Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-05-05

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All times shown according to UTC.

Time Nick Message
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11:04 fraWii Hi all, I have another problem...
11:05 fraWii I would like my script recognize if am reading a DNA, an RNA or an Amino acid sequence....
11:05 fraWii I have did:
11:05 fraWii http://codepad.org/J5BqYBuz
11:06 fraWii but is not working..
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14:10 abooz How is gff3 parsing in bioperl?
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17:56 jhannah abooz: how is it?
17:56 jhannah fraWii: did you figure it out?
17:56 jhannah abooz: I don't understand your question.
18:04 abooz jhannah: I was asking about the quality of GFF parsing.
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18:28 jhannah I think GFF was born from BioPerl authors, so I assume the GFF parsing in BioPerl is excellent.
18:28 jhannah I personally find GFF confusing. (the columns on the far right.) I have apparently not spent enough time with it.
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19:39 BelijAi hello world
19:39 rbuels hi
19:40 BelijAi wanna talk?
19:40 rbuels heh, i'm not interested in *talking* per se, i've got a lot of work to do.  :-)  but we can answer bioperl questions here
19:41 BelijAi what's the theme?)
19:43 rbuels um ... bioperl.
19:43 rbuels like it says in the channel topic
19:43 BelijAi is it cool think? i dont know what it is
19:43 was kicked by jhannah: general chat elsewhere
19:44 jhannah rbuels-- # feeding the clueless
19:44 * rbuels spanks jhannah with a wet something
19:45 * jhannah awakes from his mst trance
19:45 rbuels you never know, some of these furriners has strange ideas about introducing questions and taking a long time to get to the point
19:45 rbuels perhaps i'm too charitable
19:46 jhannah uh, every time I've seen an intro like that on IRC it's turned into spam or porn
19:50 jhannah BAH! HUMBUG!   YOU KIDS GET OFF MY LAWN!
19:51 * dnewkirk begins to cry
19:51 rbuels lol
19:52 * jhannah re-enacts various scenes from Sweeny Todd
19:53 * jhannah Smolders everyone that looks at him funny
19:56 jhannah i'm surprised my smolder emails haven't drawn more interest or spoiled produce
19:57 jhannah also interesting that they arrive on the mailing list an hour after I sent them, in the wrong order, and separated by 30m
19:57 * jhannah was expecting more bikeshedding on this
19:58 * rbuels is too busy for foolishness
19:59 jhannah ah, that's better. only more accusatory and insulting please
19:59 jhannah :o)
19:59 jhannah what's gotten into me today?
19:59 jhannah my humour is darker and even less funny that usual
20:00 * jhannah lashes out some more
20:00 rbuels you are a bit punchy today.
20:00 jhannah must be this log4perl re-org
20:05 perl_splut whee...
20:05 perl_splut almost finished converting a perl script from a desktop app to a web interface
20:05 jhannah oh ya? Catalyst?
20:06 perl_splut catalyst?
20:07 jhannah catalyst.perl.org is my web dev framework of choice. just wondering what you used
20:07 perl_splut vim
20:07 jhannah perl_splut++
20:09 perl_splut most of the time I used up was in trying to figure out (since it's been years since I wrote in php) doing form validation so that the user has a really hard time sending my code something that will screw up the system
20:09 jhannah ah, php.  :)
20:10 perl_splut yeah. php drives the frontend and the perl/bioperl stuff does the real work
20:23 jhannah cool. URL?
20:23 jhannah in github?  :)
20:26 rbuels i don't understand why you use PHP if you're already using perl
20:26 rbuels it just makes you have to write more code
20:26 jhannah cause limesurvey was already written in PHP   :)
20:27 rbuels perl_splut wrote/uses limesurvey?
20:27 * rbuels is confused
20:28 jhannah lol
20:29 jhannah i was the last to speak, so you were accusing ME of using PHP recently. which I have. limesurvey.   ;)
20:29 jhannah jhannah: be less annoying today. you're getting on my nerves
20:30 was kicked by rbuels: mine too
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20:31 deafferret mwoohahhahah
20:33 rbuels o_O
20:34 deafferret rbuels: so you super-busy w/ SoC still? or is that load on the mentors now, or...?
20:34 rbuels erm, i haven't done anything for soc in a while
20:34 rbuels the load is mostly on the menros
20:34 rbuels er,
20:34 rbuels the mentors
20:34 rbuels (the freshmaker?)
20:35 rbuels kind of in a lull right now, the 'community bonding' period
20:46 perl_splut I wrote the frontend in php as I more familiar with working with that language when writing web pages
20:46 perl_splut I wrote the app in perl as I'm making heavy use of bioperl objects
20:46 perl_splut and the app was developed over 2 years. the frontend in a week
20:47 perl_splut not because the app was hard, but because new ideas kept making parts of it be rewritten to handle new ways of doing things
21:02 perl_splut oh joy
21:03 perl_splut well, I'd give you a URL to check it out, but it seems that I no longer have the correct password to the site to upload it to, heheh
21:04 deafferret :)
21:05 perl_splut the reason I need a webinterface for it is that a paper is being published and my boss would rather they come to our server than release the code, in any form, to the world, heheh
21:11 deafferret well, I'll take a functional website over a ball of half-baked super ugly source spewed onto sourceforge and abandoned
21:12 deafferret not saying your project is either, just those are far too popular options
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23:37 abooz question about gff. I'm reading a gene from a gff file.When trying to get the features from the Bio::FeatureIO::gff object i this error message:get MSG: Calling end without a defined start position...
23:39 abooz and of course when calling to see the actual features from the Bio::SeqFeature::Annotated object i only get the seq_id. The rest are apparently not read...
23:39 abooz Any ideas? I don't see where the end position is called without a start...
23:42 deafferret abooz: nopaste your code and errors
23:42 abooz ok.
23:48 abooz http://codepad.org/BowGbuAv
23:55 deafferret installing deps
23:59 deafferret ok, this now passes for me    bioperl-live$ perl -Ilib t/SeqFeature/SeqFeatAnnotated.t
23:59 deafferret so now I have to find the difference between that data and yours

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