Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-05-28

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All times shown according to UTC.

Time Nick Message
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04:30 CIA-95 biome: Chris Fields cleanup_roles * rfb31dc5 / (2 files in 2 dirs): add Delegate role (not sure this is a keeper, but has tests, so retaining for now) - http://bit.ly/aCRNT7
04:30 CIA-95 biome: Chris Fields cleanup_roles * rba28c06 / (t/Role/IO.x t/Role/IO.t): moved incomplete tests to .x for now - http://bit.ly/9m1cWQ
04:30 CIA-95 biome: Chris Fields cleanup_roles * r03f2d68 / t/Segment/SegmentContainer.t : IN-BETWEEN, not BETWEEN - http://bit.ly/aoDiw8
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10:11 dave_messina Hey, has anyone found a good Git GUI for the Mac?
10:31 kai dave_messina: I'm a command line user :)
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11:46 kai dave_messina: though my boss uses eclipse for his perl coding and uses the eclipse git plugin, that combination should work on a mac
11:47 dave_messina ah okay thanks, Kai.
11:48 kai my pleasure
11:48 dave_messina I've tried several of the available options: GitX, GitY, etc. and haven't found one that "fits" yet. So I thought I'd ask around.
11:57 kai for me, git add --interactive, git am --interactive and git rebase --interactive are all the GUI I need
11:57 kai gitk, if I really want to look at the commit history
12:11 dave_messina Yep. With subversion I used the command line for a long time but came to prefer Versions (a GUI svn app).
12:11 dave_messina I'm sure I can get by doing git on the command line — probably good while I'm learning it, especially — but if there's a good GUI alternative I'd probably switch.
12:21 kai the eclipse plugin probably just makes sense if you use eclipse anyway
12:37 dave_messina Agreed. I don't use Eclipse, though. :)
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16:28 deafferret I've spent very little time in either, but prefer GitX to gitk on my Mac so far
16:28 deafferret dave_messina__: ^
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16:32 dave_messina deafferret:  did you just ping me?
16:32 deafferret 11:28 <@deafferret> I've spent very little time in either, but prefer GitX to gitk on my Mac so far
16:32 dave_messina ah great, thanks.
16:33 deafferret natch
16:33 dave_messina I've played with it a bit, but it still seems pretty limited
16:33 * dave_messina compared to Versions for svn, that is.
16:34 dave_messina hmmrph.
16:34 dave_messina I guess I'll just have to wait.
16:34 dave_messina Seems like somebody would've gone a little further with it by now.
16:39 rbuels there's not that much call for gui stuff in version control ....
16:40 * rbuels finds doing anything with a gui frustratingly inefficient
16:43 perl_splut guis are ok for some things
16:43 perl_splut not for repetitive tasks
16:43 perl_splut creating the GUI interfaces is even more annoying
17:09 * deafferret finds branch merger histories in GitX mesmorizing
17:09 deafferret histories meaning the cool little lines that merge into each other
17:09 deafferret the graphics of mergers
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18:29 deafferret you know. merger graphics.
18:29 perl_splut The only thing congress understands... pretty picture
18:29 perl_splut pictures
18:30 deafferret ooo... pretty!
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18:44 deafferret rbuels is enabled by spatial and temporal patterns of gene expression which in turn are driven by transcriptional regulatory networks
19:00 perl_splut I'm enabled by quantum fluctuations of the quantum foam creating fluctuations in complex multi-path networks
19:04 * deafferret high fives perl_splut for his awesome
19:06 perl_splut protein and dna is so 4 billion years ago
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21:21 kblin evening folks
21:28 * rbuels waves at kblin
21:38 spekki01 what do i need installed on my system to download stuff off of github from a terminal i know theres some package i need.
21:40 kblin you need git
21:40 kblin some systems (debian and ubuntu) call the package git-core
21:41 spekki01 thanks, i'm looking it up now :)
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21:56 deafferret spekki01: telling us your OS might be relevant  :)
21:56 spekki01 rhel 5
21:57 spekki01 im attempting to isntall git via yum, but im missing a bunch of dependencies so im going through them atm getting each
21:58 kblin should yum do that automatically?
21:59 spekki01 i thoght so but here, ill post what is going on
21:59 dnewkirk only if they are all present in the repo
22:00 spekki01 http://codepad.org/e7Rhiwv5
22:10 kblin great
22:11 kblin if you can live with your subversion installation not working, you can skip those deps
