Camelia, the Perl 6 bug

IRC log for #bioperl, 2012-09-14

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All times shown according to UTC.

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18:21 rjg_ hello- I got some fantastic help from here (from rbuels) yesterday, and I was wondering if anyone could answer a little question I have...?
18:22 rbuels rjg_: i'm here again
18:22 rbuels (mentioning my name makes my IRC client blink and gets my attention)
18:22 deafferret rbuels: like this?
18:23 deafferret all hail the king of jBrowse!!
18:23 rjg_ lol, you guys....
18:23 rbuels deafferret: why yes, like that!
18:23 rbuels deafferret: aren't you a smart boy!
18:23 rjg_ hi rbuels, you star you
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18:23 deafferret rjg_: rbuels is not "you guys". he's "Your Grace"
18:24 * deafferret also grovels before the mighty py<TAB>
18:24 rjg_ my deepest apologies your grace and you guys :p
18:24 deafferret :)
18:24 pyrimidine More like Your Highness
18:24 deafferret rjg_: I'm just teasing.
18:24 rbuels omg pyrimidine, deafferret, and rbuels all in the channel at the same time
18:24 rbuels it must be friday.
18:24 pyrimidine Your Heinous?
18:24 pyrimidine :)
18:24 deafferret hi-knee-ass
18:24 rjg_ lol friday or part-day?
18:24 rbuels yes, i do prefer Your Heinous is more like
18:25 rjg_ lol I seem to have kicked things off a little bit here
18:25 pyrimidine rjg_: both.  neither.  I need a beer
18:25 * rbuels writes up #bioperl court protocol on the wiki
18:25 deafferret <-- court jester
18:25 deafferret <--- but not funny
18:25 rbuels deafferret: oh, you're funny.
18:25 rjg_ so I don't know if you remember the script you showed me yesterday- it was getting the taxon ids for Gi numbers
18:26 rjg_ it worked beautifully (of course it did) but it got me to wondering, how do I modify it to get the same thing but for accession numbers?
18:26 pyrimidine rjg_: are you using entrez queries for this?  Or local DB?
18:27 * deafferret plays the rbuels walk-to-the-boxing-ring theme song https://www.youtube.com/watch?featur​e=player_embedded&amp;v=ebBXEeeSfn4
18:27 rjg_ hmm entrez I think....
18:27 deafferret (anything with Ace Hood)
18:27 rjg_ no definitely entrex
18:27 pyrimidine ok
18:27 rjg_ not a local db
18:27 rjg_ entrex...who's with me that sounds better than entrez?
18:28 pyrimidine o/
18:28 rbuels deafferret: the ad they ran me in front of that was for Capital One Strategic Consulting
18:28 rjg_ ...noone... ok i'll just go sit over there....
18:28 * rbuels chuckles
18:28 rbuels pyrimidine: see the backscroll for my gist from yesterday
18:28 pyrimidine ok
18:28 deafferret rbuels: oh? i didn't get an ad. sorry
18:29 rbuels good old ace hood
18:30 rjg_ oh no! don't scroll back otherwise they'll all see I'm using windows!!! :( :(
18:30 rjg_ they'll never let me come bac!
18:30 pyrimidine rbuels: there is a faster way to go from GI to TaxID
18:30 pyrimidine ftp://ftp.ncbi.nlm.nih.gov/p​ub/taxonomy/gi_taxid.readme
18:30 deafferret rjg_: masochists are allowed. fear not. ;)
18:30 rjg_ lol glutton for pain, it has been said before...
18:31 rbuels pyrimidine: he said he didn't want to download that
18:31 * rbuels shrugs
18:31 pyrimidine ah
18:31 rjg_ yes the nuc one is huge
18:32 pyrimidine nah, that
18:32 pyrimidine 't not huge
18:32 * pyrimidine having a fat finger day
18:32 rjg_ oh it doesn't look huge there...
