Camelia, the Perl 6 bug

IRC log for #bioperl, 2009-07-22

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All times shown according to UTC.

Time Nick Message
00:23 rbuels huh?
00:23 * rbuels goes and looks at the current issue
00:24 deafferret sorry. can't help giggling like a 12-year-old whenever i see PNAS
00:24 deafferret this seems to only occur to *me* for some reason
00:25 rbuels we could play a game to publicize it
00:25 rbuels it's a good journal
00:25 rbuels we could take turns shouting PNAS
00:25 rbuels at increasing volume
00:25 deafferret I am totally not going to get rolling on PNAS.  :)
00:25 rbuels thus raising awareness of its importance in the landscape of modern biological research
00:25 * deafferret titters
00:26 rbuels i fail to see the humor.
00:26 deafferret 30 FAILs! ouch http://static.cpantesters.​org/author/J/JHANNAH.html
00:27 deafferret PNAS -> penis. Hilarity ensues.
00:27 rbuels what?
00:27 deafferret I told you I'm 12.
00:28 kyanardag joined #bioperl
00:30 deafferret Ever get the feeling you have a hole in your LWP::UserAgent cookie jar? I do.
01:51 deafferret ooo... much better
01:58 * rbuels shouts PNAS
02:02 deafferret i fail to see the humor
02:24 * deafferret titters
02:56 rbuels heh.  you said, like, tits or something.
04:02 ptl joined #bioperl
08:29 rbuels faceface: ping?
08:30 rbuels what, aren't you into work yet.  i swear, you scotsmen.  always late.
08:34 rbuels heh, i'll just send you an email
08:34 rbuels i've gotta go to bed, it's 1:30am here ;-)
08:34 rbuels bed &
10:27 faceface rbuels: pong... too slow ;-)
10:27 faceface I was in work at 8:30, but I didn't check my chat until now... for the record ;-)
10:27 faceface just saw your email dated "1 hour ago" ... I'll reply there
12:24 kyanardag joined #bioperl
16:14 faceface yo rob
16:15 * faceface talks in a 'street' accent
16:15 rbuels sup g
16:16 rbuels ;-)
16:16 rbuels faceface:  ^^^^^^^^^
16:16 * faceface makes some elaborate hand gestures
16:16 rbuels hehe
16:16 faceface how is it going?
16:16 rbuels not bad
16:16 rbuels you getting me the info on the other 2 libraries?  ;-)
16:17 * rbuels knew there must be other potato bac libraries somewhere....
16:17 faceface rbuels: right...
16:17 faceface but only recently
16:17 faceface GB actually stands for 'glenn bryan' (to his embarrasment)
16:17 faceface it just 'stuck'
16:17 rbuels i've gotta get records for them in the db to hook them into the rest of the genome system
16:17 rbuels oh that's funny
16:17 faceface don't know anything about the JP one
16:17 rbuels is RH Roeland Van Hamm?
16:17 rbuels lol
16:18 faceface hehe
16:18 rbuels i'll rib glenn about that next sol meeting
16:18 faceface Actually, my supervisor is called David Martin, and we are now working on DM
16:18 faceface ...
16:18 rbuels heh
16:18 faceface I meet with Glenn quite regularly, he is really great
16:19 rbuels yeah i like him too
16:20 faceface I didn't forward the part of Theo's email where he said 'its not me who deals with this' - sorry about that
16:20 faceface not sure why he cc'ed Richard Visser / Christian Bachem in his reply, but C was on a phone conf today and he didn't mention it
16:20 * rbuels shrugs
16:21 faceface so long as you can get what you need... any other buggy bacs?
16:23 rbuels nope they look OK.  i'm successfully snarfing data from both genbank and the bacregistry thing, now i've got to write the code to get them correlated, assign version numbers, keep the mapping of bac identifiers -> genbank accessions, etc
16:23 faceface hmmm...
16:23 faceface that mapping should be in genbank
16:24 rbuels it is, but I have to keep it here
16:24 rbuels also
16:24 faceface i.e. according to the standards we were given for naming bacs for GB upload
16:24 faceface rbuels: OK - just wondering if you were thinking to blast to get correspondance
16:24 rbuels haha no no
16:24 rbuels that would be ridiculous
16:25 faceface right
16:25 rbuels if i had to do that, i would start sounding as pissed off as Theo
16:25 faceface but if you didn't know the mapping existed... extreeme measures...
16:25 faceface heheh
16:25 rbuels anyway, i have to get going, got to read over some stuff for a conf about a different project