22:11 kblin git only needs subversion for git-svn
22:11 spekki01 works for me
22:20 kblin night folks
22:21 deafferret o7
22:21 spekki01 bye
22:23 spekki01 hmmm im confused i want to get http://github.com/bioperl/bioperl-hmmer3 via git do i just use git clone "url"?
22:24 spekki01 sry im just not sure what url to use to download this stuff off of github
22:25 spekki01 sigh nm
22:26 spekki01 i should just pay attention more
22:28 deafferret :)
22:32 spekki01 night guys have a good weekend
22:32 deafferret o7 again   :)
22:32 deafferret oh, wait, that was kblin last time
22:32 deafferret have a good one  :)
22:33 deafferret just remember: [ENSG00000164379][ENST00000296839][312675]
22:33 deafferret some day you'll thank me
22:37 * rbuels tattoos it on the back of his hand
22:38 deafferret err... correction:  ENST00000426700|ENSG00000137434|180200|196318|-1   cross out that other one
22:38 deafferret sorry
22:39 deafferret (Bio::SeqIO)++
22:49 * deafferret wonders how to record what chr any given enst came from in ensembl data
22:50 deafferret hmm... maybe one of these is parsed
22:50 deafferret AC   chromosome:GRCh37:HSCHR6_MHC_DBB:1000001:1623040:1
22:50 deafferret XX
22:50 deafferret SV   chromosome:GRCh37:HSCHR6_MHC_DBB:1000001:1623040:1
22:54 deafferret umm... does this tell me a chr #?
22:54 deafferret Homo sapiens chromosome HSCHR6_MHC_DBB GRCh37 partial sequence
22:54 deafferret thats chr6?
22:55 dnewkirk yes, that's ncbi notation
22:58 deafferret hoo boy...
22:58 deafferret DESC|Homo sapiens chromosome HSCHR6_MHC_DBB GRCh37 partial sequence 27080295..28080294 annotated by Ensembl
22:58 deafferret ENST00000244601|ENSG00000124635|19801|20269|-1
22:59 deafferret so that ENST starts at chr6 27100096
23:02 deafferret woot! only off by 1   http://uswest.ensembl.org/Homo_sapiens/Tr​anscript/Summary?db=core;g=ENSG0000012463​5;r=6:27100095-27100563;t=ENST00000244601   :)
23:16 * deafferret wonders why Homo_sapiens.0.dat starts on chr6
23:19 rbuels deafferret: is it sorted by size?
23:20 dnewkirk 6 isn't the smallest though
23:21 deafferret rbuels: in what way would sorting by size make 6 first?
23:22 * rbuels has no idea what the relative sizes of human sequences are
23:23 deafferret the reason chr6 is numbered '6' is because it's the sixth largest   http://www.daviddarling.info/​images/human_chromosomes.jpg
23:31 deafferret i try asking this question every year or so:   is the designation of the sense vs. anti-sense strand an arbitrary distinction someone made up after the first assembly? or is there an actual biological different wherein you can KNOW which is the sense strand with no reference?
23:33 rbuels as far as i know, it is arbitrary
23:33 * rbuels also flips on his big neon "knows nothing about biology" sign
23:33 deafferret that's what I was thinking, but I get these handwavy yet unsatisfying 'explanations' from biologists occasionally
23:34 deafferret rarely will a biologist admit they don't know, in the circles 'round here
23:34 rbuels yes, it's often hard to get that out of them.
23:35 rbuels i think they might be a little sensitive about it because the gaps in how much is known in biology are so large
23:35 deafferret once someone says "that's the forward strand" then forever and ever amen all other references will parrot that designation, but i'm thinking the original designation (for the first reference) was arbitrary
23:36 deafferret ya, it seems like biologists tend to stretch for 'probably' explanations a lot
23:37 deafferret maybe i just hang out with the wrong bio* people   :)
23:37 rbuels ah, hmm
23:38 rbuels kalmia says sense and antisense only make sense (ha) in relation to a gene
23:38 rbuels or other translated snippet of stuff.
23:38 rbuels but isn't really applicable for a whole genome
23:39 deafferret right -- but each gene is labelled 'on the forward strand' or 'on the reverse strand' as if the whole genome has that inherent polarity
23:39 deafferret and I think that inherent polarity was arbitrary when first chosen
23:40 deafferret so the fact that 50,000 genes are on the 'forward' and 37,000 are on the 'reverse' and not vice-versa, was a historical coin flip
23:40 deafferret (whatever the real numbers are)
23:44 rbuels http://en.wikipedia.org/wiki/Antisense has some discussion ...
23:47 rbuels deafferret: really, sense and antisense are only in relation to a transcript sequence, sounds like
23:47 rbuels based on that article
23:48 deafferret ... every feature on every genome everywhere is labelled as living on the 'forward' or 'reverse' strand
23:49 rbuels yeah, that's arbitrary
23:49 rbuels but people do need to pick one as the canonical forward one, lol
23:51 deafferret ya.
23:51 deafferret doh...   'Homo sapiens supercontig GL000191.1 full sequence 1..106433

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