Camelia, the Perl 6 bug

IRC log for #bioperl, 2011-03-01

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All times shown according to UTC.

Time Nick Message
00:04 rdesfo left #bioperl
00:44 CIA-44 bioperl6: takadonet master * r7c8a961 / lib/Bio/Tools/CodonTable.pm : Hardcored IUB hash from IPUAC.pm for now. Can translate ambiguous codons . Passing a few more tests. - http://bit.ly/eusks8
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01:45 CIA-44 bioperl-live: Florent Angly master * r444aa40 / Bio/SeqFeature/Lite.pm : Merge branch 'master' of github.com:bioperl/bioperl-live - http://bit.ly/g4bRJh
01:45 CIA-44 bioperl-live: Florent Angly master * rf4d9ccf / (Bio/PrimarySeq.pm t/Seq/PrimarySeq.t): Improved detection of protein sequences in Bio::PrimarySeq::_guess_alphabet - http://bit.ly/eUAzkm
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06:36 CIA-44 bioperl-live: Florent Angly master * r1c8616f / (Bio/PrimarySeq.pm t/Seq/PrimarySeq.t t/data/sbay_c127.fas): Bio::PrimarySeq:_guess_alphabet is now IUPAC-compliant and does not count X as a valid DNA letter - http://bit.ly/dWv3rx
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13:54 pyrimidine takadonet++ # bioperl6
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14:42 deafferret :)
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18:33 pdc joined #bioperl
18:35 pdc Hi - I'm trying to get BioPerl reinstalled on a Windows 7 Machine - 64Bit, Quad-Core, 18Gb RAM. First problem - the version of nmake that is linked in the installation instructions will not run on a 64bit machine, is there a 64bit nmake?
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18:42 deafferret 7 minutes  \o/
19:01 * rbuels finds it amusing that they've bought a big beefy machine and are running windows on it
19:02 pyrimidine pshah, 18 GB.  I spit on your 18GB of RAM.
19:02 rbuels well yes, it's not *that* beefy
19:34 dbolser cluster for windows ^{TM}
19:42 rbuels haha
19:48 pyrimidine rbuels: do we have an OBF projects page started for GSoC?
19:48 rbuels pyrimidine: sigh, not yet
19:48 pyrimidine snap snap!
19:48 * rbuels has been sitting on his butt
19:49 * rbuels drags his butt over to open-bio.org
19:49 * rbuels sighs, groans, looks sidelong at pyrimidine
19:49 * rbuels picks his nose
19:49 pyrimidine I think the BioRuby folks have already started something
19:50 rbuels wtf?  http://www.open-bio.org/wiki/Shi​t_man_thermite_your_harddrive_30
19:50 rbuels this wiki is getting spammed
19:51 pyrimidine just a tad bit
19:51 rbuels although that's a rather fun article
19:51 pyrimidine yeah, http://www.open-bio.org/wiki/We_give_quotes_for_​Auto_Life_Home_Business_and_Health_insurance_30 isn't as fun
19:52 rbuels i like the soccer players
19:53 pyrimidine I think those pages are meant to warp people's minds.  "Place a pinch of sugar on a plate. Add some few drops about water to kind a sugary solution. Carry the steel wool pad in your turn and dip the available ended strand in the sweets water"
19:58 * rbuels starts sitting in #obf-gsoc
20:09 rbuels oh wait, obf-soc
20:17 pyrimidine here ya go:
20:17 pyrimidine > my $dna = "ttaagg"; sub translate($dna) { "FFLLSSSSYY!!CC!WLLLLPPPPHHQQRRRRIIIMT​TTTNNKKSSRRVVVVAAAADDEEGGGG".comb[map { :4($_) }, $dna.trans("tcag" => "0123").comb(/.../)] }; say translate($dna)
20:17 pyrimidine LR
20:18 pyrimidine some perl6 for you
20:18 pyrimidine ('LR' is the output)
20:19 * deafferret grunts, wonders if that's shinier than perl5 in any way
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21:22 pyrimidine deafferret: naw, it's basically perl golf, but the description on what it means is pretty nice:http://strangelyconsistent.org/blog/​the-genetic-code-oneliner-in-perl-6
21:22 pyrimidine at least gives you an idea on what is going on
21:23 deafferret ha   <TimToady> course, where not /<-[ACGTactg]>/ might beat all those
21:23 deafferret ah, i remember life before ambiguity codes etc etc etc
21:24 deafferret when dna was simple
21:25 deafferret huh... so FFLLSSSSYY!!... is some sort of condensed translation result map for all possible dna combinations?
21:26 deafferret don't think i've seen that before