18:32 rjg_ i downloaded it and it unzipped to about 3 gb
18:33 rjg_ maybe I pixied the wrong thing
18:34 pyrimidine I just bulk load that into a DB (MySQL, SQLite, whatever), index, and query
18:34 rjg_ you see my grand idea if I can put it that way is to develop a pipeline that people can access from the web without the need to download a large datafile- it's probably a silly idea that noone will ever use but it might be fun for some people
18:35 pyrimidine .oO( isn't that genbank? )
18:35 pyrimidine :)
18:35 rbuels pyrimidine: party pooper.
18:35 rjg_ lol yes, but genbank doesn't do what I want it to do....
18:36 pyrimidine Okay, so what do you want it to do?
18:36 * rbuels grumbles about these people always injecting "reality" and "practicality" into everything
18:36 * pyrimidine is a pragmatist
18:36 * rbuels goes loco with the cake
18:36 * pyrimidine prefers pie
18:37 pyrimidine strawberry rhubarb in particular
18:37 rjg_ well, at the risk of giving away all my precious ideas I want to see if I can determine the life history of a bacteria by the mobile elements it has acquired from elsewhere
18:38 pyrimidine ok
18:38 rjg_ lol, I think it's a precious idea because its been occupying 90% of my time recently
18:38 rjg_ and thats including time spent asleep :s
18:39 pyrimidine sounds like a good idea.  Don't tell anyone… oh, wait...
18:40 rjg_ you guys are hilarious.  It'ts taken my a while to read over the things you've just written, where do you find guys like you?!
18:40 rjg_ (aside from a bioperl irc channel?)
18:40 rbuels i find me sitting in my lap
18:40 rjg_ lol if it was such a good idea someone would have done it by now....but thats not putting me off!
18:41 deafferret rjg_: you'll find me rubbing rbuels' chin thoughtfully
18:41 rjg_ everyone needs a muse
18:41 rbuels i will sometimes also by found rubbing my own damn chin
18:41 rjg_ don't rub it too much, you'll wear it thin, there's two of you at it!
18:42 rjg_ guys I've timed my question so badly, I'm being prodded by my SO to go and make the dinner.....
18:42 rjg_ I'll be back, sorry to have to skip like this
18:42 pyrimidine I'm in between my laptop and my seat, 2nd floor in a glassy building in the midwest
18:43 pyrimidine ah, corn and soy, how I hate thee
18:47 deafferret "corn is a fucker" --rbuels
18:47 * rbuels nods sagely
18:47 * rbuels starts production on The Innocence of Corn
18:47 deafferret pyrimidine: you should try mock duck (wheat gluten). delicious when prepared correctly
18:49 pyrimidine may have to do that, been reducing my duck intake for a while now
18:49 * rbuels casts deafferret as Barbara McClintock
18:51 deafferret (type casting)--
18:51 rbuels deafferret: i'm sorry, but people really identify you with these kinds of roles!
18:51 deafferret zomg http://sluttyscientists.tumblr.com/
18:52 deafferret damn you google
18:52 rbuels naaaaaaaaagh!
18:52 deafferret rbuels: i understand. it's the abs.
18:53 rbuels the darwin and venter ones are the best
18:56 rjg_ sagan has my vote
18:57 rjg_ so from the look of the database, it it safe to say that you can't directly query for taxon id using accession number- you'd have to have the GI?
18:57 rjg_ or have i got that wrong?
18:59 pyrimidine rjg_: yes
18:59 pyrimidine you can go from acc->GI->taxID
19:00 pyrimidine rjg_: http://www.bioperl.org/wiki/HOWTO:EUtilitie​s_Cookbook#Get_GIs_for_a_list_of_accessions
19:01 rjg_ ahh thats great, I thought I was being a retard
19:01 rjg_ thanks, I have seen that (I'm very much just 30 hours old when it comes to bioperl, but I've been giving that particular document some thorough consideration
19:02 pyrimidine It's generally better to use this one if you need to track which acc goes with which GI: http://www.bioperl.org/wiki/HOW​TO:EUtilities_Cookbook#Get_GIs_.28as_well_as_other_informatio​n.29_for_a_list_of_accessions
19:02 rjg_ fantasic, thank you for the direction
19:02 rjg_ do you guys work together? or do you just know each other from here?>
19:05 * deafferret is just a fanboi / hang-around
19:06 deafferret they're, like, smart and stuff
19:06 pyrimidine same here
19:06 pyrimidine well, except the hanging around part, not on IRC as much as I used to be
19:08 rjg_ lol deafferret- i wish I could call myelf a fanboi like you....at the moment I'm more like something you've scraped off your shoe!  But I'll get there.... one day...
