Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-08-13

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All times shown according to UTC.

Time Nick Message
00:35 genehack L7
00:36 deafferret Bricks Are Heavy
00:37 genehack so, if anybody should happen to have some code that uses Bio::SeqFeature::SimilarityPair, it needs a bit of a doc update -- happy to do that, but I'd like to look at some Real Working Code first (and there's none in the test suite... 8^/ )
01:03 Yksi joined #bioperl
01:15 rbuels that's a very nice frown face
01:15 rbuels heh
01:43 deafferret ehe
02:29 rbuels what?  is this *opposite day*?!?!
02:29 rbuels oh ho ho look at me i'm deafferret and i'm so opposite!
02:29 * rbuels capers about
02:33 deafferret do not release the anti-gnomes
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07:58 dbolser genehack: I'd like to use that for agp parsing I think...
09:06 genehack actually, since i've let the goatee grow back in, a more accurate representation would be 8^/=
09:13 kblin genehack: it's no fun until it's a long goatee, 8^/=-
10:10 dbolser seen this...   c|:-{     and     =|:-?
10:21 kblin so one is a guy with a bowler hat and a moustache, the second is sylvester stallone wearing a cylinder
11:04 genehack kblin: it's been a long goatee in the past; it ends up being $WORK-environment dependent.
11:04 genehack the long goatee scares the straights.
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13:41 kblin genehack: yay for working at university, I guess
13:48 rbuels hahaha
13:49 rbuels yeah, working in academia is definitely better than industry where things like that are concerned
13:49 rbuels but the money is crap.
13:50 rbuels (for developers)
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15:18 deafferret ..o.
15:19 deafferret you can't BUY happiness (excessive facial hair)
15:19 deafferret unless you're Primus.   http://www.primusville.com​/img/2010-primus-band.jpg
15:22 Jun Hi, is bioperl-l@bioperl.org the same with bioperl-l@lists.open-bio.org?
15:22 deafferret yup
15:24 Jun ok ... cheers
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15:54 pyrimidine mst is in a good mood today :)
15:55 deafferret :0
16:08 kblin deafferret: it's not excessive...
16:08 pyrimidine deafferret is excessive
16:08 kblin it's like :-#
16:08 kblin not like :-######
16:09 kblin I know some people with beards like that, but they're all theoretical astrophysicists, and die-hard Unix geeks
16:10 deafferret err   I meant  :)
16:10 deafferret slow on the shift key apparently
16:11 * deafferret is causing trouble in #dbix-class this morning
16:11 pyrimidine =-O
16:23 Jun Hi, pyrimidine. It seems now SimpleAlign has passed nearly all the old tests,except the end position test
16:24 Jun The reason is in my email to the bioperl mail list... it is not easy to solve
16:25 pyrimidine my feeling is, truthfully, that the sequence should be immutable
16:26 pyrimidine and that any calls to modify the seq using $ls->seq('ATTTGA') beyond the constructor should ie
16:26 pyrimidine *die
16:26 pyrimidine this solves a LOT of problems
16:26 Jun yep ... sounds cool :D
16:27 Jun Then everytime when you modify a sequence, you can start a new sequence object. This may solve some problems
16:27 pyrimidine any methods that modify the sequence should return a new LocatableSeq with the modifications
16:27 pyrimidine yes
16:27 pyrimidine beat me to it
16:27 pyrimidine :)
16:30 pyrimidine I posed that question to Heikki L. at BOSC (switching to mainly immutable objects) and his initial though was 'isn't that a lot of work'
16:30 pyrimidine then, after thinking it over, he realized it solves a lot of state-based problems in bioperl
16:31 Jun yep, that is true. It makes sense
16:31 pyrimidine one issue: setting the sequence and start or end is probably fine, but setting seq, start, and end is tricky
16:32 Jun Because when you modify the sequence, the sequence is changed, and it is no sense to use the old information
16:32 pyrimidine right
16:33 pyrimidine but,
16:33 pyrimidine $ls = Bio::LocatableSeq->new(-seq => 'ATGA-AG', -start => 2, -end => 7)
16:33 pyrimidine is a bit of a snare
