Camelia, the Perl 6 bug

IRC log for #bioperl, 2009-10-06

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All times shown according to UTC.

Time Nick Message
00:00 rbuels where the %s is your accession
00:00 rbuels and fill in the email and tools to not blame it on me
00:00 deafferret rettype=gbwithparts ? I don't see that in eutils docs
00:00 rbuels docs??
00:00 rbuels DOCS???????
00:00 rbuels in bioinformatics?????
00:00 rbuels you've gotta be kiddin
00:00 deafferret but but but
00:01 deafferret i was totally going to write a SYNOPSIS today and everything
00:01 rbuels fuck that shit.  pabst blue ribbon.
00:01 deafferret but I want pyrmiwhatever to like me!
00:01 rbuels i have to go to my piano lesson now.  i need to make sure my pink tutu is clean.
00:01 deafferret oh? are you going to tour with Coldplay?
00:01 deafferret they're a good show
00:03 deafferret damn you're good
00:06 rbuels &
00:22 deafferret & commute
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04:22 Banff Is anyone here familiar with BioPython?
07:59 faceface oh that trixter!
08:03 faceface deafferret: the Eutils docs sucks
08:03 faceface why isn't everythign wiki?
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10:39 Biome biome: Siddhartha Basu master SHA1-9558714
10:39 Biome Added location type
10:39 Biome http://bit.ly/AlWaK
10:39 Biome biome: Siddhartha Basu master SHA1-00f6cff
10:39 Biome Removed swap file
10:39 Biome http://bit.ly/XAaaE
10:39 Biome biome: Siddhartha Basu master SHA1-d68c0ca
10:39 Biome removed .dotest folder
10:39 Biome http://bit.ly/uhPj8
10:39 Biome biome: Siddhartha Basu master SHA1-84ec9f1
10:39 Biome Merge branch 'master' of git@github.com:cjfields/biome
10:39 Biome http://bit.ly/1HhSr
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13:06 deafferret faceface: you're asking why isn't the NCBI website wiki?  :)
13:06 deafferret in my limited experience, homie don't play that
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16:55 perl_splut wiki's are ok, but the data on NCBI needs to be far less freeform than most wikis usually allow.
17:00 deafferr1t faceface_: see? homie defnt'ly don't play that
17:01 * deafferret flexes
17:02 deafferret <- @ ftw
17:06 perl_splut sigh... not even near lunch and stomach is growling...
17:07 perl_splut and I have $1 to my name
17:09 * deafferret spots perl_splut
17:32 faceface_ deafferret: perl_splut: Agreed, but still, there are wikis and there are wikis
17:32 faceface_ why is my face distended?
17:32 faceface thats better
17:55 pyrimidine deafferret: what you talkin' bout, my Eutilities has no docs?!?
17:55 pyrimidine ;)
17:56 deafferret pyrimidine: oh, there's LOTS of docs. but the SYNOPSIS seems a touch sparse.  :)
17:56 deafferret "how to use this" docs seems lacking a bit you see
17:57 deafferret I didn't realize that Bio::DB::GenBank and EUtilities backend the same way nowadays (always?)
17:57 pyrimidine deafferret: let me know the ones and I'll improve them (lots of modules involved)
17:58 pyrimidine deafferret: also, did the HOWTO cookbook help at all?
17:58 * pyrimidine thinkin' I need to port eutilities over to moose
18:00 deafferret didn't see the HOWTO on it
18:00 deafferret Bio::DB::EUtilities SYNOPSIS
18:00 deafferret I was going to add an efetch example from the t/ directory, but I couldn't seem to grab the format I happened to want (Genbank)
18:00 deafferret rbuels gave me the rettype=gbwithparts trick
18:00 deafferret not sure if that passes all the way through somehow
18:00 * deafferret checks the HOWTO
18:01 deafferret laugh   http://www.bioperl.org/wiki/HOWTO:EUtilities
18:01 rbuels deafferret indicated that he just wanted to save gb documents to disk, and that sounded like round-tripping that stuff through bioperl would be unnecessary and probably lossy
