Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-08-16

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All times shown according to UTC.

Time Nick Message
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02:57 CIA-95 biome: Chris Fields topic/default_locations * ra683fda / (4 files in 2 dirs): remove extraneous roles - http://bit.ly/cmEyDT
03:53 CIA-95 biome: Chris Fields topic/default_locations * r7b581e2 / (2 files): split locatable logic and strandedness out into separate roles - http://bit.ly/cvIJqg
03:53 CIA-95 biome: Chris Fields topic/default_locations * r13bb751 / (6 files in 2 dirs): split strandedness out into a role, include where needed - http://bit.ly/8YNKgi
03:53 CIA-95 biome: Chris Fields topic/default_locations * rb25d3f4 / (6 files in 5 dirs): clean up types to match changes - http://bit.ly/93G6yQ
03:53 CIA-95 biome: Chris Fields topic/default_locations * r59119f6 / t/Location/Simple.t : remove extraneous space - http://bit.ly/cdJ4pU
04:31 CIA-95 biome: Chris Fields topic/default_locations * r7d6c7a7 / (5 files in 3 dirs): get split locations running again - http://bit.ly/aa8gR3
04:36 CIA-95 biome: Chris Fields topic/default_locations * r64f5d0e / (3 files in 2 dirs): cleanup - http://bit.ly/cH6pUk
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15:23 CIA-95 biome: Chris Fields master * r64f5d0e / (3 files in 2 dirs): cleanup (+13 more commits...) - http://bit.ly/cH6pUk
15:25 CIA-95 biome: Chris Fields master * ra899816 / MANIFEST : update MANIFEST - http://bit.ly/baNujP
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15:52 deafferret .o.o
16:00 Jun should i report something if I fixed a bug?
16:00 Jun e.g. modify the status in Bugzilla?
16:00 kblin usually, yes
16:02 deafferret if you resolved a Mozilla bug, then change the status of that bug to 'resolved'   :)
16:02 dbolser hello
16:02 dbolser if I have a bunch of features in an array, how can I 'select' from the features by type, etc?
16:03 dbolser I figure I should load it into an in memory collection or just start looping?
16:04 rbuels dbolser: usually you would want to use a hash to index the features by how you want to look them up
16:04 rbuels dbolser: it sort of depends on how many lookups you will be doing
16:04 rbuels dbolser: if you're just going to do it once, just loop through them
16:04 dbolser rbuels: I see, just loop once and hash them how I want them?
16:05 rbuels dbolser: yes.  but it's only worth hashing them if you are going to be repeatedly looking up from that hash.
16:05 dbolser I am querying from a SeqFeature::Store, so I could just select them directly, but it feels like it will be more efficient to get all relevant features for my region of interest first, and then 'do the work'
16:05 rbuels dbolser: if the hash starts getting too big, DB_File.
16:05 rbuels dbolser: no, it's not more efficient.
16:06 rbuels dbolser: if you are using seqfeature::store, just do a query each time.
16:06 dbolser ic, so if I want 'wibble gaps' I should just hit the SeqFeature::Store
16:06 dbolser cool
16:06 rbuels yeah i think that's usually going to be better.
16:06 dbolser does it make any sense to create a tempoary memory adaptor (because my regions are always small)
16:06 dbolser small ish
16:07 dbolser anyway, I have enough to get back to work ;-)
16:07 rbuels well if they're always really small, it might not make that much sense to use seqfeature::store
16:07 rbuels i dunno.
16:07 rbuels you also have to factor in your own time here
16:07 rbuels computer time is cheap.
16:07 rbuels your time is expensive.
16:08 dbolser Ive wasted my life! ;-)
16:10 rbuels lol
16:12 deafferret you have to ask yourself: with my remaining time on this pale blue dot would I rather implement a temporary memory adaptor, or go scuba diving?
16:14 dbolser the former
16:17 Jun Cheers~
16:18 deafferret very well. less crowded oceans for us slackers  :)
16:19 * dbolser begins to understand bioperl better ;-)
16:29 pyrimidine dbolser: if you have an array of features, grep works.  From DB::SF::Store, there are lots of ways to get what you want
16:30 pyrimidine something like: grep {$_->primary_tag eq 'foo'} @feats;
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19:14 CIA-95 bioperl-live: Chris Fields topic/leto_interpro_relationship * rf5c7c98 / Bio/OntologyIO/Handlers/InterProHandler.pm :
19:14 CIA-95 bioperl-live: interim fix for inverse IDs, uses cache of marshalled IDs to check for
19:14 CIA-95 bioperl-live: previously viewed relationships, instead of a more expensive lookup. TODO:
19:14 CIA-95 bioperl-live: should perform lookup after this to check for defined inverse relationships, but
19:14 CIA-95 bioperl-live: for now just returns - http://bit.ly/aQqAf9
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19:23 pyrimidine dukeleto: committed an interim fix for that bug on topic/leto_interpro_relationship.  passes tests, but we should probably add a check in there for proper inverse relationship, JIC
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