16:34 pyrimidine end is defined based on the sequence itself
16:34 Jun yep
16:34 pyrimidine so, I think passing in end should be more a validation step instead of a set
16:34 Jun This is one is ok, it will still pass the check from $ls->end($ls->end)
16:36 pyrimidine calling end() and length() should probably just use the ungapped length (with end offset by the length)
16:36 pyrimidine oops
16:36 pyrimidine end offset by the start and the length
16:36 Jun yep, this is the current check in end()
16:36 pyrimidine so, what do we do in this situtation:
16:37 pyrimidine $ls = Bio::LocatableSeq->new(-seq => '', -start => 2, -end => 7)
16:37 pyrimidine (a virtual sequence)
16:37 pyrimidine I tend to think, in this case, we don't use LocatableSeq
16:38 pyrimidine have something else
16:38 pyrimidine and keep the logic for that separate
16:38 Jun ok
16:39 pyrimidine this popped up with MUMmer I think
16:40 Jun Yes, we should have the location information stored in a seperate object in some case
16:41 Jun Location for every residue in the current sequence from the original sequence
16:41 Jun But thi will make things even more complicated
16:41 pyrimidine well, in that case you could switch to using features
16:42 Jun But anyway, it is the basic idea I have for the new Bio::DB::Seq, a location based module to store alignment sequences
16:42 pyrimidine sounds good
16:43 Jun BTW, I dont think i will have time to implement that before the end of August
16:43 pyrimidine that's fine
16:44 pyrimidine you got a lot of work done
16:44 Jun But my idea on that is pretty clear now. I will give a go in September. I can try with a few alignment formats. If it works, we can proceed.
16:45 Jun Thx :D
16:46 pyrimidine np
16:47 Jun I am not very happy with myself, because i didnot get 100% devoted to the GSoC project. It is just because this is the busiest summer I've ever had...
16:48 Jun Actually, I am involved in more thant 6 projects... really hard to manage time and work progress
16:50 Jun But anyway, I've learned a lot during this project. ANd, the more important thing is, I am more confident to do something in Perl/BioPerl now.
16:50 Jun It feels like this project has opened a new world for me :D
16:53 Jun One more thing, how can I create a new page in BioPerl wiki? I need to make a new HOWTO for SimpleAlign
16:54 Jun and, also for other Alignment modules
16:54 pyrimidine sure, go ahead
16:54 pyrimidine I think you made enough progress in the classes you currently have
16:55 pyrimidine we'll likely have to tie the deprecation warnings to a specific Root version of bioperl
16:55 pyrimidine but that's down the line
16:58 Jun do you mean I should specify -warn_version, and -throw_version in $self->deprecated?
16:59 pyrimidine possibly
17:00 pyrimidine we would need to think about what version we want warnings to start showing up, and when we need them to actually throw
17:01 pyrimidine it's okay for now, though
17:01 pyrimidine we can parse through bioperl to find any deprecated calls and globally replace them
17:02 Jun ok, good
17:02 Jun btw, do you know how to create a new page in BioPerl wiki?
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17:04 rbuels Jun: it's like any other wiki i think ... are you having permission issues?
17:04 Jun I dont know ...
17:05 Jun I think I can modify pages, but I havenot found where to start a new page
17:05 rbuels Jun: in the bioperl wiki, and on most wikis, you can start a new page just by trying to view a nonexistent page.  it will let you create a page if it does not already exist.
17:06 rbuels Jun: you could do this, for example, by trying to visit http://bioperl.org/wiki/My_New_Nonexistent_page
17:06 Jun ok, i see
17:07 rbuels Jun: wikipedia works the same way
17:07 rbuels Jun: and other wikis mostly do also
17:07 Jun done... interesting :D
17:08 Jun Yep, we have a wiki in our group, but I seldom use it :p
17:40 Jun Ok, see u guys. I think you will have the test files for the new packages and a HOWTO next week :D
17:40 Jun Have a nice weekend.
17:41 pyrimidine thanks Jun
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