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21:38 dnewkirk That's pretty cool.
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22:06 rbuels is now known as troll
22:06 troll is now known as rbuels
22:07 pyrimidine rbuels: troll
22:07 * rbuels chuckles
22:08 * rbuels trolls fejes in #bioinformatics
22:09 pyrimidine I never check in there; when I did I never saw anything bioinformatics-related
22:10 rbuels eh, yeah, there's a lot of off-topic-ness there
22:10 pyrimidine that never happens here ;-)
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23:35 deafferret 3rd Rock from the Sun is streamable on Netflix now.  woot!
23:35 deafferret aliens are very bioinformatical
23:41 DeniseM joined #bioperl
23:41 DeniseM Greetings everyone
23:42 DeniseM I have a list of Refseq mRNA IDs that I want to get the sequence for.  I don't want to use Bio::DB::Refseq though because I don't watn to have to hit a remote database.  I have a local copy of the refseq flatfile.  How do I get Bio::DB::Refseq to use the local flatfile?
23:43 deafferret how many IDs are you searching for? a few or thousands?
23:43 DeniseM I've looked at the Bio::SeqIO package, but that doesn't seem to allow me to retrieve particular information via query rather than cycling through all of the refseq ids
23:43 DeniseM thousands
23:43 rbuels DeniseM: you probably want Bio::Index::Fasta
23:44 DeniseM thanks, I'll look that up :)
23:44 * rbuels uses that a *lot*
23:45 DeniseM What about Bio::DB::Fasta?
23:46 rbuels DeniseM: that could work too.  i haven't used it though
23:47 DeniseM Ok.  really what I'm aiming for here overall is that I have a list of insertions at chromosome positions and I've mapped that chromosome position to a particular refseq, then I want to use bioperl to retrieve the sequence, insert the insertion, and then use the translate function to see what the impact is of the insertion on the protein of that refseq
23:47 DeniseM Seems like that's a reasonable way to do it, but maybe you have a better suggestion?
23:47 rbuels wow, you gave us the backstory without us having to pry it out of you!  DeniseM++ !
23:48 * rbuels thinks about this problem
23:48 DeniseM hehe.. thanks :)
23:48 * deafferret rubs rbuels' chin
23:49 rbuels DeniseM: yeah, i think you're probably going about it in the right way.
23:49 DeniseM Ok, thanks :)
23:50 rbuels DeniseM: and probably either Bio::Index::Fasta or Bio::DB::Fasta would work.  Bio::DB::Fasta would probably be more efficient if you are querying for subsequences, and their performance would probably be about the same if you're querying for whole sequences
23:51 DeniseM Think I'm probably going to end up querying for whole sequences, so I'll start with the index and if I need it I'll use the DB
23:51 * rbuels nods
23:51 DeniseM thanks for your help :)
23:52 rbuels DeniseM: no problem.
23:52 rbuels DeniseM: you work at ISB in seattle?
23:52 DeniseM I do
23:52 rbuels DeniseM: postdoc?  technician?
23:52 rbuels DeniseM: PI?
23:52 rbuels i'm just down the road in portland
23:52 DeniseM Lowly software engineer ;)
23:53 DeniseM Cool.  You've been getting the same terrible weather we have
23:53 * rbuels nods
23:53 deafferret 60 deg in Omaha! woot!
23:53 * rbuels is also a software engineer
23:54 rbuels DeniseM: so software devs are lowly at ISB?  no that it's unusual for that to be the case.
23:54 rbuels s/no/not/
23:54 DeniseM Nope, just me.  I'm starting a new project and feeling like I'm swimming upstream currently
23:55 deafferret it's either that or freefalling downstream over the waterfall  ;)
23:55 rbuels DeniseM: ISB needs to open a branch in portland
23:56 rbuels DeniseM: lots of good perl devs down here
23:56 rbuels DeniseM: dukeleto and I are both here, we telecommute for http://solgenomics.net
23:56 * rbuels snaps his fingers to cause this to materialize
23:56 * rbuels chuckles
23:56 DeniseM That looks like an interesting place :)
23:57 deafferret DeniseM: Don't ask him about the corn genome though. You don't want to know.
23:57 rbuels hehehe
23:59 DeniseM uh oh! :o
23:59 rbuels DeniseM: if you do any online database stuff, you might be interested in #gmod, also on this server

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