Camelia, the Perl 6 bug

IRC log for #bioperl, 2011-02-10

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All times shown according to UTC.

Time Nick Message
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09:40 CIA-67 bioperl-live: Jonathan "Duke" Leto master * r8bd382a / (3 files in 2 dirs): Add warnings to some StandAloneBlast files - http://bit.ly/e6wlf5
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16:47 Dezin anyone here?
16:47 Dezin this time i swear i have a doosey of a problem
16:48 pyrimidine Dezin: okay
16:48 pyrimidine what is it?
16:48 rbuels how does one spell that?  is it really "doosey"?
16:48 * rbuels always thought it was "doozy"
16:49 Dezin lol
16:49 Dezin so how i am looking at the feature annotation wiki
16:49 Dezin and I cant figure out how to get the CDS location info
16:50 Dezin specifically the info on the same line as the CDS in a genbank file
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16:52 Dezin do you get what i mean?
16:52 rbuels o_O
16:53 pyrimidine Do you want the location string, or the Bio::Location object?
16:53 rbuels hmm, well question 1 is whether that is being parsed out, and question 2 is, if it is, what are the accessors for it
16:54 * rbuels waves his arms vaguely while pyrimidine solves the problem
16:54 Dezin i was trying the location object but i couldnt get it to work. Do i get the location object from the feature object?
16:54 pyrimidine Dezin: yes
16:54 pyrimidine I think it's '$sf->location'
16:57 Dezin lol
16:57 pyrimidine So, grab the features from the Bio::Seq instance with 'my @sfs = $seq->get_SeqFeatures('CDS');
16:57 Dezin not so much a doosey
16:57 Dezin i swear i tried this
16:57 Dezin thx pyrimidine
16:57 pyrimidine np
16:57 pyrimidine now, if you want that stringified, you would need Bio::Factory::FTLocationFactory
16:58 Dezin i jsut did $feature->location->start and it worked
16:58 pyrimidine ok
16:58 kai which reminds me
16:58 pyrimidine ...
16:59 * pyrimidine waiting for the other shoe to drop...
16:59 kai Bio::SeqIO::FTHelper::from_SeqFeature() returns a list of FTHelpers, right?
17:00 pyrimidine yes, I think so.  I don't think most parsers even use that, except the most important ones of course :)
17:00 kai and the fth->key comes from the primary tag of the feature?
17:01 kai so if I get a warning about if ( $fth->key eq 'CONTIG') being an empty comparison, there's a problem with a primary tag in a sequence?
17:01 pyrimidine yes, I would assume so.
17:01 kai ok, will have a look at my code again
17:02 kai thanks :)
17:02 pyrimidine Personally I don't like using FTHelper.  I think it's ironically named.
17:05 Dezin so does anyone know about successful uses of neural nets to predict gene structures?
17:05 Dezin not predict but identity
17:05 Dezin *identify
17:09 pyrimidine Dezin: no
17:09 pyrimidine not familiar, but sounds interesting
17:09 Dezin lol yeah
17:09 Dezin i was thinking of attempting it to try and classify specific poxviridae
17:11 Dezin maybe use two seperate nets one to id transcribed sequences and another to id control sequences
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18:48 deafferret rbuels: re: tweet: what frustrates me about these sorts of things is that it's missing a single concrete change that should be made to the system
18:48 rbuels hah
18:48 deafferret lots of good ideas, no concrete call to action
18:49 deafferret because Education's financial model doesn't work without lots of what they already do
18:49 deafferret and pass/fail diploma/no_diploma
18:51 deafferret i have the same complaint about Sam Harris' books
18:58 rbuels i think action will naturally follow from these idea-exposition things.
18:58 rbuels the ideas just have to percolate through society.  which takes years.
18:59 pyrimidine decades
18:59 * rbuels nods
19:06 deafferret seems to me nothing tangible can percolate until someone offers something concrete as a catalyst for change
19:07 * pyrimidine nods, but doesn't know what the hell we're discussing
19:07 pyrimidine :)
19:07 deafferret http://www.youtube.com/watch?v=zDZFcDGpL4U
19:10 deafferret the "ooo! shiny idea!" part of my brain loves that stuff.  the "put up or shut up" part of my brain abhors it
19:10 deafferret and the latter is angry
19:10 deafferret :)
19:21 pyrimidine just finished most of it.  I've seen his talks before (on TED I think)
19:23 pyrimidine he actually has some great ideas (the talk is heavily edited), problem is the current system is so ingrained it would have to be completely dismantled.
19:23 pyrimidine Hell, we still have summer breaks in most of the country, so the little kiddies can go help ma and pop on the farm
19:24 rbuels hehe
19:24 rbuels there are stepwise things that could be done
19:24 rbuels like eliminating age-based grades.
19:24 rbuels i.e. "8th grade", etc
19:25 pyrimidine but look at the resistance to relatively minor changes, like block scheduling or paying for after-school programs
19:27 rbuels yep, and that's why ideas have to percolate
19:27 rbuels so people say "you know, that's probably a good change"
19:28 pyrimidine right, but people are naturally resistant to change
19:28 rbuels and rightly so.  there should be some resistance, to avoid flailing about.
19:30 pyrimidine unfortunately, incremental changes in something as broken as the american education system won't address the current problem, namely that there just isn't enough money for public education to be sustainable
19:32 pyrimidine if you can't tell, the wife's a HS teacher.
19:32 * deafferret buys pyrimidine a beer, prepares for a 3 hour conversation
19:32 deafferret oh, wait... no, i'm at work in Omaha. nevermind
19:33 pyrimidine and she's Canadian (where they actually pay teachers)
19:33 pyrimidine :)
19:33 pyrimidine will have to take the beer some other time
19:34 pyrimidine trying to work out why the GBrowse upgrade borked displaying our seq data
19:34 deafferret GGCATCGTCGTAGCborkGTACGTAGCTAAAGCborkACGTAGCATGCT ?
19:35 deafferret hmm... should probably gap it     GCATGCAT-bork-CAGATTAAC
19:37 dnewkirk You've discovered Bork motifs
19:37 dnewkirk I sense a Science paper coming up...
19:37 pyrimidine The DNA came from the Swedish Chef
19:38 dnewkirk DNA... it's what's for dinner?
19:38 deafferret http://www.youtube.com/watch?v=sY_Yf4zz-yo
19:38 pyrimidine http://www.youtube.com/watch?v=mbs64GvGgPU
19:39 pyrimidine muppets are awesome
19:39 deafferret (GBrowse upgrade)++
19:45 rbuels pyrimidine: got a url of the borked sequence display?
19:46 pyrimidine rbuels: posted an image to the list (I'm behind a firewall at the IGB, so it's only visible on-campus, with is a PITA)
19:47 * rbuels looks at the list
19:50 pyrimidine rbuels: see #gmod for scott's response
19:51 pyrimidine hah, deafferret got RTFM'd
22:17 dukeleto does anybody actually use Bio::Tools::Run::StandAloneNCBIBlast ?
22:24 rbuels heh
22:26 pyrimidine the question is, should we burn the whole mess down and start over?
22:27 rbuels ncbi already did that with the underlying C codebase, lol
22:27 * pyrimidine -> home
22:35 deafferret i got RTFM'd where?  #moose?  lazy++
22:35 deafferret pyrimidine: ^
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23:39 CIA-67 bioperl-live: gjuggler topic/tree_api_refresh * r2bee2b5 / (74 files in 35 dirs): Fix merge conflicts (+23 more commits...) - http://bit.ly/f4QvE2

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