18:01 pyrimidine 'gb' also works in most cases, but 'gbwithparts' is better.  Also, if you're pulling down very large files I wouldn't use Bio::DB::GenBank
18:01 pyrimidine rbuels: agreed
18:02 deafferret disk or via Bio::Seq. I don't know since the requestor is vague
18:02 rbuels hit them on the head with a hammer, see if that helps
18:02 deafferret EHANDTHATSORTOFFEEDSMEBARELY
18:03 rbuels lol
18:03 rbuels ETHESECSTYLEERRORCONSTANTSAREKINDOFRIDICULOUS
18:03 pyrimidine yes the eutilities HOWTO is blank; the Eutilities cookbook isn't.  I'll remove that link...
18:04 pyrimidine done
18:04 deafferret oo! HOWTO:EUtilities_Cookbook++
18:04 deafferret $factory->set_parameters(-rettype => 'gbwithparts');
18:05 * deafferret wonders if all the Bio::DB::EUtilities* POD and wiki pages should link to HOWTO:EUtilities_Cookbook
18:06 pyrimidine deafferret: will be doing that, yes
18:06 deafferret or at least SYNOPSIS should refer there
18:06 deafferret pyrimidine++
18:06 deafferret rbuels: do take a note of that karma increment
18:07 rbuels i'll increment your big fat face
18:07 * deafferret wonders if they even sell xxxXl helmets...
18:08 deafferret circusfreakhats.com
18:08 rbuels lol
18:08 rbuels ok enough tomfoolery i have a *lot* of stuff to do
18:08 * rbuels continues grinding his nose
18:28 * pyrimidine also thinking about rewriting the hell that is StandAloneBlast
18:30 * deafferret never drank that punch
18:35 pyrimidine deafferret: don't.  No rainbows and unicorns there (unless they're of the quentin tarantino variety)
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18:44 Topic for #bioperlis now http://www.bioperl.org - You can get help here, but you must be patient.  Paste to http://gist.github.com/.
18:59 * rbuels will now always be reminded of the song 'Stuck in the Middle With You' when thinking about StandAloneBlast
19:03 deafferret hmm... I wonder why it takes 3 hours to find my head in my ass? maybe because we configure DNS like this?  dev -> l3oedsdev1 -> l3qaoeds1 -> 10.0.97.39 (owsDEV); qa -> l3oedsqa1 -> 10.0.97.91 (owsQA)
19:05 rbuels is that turkish?
19:05 rbuels i have no idea what you just typed.
19:05 perl_splut Well, it stops being a Wiki once you force a lot of programmatic constraints on the format of the data
19:05 deafferret ya. me neither.
19:06 deafferret you see, l3oedsqa1 is QA while l3qaoeds1 is DEV.
19:06 deafferret duh
19:08 deafferret presumably l3oeTRAININGds1 will be PRODUCTION
19:18 * pyrimidine still thinks it's turkish
19:19 * ptl_ finds it more like greek
19:22 pyrimidine да
19:47 perl_splut looks like a bunch of anames and cnames for various systems
19:50 deafferret indeed. the suck abounds.
19:50 * deafferret abides
20:00 * deafferret sticks the shotgun in the Java's face
20:04 * pyrimidine again thinks of quentin tarantino
20:43 * rbuels slices off the DNS server's ear with a razor
20:52 * ptl gets the server's ear from the floor and auctions it on ebay
20:53 perl_splut using DNS is an advantage as resources can be moved around by repointing the name elsewhere while not having to do things like rename the machine itself
20:54 deafferret indeed. and it helps if you're not on crack when you load the entries.
20:55 pyrimidine crack is whack
20:55 perl_splut meth is better
20:55 pyrimidine that doesn't rhyme, though
20:56 perl_splut so
20:56 deafferret kick him!
20:56 * deafferret laughs evilly
20:56 deafferret evillllllllly
20:56 * perl_splut kicks pyrimidine *
20:56 pyrimidine \kick perl_splut
20:56 deafferret oooo... close call
20:57 pyrimidine just a backtick off ;)
20:57 was kicked by pyrimidine: pyrimidine
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20:57 pyrimidine heh
20:57 perl_splut ,,|,,
20:57 deafferret lol
20:58 deafferret where's the thumb?
20:58 deafferret oh... 5 digits. right
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