16:26 rbuels will be looking for the lib information ;-)
16:26 faceface where?
16:26 faceface enjoy your conference?
16:27 rbuels in my email inbox?
16:27 faceface s/\?/!/
16:27 rbuels oh.  phone conference.
16:27 faceface just habbit???
16:27 faceface sorry
16:27 faceface er...
16:27 rbuels or hobbit.
16:27 faceface I'll try to see what I can find
16:27 * rbuels has hair on his toes
16:27 rbuels ok ttyl
16:27 faceface rbuels: have you been informed about the tomato ngs assembly strategy?
16:28 faceface bb
16:28 rbuels ...
16:28 rbuels no i haven't
16:28 rbuels have you?
16:28 rbuels lukas may have been
16:29 rbuels reading stuff &
16:30 faceface I wanted to crash the conf, but I ran out of time
16:31 faceface I'm sure I've got a tomato hat around here somewhere
18:43 Emos joined #bioperl
18:44 Emos Hello there
18:44 Emos I have a question for you
18:45 Emos I want to create a loop that verifies if a condition is met, and runs until it is met
18:45 Emos but the condition is pretty long
18:45 Emos 5 rows of code
18:45 Emos how can I write the loop?
18:55 deafferret nopaste the condition at http://pastebin.com or somewhere
19:09 Emos the condition is genome_coords($rand_id, $db, $ua) to be true
19:09 Emos but if it is not true, it has to do $rand_id = int(rand($range));
19:10 Emos and then check again
19:18 deafferret and when does it stop trying?
19:20 Emos when it is true
19:24 deafferret so try forever?
19:25 Emos no, the pseudocode id: try if genome_coords($rand_id, $db, $ua) is true, if it true, do what I want. If it is not true, do $rand_id = int(rand($range)); until genome_coords($rand_id, $db, $ua) is true
19:26 Emos is that possible?
19:26 deafferret while (! genome_coords($rand_id, $db, $ua)) { $rand_id = int(rand($range)) }
19:26 deafferret # Yay! do what Emos wants.
19:27 Emos thanks!!! I didn't think of creating a new loop
19:27 deafferret sure. that leaves you nice and stuck in the while loop forever -- until genome_coords() becomes true  :)
19:27 Emos !
19:27 Emos means not?
19:27 deafferret yup
19:28 Emos ok
19:28 deafferret not also means not, if you prefer that
20:34 perl_splut joined #bioperl
22:39 Emos joined #bioperl
22:39 Emos sorry
22:39 Emos I have another problem here
22:39 Emos :-((
22:39 deafferret :)
22:40 Emos this time I have to make an if statemente
22:40 Emos if ( genome_coords($geneid, $db, $ua) ) {
22:40 Emos doensn't work
22:40 Emos syntax error at genome.pl line 35, near "$geneid ( "
22:41 deafferret go to pastebin.com and put your code in there, then tell us the URL
22:43 Emos I'http://pastebin.com/d59478580
22:45 deafferret http://pastebin.com/m619178e5
22:45 deafferret you were missing the last curly brace. Avoiding tabs and clear indention make that easier to spot
22:48 Emos I can't see any difference between my and yours code
22:48 deafferret Mine has a curly brace at the end. And has no tabs.
22:49 deafferret and is indented
22:51 Emos I counted them
22:51 Emos they are 6
22:51 Emos in yours and mine
22:52 Emos where did you add it?
22:53 deafferret oops, my bad. I guess my copy/paste failed. let me try again
22:53 deafferret huh. when I copy/paste yours it runs fine.
22:54 deafferret the indention's just off. But perl doesn't care about that, only humans do
22:54 deafferret so it looks like I can't reproduce your syntax error
22:54 deafferret try pasting the whole file instead of just 8 lines
22:57 Emos I think I found the problem
22:57 Emos wait a sec
23:03 Emos I cannot
23:04 Emos here's the entire script
23:04 Emos http://pastebin.com/d1eac8489
23:05 deafferret you need a semi-colon on the end of line 31
23:06 Emos nooooooo
23:06 Emos THANKS!!!!
23:06 Emos it's such a stupid error!
23:06 deafferret the problem is always right above whatever you paste the first time  :)
23:11 Emos thanks again
23:15 biomoose joined #bioperl
23:15 biomoose biomoose: Siddhartha Basu master SHA1-0ecf66a
23:15 biomoose Added bunch of roles,  most of them are interface centric and needs only requires keyword.
23:15 biomoose http://bit.ly/2kzxS8
23:15 biomoose left #bioperl
23:19 deafferret another cfields bot drive-by   ;)
23:27 kyanardag joined #bioperl

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