Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-04-05

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All times shown according to UTC.

Time Nick Message
00:02 brunov joined #bioperl
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10:15 driveby_bot joined #bioperl
10:15 driveby_bot /home/svn-repositories/bioperl: r16945 (dave_messina) : Fix for bug #3040. dS=nan is now parsed. As far as I can tell, allowing this non-numeric value isn't causing any downstream problems. All tests pass.
10:15 driveby_bot Diff: http://tinyurl.com/ybqczh2
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17:17 deafferret ..o
17:31 rbuels .@o..
17:35 pyrimidine .......
17:41 rbuels pyrimidine, deafferret does javascript have closures?
17:41 * rbuels times out in 10 seconds and gets book down from shelf
17:42 deafferret no clue. my js guy isn't here today
17:42 pyrimidine there is this:
17:42 pyrimidine http://blog.morrisjohns.com/java​script_closures_for_dummies.html
17:42 rbuels oh, it does
17:42 deafferret OH SNAP! Dummies!
17:42 * deafferret grabs some popcorn
17:42 * rbuels snaps his ... something
17:43 deafferret FIGHT FIGHT FIGHT
17:43 pyrimidine I snapped a long time ago...
17:43 * rbuels beats his .... forehead
17:44 * rbuels fixes a js error in gbrowse
17:45 pyrimidine just thinking out loud, but we had several SoC prospects on bioperl-l that... evaporated
17:45 rbuels did we chase them away? discourage them?
17:45 pyrimidine No, we responded to them on the list, just haven't heard back
17:45 rbuels (but also, if they are that easily discourage, probably not such great prospects anyway)
17:46 rbuels well, maybe their apps will be coming in
17:46 rbuels the deadline effect
17:46 pyrimidine yes, but we only have one bp-specific proposal
17:46 rbuels nuba's still here  :-)
17:46 rbuels he said he's be applying for the reorg
17:46 pyrimidine okay
17:46 * rbuels points at nuba
17:47 * pyrimidine throws the phant at nuba
17:47 nuba yeah
17:47 pyrimidine how's that coming along?
17:47 pyrimidine ;-)
17:49 nuba i hope to write and post that proposal until wednesday
17:49 pyrimidine okay
17:49 pyrimidine wfm
17:49 deafferret wfm? wait for me?
17:50 pyrimidine works for me
17:50 deafferret oic
17:50 rbuels o rly?
17:50 pyrimidine that's much better than wtf :)
17:50 rbuels true
17:50 nuba btw, should it go for TPF or the OBF?
17:50 pyrimidine OBF
17:50 rbuels obf probably
17:51 pyrimidine Of the proposals we have, this is one that could go for both, but i think it has a better chance with OBF
17:53 nuba ok
17:55 nuba is there anyone else (student-wise) interested in the reorg project?
17:55 pyrimidine Not ATM
20:20 deafferret $work[1] $mentor suddenly talking about locking down all of our research until publication (which tends to be never). Makes me sad.
22:03 spekkio joined #bioperl
22:20 spekkio I'm having a bit of trouble catching an error, whenever i run this code http://codepad.org/XgkdIy23 i get "Use of uninitialized value in hash element at run in parallel.pl line 12  and line 12 is $gorganism = $record->species->species; it has something to do with a improper species name for certain bacteria. Anyway im just wondering how do i properly catch this error so it's not spamming the output and i can email somone about it instea
22:21 spekkio im assuming some kind of if statement but im just not sure what to check for
22:28 deafferret so $record->species is undef, I'm guessing, which means you can't call ->species on it
22:28 deafferret so you need to do some sort of handling...
22:29 deafferret if ($record->species) {
22:29 deafferret $sp = $record->species->species;
22:29 deafferret what's the genbank ID in question?
22:34 spekkio one sec lemme look it up
22:35 deafferret print $record->id
22:35 deafferret or ->display_id
22:42 spekkio the $record->id gives me NP_032443
22:46 spekkio here is a link to what it is http://www.ncbi.nlm.nih.gov/protein/157012015
22:48 spekkio i used $record->primary_id() and it gives me a gi number which i just did a search for in protiens
22:49 deafferret hmmm... I get "musculus"
22:49 spekkio yep thats right
22:49 rbuels left #bioperl
22:49 spekkio its the whole sub family thing i think its not properly named as a species yet
22:50 deafferret uh... I'm not sure how to help you if I can't reproduce your problem...
22:50 deafferret ->species->species works fine for me...
22:51 spekkio hmmm k maybe im doing something wrong gimme a moment sry
22:51 deafferret no worries  :)
22:53 deafferret http://github.com/jhannah/s​andbox/tree/master/spekkio/
22:54 bag joined #bioperl
22:57 spekkio yeah your feeding it the same record as i am
22:59 spekkio lemme try it again
23:10 spekkio oh oh i think its something else, give me a few min ill try post the code narrowing it down.
23:22 * deafferret nods
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