Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-04-06

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All times shown according to UTC.

Time Nick Message
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15:35 deafferret ..@@\
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17:18 kyanardag_ anybody familiar with gbrowse2 configuration?
17:18 kyanardag_ i installed it, the demo works fine but my own data does not work (no image)
17:21 deafferret kyanardag_: nopaste your config?
17:21 kyanardag_ i have pastebin..
17:21 kyanardag_ http://pastebin.com/SBPuLRSr
17:22 deafferret do you have anything else working w/ Bio::DB::SeqFeature::Store?
17:23 kyanardag_ yes it works..
17:23 kyanardag_ http://128.146.132.29/cgi-bin/gb​2/gbrowse/maize4a53_filteredset/
17:24 deafferret no image at all? or nothing on the image?
17:24 kyanardag_ this is the page
17:24 rbuels kyanardag_: lol, 2 channels at once?
17:25 rbuels sudo deafferret go to #gmod
17:25 kyanardag_ yes, i asked there too first, then came here thinking nobody will respond..
17:26 kyanardag_ i hope it's not bad, doing that..
17:26 kyanardag_ in examples, if you choose Chr, it says its not recognized, but if you select gene names (GRM....), it finds its location but does not show the image..
17:28 * deafferret assumes #gmod is handling it, wanders off
17:28 kyanardag_ deafferret, thanks..
17:28 kyanardag_ for your help/interest..
17:28 deafferret kyanardag_: you're welcome for all that non-help I gave you  :)
17:29 kyanardag_ at least you wondered about the error and config :)
17:30 deafferret heh.... i just barely resisted re-delivering a lightbulb joke from an hour ago
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17:58 spekkio when dealing with lots of records 2000+ i use epost with the -db=>protein switch then efetch to submit gi numbers and get the data back in batches of 500 like the docs online say. is it possible to do this same thing use epost with the -db=>nucleotide and submit a bunch of nucleic acid accesion numbers and use efetch to get the data back?
17:59 spekkio cause i feel im doing something funny cause i get the error NCBI epost fatal error: IDs contain invalid characters which was treaded as delimiters.
17:59 spekkio whenever i attempt to do this
18:00 deafferret uh... is the nucleic ID character set different than the protein ID character set? that sounds fishy, like you've got a glitch somewhere...
18:01 deafferret if you nopaste your code and the specific ID you're trying to fetch I could try to reproduce
18:01 spekkio k that's what i was thinking, cause in theory i should be able to do epost/efetch with the id's for the nucleic acids right?
18:01 deafferret that would be my guess, yes
18:02 spekkio k thanks very much, i'll have to try post it when i get back, i gotta run to work.
18:02 deafferret oh, you were doing that for fun?  ;)
20:32 deafferret yay, open-bio SVN is up!
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