Camelia, the Perl 6 bug

IRC log for #bioperl, 2011-03-02

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All times shown according to UTC.

Time Nick Message
00:00 DeniseM I do sometimes, but usually I end up downloading flatfiles and processing myself due to the number of hits I'd end up subjecting the poor server to
00:00 rbuels DeniseM: google summer of code is coming up also, if you're interested in working with a summer student
00:01 rbuels DeniseM: #obf-soc for that
00:01 DeniseM Cool
00:30 * dukeleto puts on a silly hat
00:35 deafferret http://search.cpan.org/~jhannah/   <-- me
00:37 rbuels wow, i've been actually *coding* all *day*.  so nice.
00:38 rbuels unfortunately, it's the exception rather than the rule.
00:42 dnewkirk Bio::DB::Fasta >> pygr
00:42 deafferret whatz pygr?
00:45 dnewkirk It's a python module set for sequence/comparative genomics analysis.
00:45 deafferret ooo... shiny?
00:45 dnewkirk It's pretty powerful
00:46 dnewkirk To be more specific, the Bio::DB::Fasta module returns sequences faster than pygr will.
00:48 dnewkirk Sorry, the more I dig into Bioperl, the more I love it.
00:49 deafferret i'm surprised the intro video doesn't have any graphing shininess  http://code.google.com/p/pygr/
00:55 CIA-44 bioperl6: takadonet master * r3d6b57c / lib/Bio/Tools/CodonTable.pm : implemented is_start_codon, is_ter_codon and is_unknown_codon methods. Passing more testsZ - http://bit.ly/fmkPEy
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01:15 rbuels dunno if i would describe very many things written in perl as 'shiny'
01:16 deafferret pygr is written in perl?  they needs lots of doc patches  ;)
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03:08 CIA-44 bioperl6: takadonet master * rde0366e / lib/Bio/Tools/CodonTable.pm : implemented method translate_strict . Passing one more test - http://bit.ly/e2tl2N
03:26 CIA-44 bioperl6: takadonet master * r5ef187d / (lib/Bio/Tools/CodonTable.pm t/Tools/CodonTable.t): Implemented method add_table. Changed API from p5 version. Passing a few more tests - http://bit.ly/hnRegM
03:37 CIA-44 bioperl6: takadonet master * r960e4f9 / (lib/Bio/Tools/CodonTable.pm t/Tools/CodonTable.t): implemented tables method. It's not a class method yet but will work for now - http://bit.ly/dYT8S4
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04:03 CIA-44 bioperl6: takadonet master * r8c83adc / lib/Bio/PrimarySeq.pm : first multi method translate done. The simple case with no parameters. - http://bit.ly/fIGKLO
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05:03 andreitudor hello
05:04 andreitudor i have a question abput bioperl and blast+
05:05 andreitudor I have been trying for a few days to make a blast+ database, but I would like to insert the gene information of the sequences in that database
05:06 andreitudor so that when I make a blastn search for example, it gives me the gene information also not only the sequence
05:06 andreitudor is it possible with bioperl or blast tools to do this?
05:09 andreitudor I know there is a bioperl object that can get the information from a genebank file
05:10 andreitudor but he searches for it online, and the computer where the database has to be setup does not have an internet connection
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08:39 dbolser andreitudor: as far as I know, you can only put such data in the fasta header
08:39 dbolser may be wrong, because I'm still using old blast not blast plus
08:39 dbolser so you just design a fasta header with all the info you want, space separated or something
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17:09 pyrimidine Bio::DB::Fasta is very fast for a good reason.  Lincoln uses that for a lot of his modules (Bio::DB::Sam, for instance).  Good example of how we could try speeding things up.
17:21 CIA-44 Bio-FeatureIO: Chris Fields master * r8c0509b / (Build.PL dist.ini): remove cruft from C&P - http://bit.ly/dQE1jM
17:21 CIA-44 Bio-FeatureIO: Chris Fields master * r180216b / (5 files in 4 dirs): Remove more cruftiness, $Id tags and such - http://bit.ly/fDQ51s
17:21 CIA-44 Bio-FeatureIO: Chris Fields master * r62ba579 / (Changes dist.ini): some more for dzil - http://bit.ly/ifgBck
17:21 CIA-44 Bio-FeatureIO: Chris Fields master * r7523ef2 / MANIFEST : update MANIFEST, though this might be removed or updated through the Build step with dzil - http://bit.ly/dSbX6O
17:21 CIA-44 bioperl6: Takadonet master * r311bfa7 / lib/Bio/Tools/CodonTable.pm : added attribute $.gap with default value '-' . Passing a few more tests - http://bit.ly/i9SaV4
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17:27 takadonet hey all
17:30 * rbuels grunts, seeks coffee
17:30 rbuels ;-)
17:37 * dbolser seeks bed
17:43 deafferret bed? i just got started!
17:44 deafferret the party ain't over till i read a page of my book and fall asleep
17:45 rbuels lol, my nights exactly.  and i don't even have kids!
18:02 deafferret really enjoying me current light read though   http://www.amazon.com/Gates-Novel-Joh​n-Connolly/dp/1439175403/ref=sr_1_2?i​e=UTF8&amp;qid=1299088938&amp;sr=8-2
18:03 deafferret err  http://amzn.com/1439175403
18:05 deafferret amazon++  "share" link
18:05 deafferret mutationgrid.com has mgd.me for permalink URLs  :)
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21:50 pyrimidine looks like open-bio is migrating bug reports to redmine on an AWS instance
23:01 CIA-44 bioperl6: takadonet master * rada5ac4 / (lib/Bio/Location/Simple.pm t/Location/Simple.t): very simple implement of attributes for the Role Location::Simple . No special subtypes for attribute yet. But somehow passing lots of tests - http://bit.ly/fdSZ9V
23:16 CIA-44 bioperl6: takadonet master * r033af1c / (lib/Bio/Location/Simple.pm t/Location/Simple.t): Added more method stubs for : to_string , is_fuzzy , length . Uncommented more tests as well. - http://bit.ly/i1N6GD
23:27 CIA-44 bioperl6: takadonet master * rc8ed3d9 / (lib/Bio/Location/Simple.pm t/Location/Simple.t): implemented length method, uncommented a test. - http://bit.ly/hdv5p4

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