way of doing it.
20:14 rbuels pyrimidine: ok, well, Bio-GFF3 will be the distribution then, we can add an actual low-level parser in there if we want
20:14 rbuels pyrimidine: alongside these little functions
20:14 rbuels pyrimidine: if you've got a good architecture for generic parsers
20:17 pyrimidine rbuels: I think for seq and feature-related data, passing information as structured bits should suffice, doing very little data munging (beyond any URI-related coding/decoding the format requires, and even that could be optional)
20:17 pyrimidine rbuels: could even keep track of file points for indexing
20:17 rbuels oooh, file points
20:18 rbuels that's a very good idea
20:18 rbuels well, these functions actually don't know anything about files, but if i write something that's high-level enough to do filehandles or something, i'll remember to include file points
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22:41 ryan__ Hello,  I'm looking for GSOC ideas and Dukeleto++ informed me that I should speak to some people in the IRC.  Does any one have any ideas?
22:53 rbuels hmmm
22:53 * rbuels considers this
22:53 rbuels ryan__: what are you good at?  perl i suppose, since you're in the bioperl channel
22:53 rbuels ryan__: any other things you Specially Know About or are good at?
22:54 rbuels ryan__: how about the beginning of a cairo-based replacement for Bio::Graphics?  oh ho ho, that would be quite a project
22:54 rbuels that's a pretty tough one
22:54 * rbuels thinks some more
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23:19 ryan__ rbuels: hello
23:19 rbuels um, yes?
23:19 ryan__ rbuels: I've used perl for alot on one liners and currently going to school bioengineering
23:20 ryan__ the Bio::Graphics sounds interestings.  I was also on the perl6 irc and they mentioned bioperl6
23:21 rbuels ryan__: yep, there's that too
23:21 rbuels ryan__: pyrimidine (who is not online at the moment) would be the person to talk to about that i think
23:21 ryan__ ok
23:39 rbuels he's often in here thouhg
23:39 rbuels during business-ish hours
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