Camelia, the Perl 6 bug

IRC log for #bioperl, 2013-05-14

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17:21 Topic for #bioperl is now Be patient! People chat here daily, but not necessarily the minute or hour you wandered in. Leave your IRC client connected. | http://bioperl.org/wiki/IRC#Getting_help | http://www.bioperl.org/wiki/Using_Git | nopaste to gist.github.com
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19:43 Topic for #bioperl is now Be patient! People chat here daily, but not necessarily the minute or hour you wandered in. Leave your IRC client connected. | http://bioperl.org/wiki/IRC#Getting_help | http://www.bioperl.org/wiki/Using_Git | nopaste to gist.github.com
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20:16 pyrimidine rbuels: around?
20:32 rbuels pyrimidine: kind of
20:32 pyrimidine heh
20:32 pyrimidine rbuels: just wanted to ask: do you want me to add some GTF hooks to Bio::GFF3::LowLevel
20:32 pyrimidine (might need a rename)
20:33 rbuels good god people are still using gtf?
20:33 pyrimidine unfortunately
20:33 rbuels it would probably be best to just make a Bio::GTF::LowLevel
20:33 pyrimidine I could do that
20:33 * rbuels knows nothing about Bio::GTF
20:34 rbuels pyrimidine: you can put it in the same dist if you want, i can give you commit on it
20:34 pyrimidine rbuels: that works for me
20:34 pyrimidine this is also to get some consistency with Bio::FeatureIO
20:35 pyrimidine (e.g. using the same low-level parser)
20:35 pyrimidine rbuels: UCSC still uses GTF over GFF3 (and BED over everything)
20:35 pyrimidine a real PITA
20:37 rbuels pyrimidine: ok, you have write access to https://github.com/solgenomics/bio-gff3
20:37 pyrimidine thanks!  will work on adding code there
20:37 pyrimidine (on a branch :)
20:37 rbuels pyrimidine: i think we should avoid making a class hierarchy or anything with these.
20:38 pyrimidine rbuels: I agree, I'm staying away from that
20:38 * rbuels nods
20:39 pyrimidine key thing is to make sure I'm not dinging performance (if that is an issue)
20:39 rbuels pyrimidine: if it doesn't share any code, you won't be dinging performance
20:39 rbuels heh
20:39 pyrimidine true
20:40 pyrimidine my thought was, you could write gff3_parse_features() as a generic gff_parse_features() that uses a version-specific callback for the attributes
20:40 pyrimidine that seems to be where the main differences are in the two formats
20:42 rbuels hmm
20:43 rbuels pyrimidine: eh, just cut and paste the code.  these things are used in such tight loops, and the code is so simple, that some kind of callback system would hurt more than it helps
20:43 pyrimidine ok
20:45 rbuels pyrimidine: and it's all super performance-tuned.  the gff3 unescaping s/// is cut and pasted all over the place, for example, because that's like 30% faster than having it in a subroutine
20:45 rbuels seriously makes the parsing like 30% faster
20:45 rbuels (which is weird)
20:46 pyrimidine huh, that is weird.  Maybe use a precompiled regex?
20:46 rbuels pyrimidine: i don't know of a way to precompile a substitution
20:47 pyrimidine I think you can use qr// for this
20:47 pyrimidine not surem though
20:47 pyrimidine *sure,
20:47 rbuels pyrimidine: but it's not a // pattern match, it's a s/// substitution
20:48 pyrimidine http://www.perlmonks.org/?node_id=910116
20:48 rbuels whoa
20:49 rbuels hrm, i might try that next time i'm working on that cod
20:49 rbuels e
20:50 pyrimidine qr// are pretty handy
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