Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-03-09

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All times shown according to UTC.

Time Nick Message
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05:42 deafferret minight R! woot!
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14:46 shellfish_gene Hi all! I have a question: Is Bio::Index::Blast known to work? It seems to always return the first hit in the Blast file, no matter what ID one specifies in the get_stream or fetch_report methods.
15:07 shellfish_gene Aha! I found it, for some weird reason the indexing module expects the queries to be separated by BLAST, or by Query= in RPS-BLAST ouputs, whatever RPS-BLAST is. But in the current version of blastall or blast+ it's only 'Query='.
15:20 rbuels shellfish_gene: could you send a report about this to the mailing list?
15:21 rbuels shellfish_gene: i'm afraid expertise and tuits are rather diffuse
15:47 Furiiku joined #bioperl
15:58 * deafferret swims about idly in his tuit lap pool
15:59 rbuels deafferret: could you take a look at the OBF and bioperl GSOC pages?  things look well-worded?  links where they should be?  http://www.open-bio.org/wiki/Google_Summer_of_Code
16:04 deafferret rbuels: curing cancer. please hold
16:04 deafferret rbuels: you left #poe? traitor
16:05 rbuels man i gotta trim my channel list
16:09 deafferret (local::lib)++
17:24 deafferret hee hee... generating .R with Template Toolkit
17:33 rbuels oh, we're just talking about this
17:33 rbuels Statistics::R is abandoned looks like.
17:33 rbuels and RSPerl is ... weird
17:34 rbuels so you're taking the approach of just making .R tempfiles and running R CMD SLAVE or whatever on them?
17:34 rbuels deafferret: ^^^
17:34 deafferret ya, cause I'm qsub'ing the runs to the cluster(s)
17:37 deafferret lol run.R.tt.Rout
17:37 rbuels deafferret: would you like to be a GSoC mentor to make a DBI-like interface to R from Perl?
17:38 rbuels my $r = Statistics::RI->new;
17:38 deafferret uh, $boss[1] has me beyond swamped w/ local students already
17:38 rbuels $r->plot(...)
17:38 deafferret $r->ucrazy('rbuels') ? "mad hatter" : "liar";
17:39 rbuels hatters are mad cause of all the mercury
17:39 deafferret and the brain aliens
17:50 faceface rbuels:
17:50 faceface /join
17:50 faceface /join #R
17:51 deafferret he was just bemoaning his long channel list  :)
17:51 deafferret luckily, I have been banned from most channels, so I'm less distracted
17:52 * rbuels bans deafferret
17:52 deafferret d:
17:54 deafferret hmmm  R CMD BATCH + commandArgs()
17:58 faceface nooooo
18:02 faceface how do I do this in such a way that spaces in file names don't bork
18:02 faceface chgrp barton `find ./ -group users`
18:02 faceface -eval I gues
18:03 deafferret or xargs
18:04 faceface -exec
18:04 faceface I never remember how to use xargs properly
18:04 faceface or -exec for that matter, but its working
18:04 faceface find ./ -group users -exec chgrp barton {} \;
18:04 deafferret find ./ -group users | xargs chgrp barton
18:04 faceface its that "{} \;" that is so fraggle
18:05 faceface ty
18:06 deafferret natch
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20:22 driveby_bot /home/svn-repositories/bioperl: r16913 (sharpton) : Importing the initial version of the SearchIO based parser for HMMER v3.0rc. Still crude, but appears to have at least basic operational functionality for hmmsearch and hmmscan outputs, both with and without alignment data. Test data and a test script are included in the root directory of the bioperl-hmmer3 package. Please direct questions to the author Thomas Sharpton at
20:22 driveby_bot Diff: http://tinyurl.com/yky5azc
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23:06 rbuels deafferret: tiny stupid templating in a __DATA__ section:  my $text = Template->new->process(\*DATA); ?
23:06 rbuels deafferret: correcto?

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