19:08 deafferret rjg_: we'll be Almost Famous together :)
19:08 rjg_ lol it's a deal!  But you've got to take me with you!
19:09 deafferret there's plenty of room in Omaha, NE. Come on down :)
19:09 deafferret /over/up
19:11 pyrimidine across
19:16 rjg_ lol across is probably the one, I'm UK myself
19:16 rjg_ and fml, have any of you ever tried to make enchiladas??
19:16 rjg_ how do you even *do* that?
19:17 pyrimidine very carefully
19:17 rjg_ the kitchen looks like a bomb has gone off in it, saying nothing for the enchiladas themselves!
19:18 rjg_ one thing I've learned today is that I better make biology pay off for myself, cos I'm not ever going to be a chef!
19:21 rjg_ Is it nice in Omaha?  Pictures make it look nice, but cold in the winter..
19:28 pyrimidine rjg_: if it's like Champaign IL it's cold
19:29 rjg_ ahh right so most of you are in the USA then?  well it's not like I've got the better deal, I live in Scotland
19:30 deafferret rjg_: ya, weather is way too hot, way too cold (nice right now for a couple weeks)
19:30 deafferret we've got the same weather as the Chicago area
19:30 rjg_ lol count yourselves lucky then, I think I've forgotten what the sun looks like
19:31 deafferret rbuels used to be in Oregon (brilliant!) but I think he moved to boston or something. bad move, weather wise
19:31 rjg_ not that its so bad, after a while you even stop missing it
19:31 deafferret haha
19:31 rbuels i would much rather still be in Portland.
19:32 rjg_ the USA is so huge isn't it, never been myself but it must be weird thinking you could be so far from a coastline when inland
19:32 rbuels i make enchiladas sometimes.  you have to clean as you go.
19:32 deafferret ya. genehack just moved out there. I assume he's loving it
19:32 rbuels actually, that goes for cooking anything more than an egg.
19:32 deafferret rjg_: ya. i'm in the dead center of nowhere :)
19:32 rjg_ yeah cleaning.... thats never something I've been very good at
19:32 rbuels your kitchen life will be hell until you learn how to clean as you go.
19:32 rjg_ still you must have some great countryside out your way deafferret?
19:33 rjg_ my gf makes my kitchen life hell, so I don't clean as retailation :p
19:33 rjg_ it's all I have!!
19:33 deafferret rjg_: oh ya, the plains are fine scenery wise
19:33 deafferret rjg_: it's rolling hills near the river, which is nice
19:34 * deafferret likes trees, dislikes flatness
19:34 rjg_ that sounds lovely.  I grew up in london where you can't see the sky for the smog
19:34 deafferret ya. no pollution issues here
19:34 rjg_ well chaps this has been great again, my kitchen buzzer is telling me its time for food!!! thanks for your help, you guys are well nice I'm sure I'll be back!
19:35 deafferret people are dirty. fewer people, fewer problems.
19:35 deafferret toodles :)
19:35 rjg_ thanks again and have a great weekend you all! Bye!
19:58 genehack deafferret: yes, it's lovely.
19:58 genehack (although I'm in Salem, not Portland.)
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21:13 deafferret genehack: hmmm.... $cities{OR} = [ 'Portland' ]  I'm afraid
21:14 deafferret heh. google maps clearly shows that's basically a rounding error. like Omaha/Lincoln
21:15 deafferret (Walla Walla)++ # existing
21:17 genehack deafferret: it's 50 miles
21:17 genehack which, yeah, in the DC metro area would be considered the same town. 8^)
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