Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-06-12

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All times shown according to UTC.

Time Nick Message
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00:42 deafferret ooo.o
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10:53 CIA-94 bioperl-live: Florent Angly master * r68ffe48 / Bio/Assembly/IO/ace.pm : Removed temporary debugging code - http://bit.ly/cT3zMc
10:53 CIA-94 bioperl-live: Florent Angly master * r3fc2a56 / (10 files in 7 dirs): Merge branch 'master' of github.com:bioperl/bioperl-live - http://bit.ly/bDfvlN
10:53 CIA-94 bioperl-live: Florent Angly master * r7c4d789 / (2 files in 2 dirs): More robust creation of cross-contigs - http://bit.ly/aD7zyg
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17:09 CIA-94 biome: Chris Fields master * r3939c39 / lib/Biome/Role/PrimarySeq.pm : type changed (aka I hate CamelCase) - http://bit.ly/94LbaY
17:09 CIA-94 biome: Chris Fields master * r1ac27fc / lib/Biome/Role/Segment/SegmentContainer.pm : clean up of a few methods - http://bit.ly/96h4hx
17:09 CIA-94 biome: Chris Fields master * r955ca05 / (t/Types/LocationTypes.t t/Types/SequenceTypes.t): tests working again, broke when changing Types and splitting up Segment types based on position or complete segment - http://bit.ly/9KNMYg
19:10 * deafferret needs a storage mechanism for subsequences ... where I can still know the absolute positions of features in the chromosome, store the sequence, etc.
19:10 deafferret Homo sapien in embl format has a description which says "chr4 400,000..600,000" and features are at "2000",  (which is chr 4 402,000)
19:10 deafferret etc
19:40 * deafferret wonders what the default GBrowse database format is
19:42 deafferret chases Bio::DB::SeqFeature::Store for a few hours
19:53 * deafferret curses the horse NFS rode in on
20:08 deafferret wow. GBrowse got a lot easier to install
20:23 * deafferret wonders if there's already an embl -> Bio::DB::SeqFeature::Store script somewhere
20:57 * deafferret wonders why no one has slapped him with Bio::DB::SeqFeature::Store before
20:58 * deafferret wonders if a new DB per organism per chr is the way to go
20:58 deafferret since I don't see chr4 anywhere in the Store
21:16 deafferret GRCh37_CHR06.sqlite me thinks
21:38 deafferret whoah... a single feature is .6MB in the database.. stored Bio::SeqFeature::Generic apparently
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21:46 CIA-94 bioperl-live: Jay Hannah master * rc659768 / Bio/DB/SeqFeature/Store.pm : Works great in Bio::DB::SeqFeature::Store::DBI::SQLite too. - http://bit.ly/cUTqpO
21:48 deafferret security breach!
22:38 * deafferret wonders how to clone feature objects
23:04 deafferret oh dear... there's no way to clone/copy ?
23:05 deafferret deafferret: patches welcome
23:05 deafferret deafferret: but but but..
23:05 deafferret deafferret: quit yur whinin
23:35 CIA-94 biome: Chris Fields master * rbfc97a8 / (lib/Biome/Type/Segment.pm lib/Biome/Type/Sequence.pm): promote Types to their own namespace - http://bit.ly/djRvgJ

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