Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-03-22

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All times shown according to UTC.

Time Nick Message
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11:51 nofutur hey guys
11:52 nofutur by any chance do you know whether it is possible to limit Blast search as to include either Vertebrata or percent identities of >50%
11:53 nofutur The trick I am seeking would hopefully produce a single blast report
11:54 nofutur Currently I am running two separate remote blast - but this makes things very messy to handle.
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14:20 space_agent Hello fellows. If I have a blast output in xml format, can I extract the parameters that were used to run it ? Like blastx -e 0.1 -w 15
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15:05 deafferret space_agent: is that information in the result file?
15:27 space_agent I am not sure about that
15:30 space_agent I did not find the parameters there.
15:39 deafferret space_agent: Bio::SearchIO just parses file into Perl data structures. If the information you want isn't there to be parsed, I don't think you'll have much luck.
15:39 deafferret Unless you're using BioPerl to launch the blast, in which case some object(s) somewhere might hold onto your parameteres
15:40 deafferret (I tend to just parse the results with BioPerl after the fact.)
15:41 space_agent The blast was sent to me from a colleague so i guess it is hopeless. Thanks for the help anyway.
15:46 rbuels space_agent: have you looked at the actual xml file?
15:46 rbuels space_agent: are the parameters in there?
15:51 space_agent The only thing I found was http://pastebin.com/7bELTV1j
15:53 rbuels space_agent: that's what you're looking for, i think
15:55 rbuels space_agent: looking at the blast.pm parser for Bio::SearchIO, i think it is parsing it.
15:55 * rbuels looks
15:56 rbuels just need to find out where it is putting it, which is always the problem with damn bioperl
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15:57 deafferret bioperl: damn you!
15:58 yannickw hehe - hello
15:58 deafferret rbuels: thank you for asking the exact same question I did earlier and getting a different answer. well done.  :)
15:58 deafferret magic!
15:58 rbuels i've got the touch.
15:58 deafferret rbuels: do you have the touch?
15:58 rbuels i has it.  i has the touch.
15:59 deafferret rbuels: do you have the touch?
15:59 rbuels ah, it puts it in a Bio::Tools::Run::GenericParameters ....
15:59 rbuels which is accessed by ....
15:59 * rbuels looks
15:59 * deafferret lools
16:00 rbuels space_agent: you can call get_parameter('expect') on the result object, i think
16:00 rbuels space_agent: do perldoc Bio::Search::Result::GenericResult
16:00 yannickw I have a bit of a naive question: I'm having some version problems... the FAQ says `perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"' ` will tell me the version... mine returns 1.006 .... does this mean 1.6?
16:01 rbuels yannickw: yes.
16:02 yannickw thanks! - but then if on my mac it returns 1.0069
16:02 yannickw but the recent release is 1.6.1?
16:03 deafferret I use bioperl-live from Subversion, so I tend not to know or care about those version numbers
16:03 rbuels 1.0069 is the just-before-1.7.0 release
16:03 rbuels deafferret: do not tell people to do that!
16:03 rbuels deafferret--
16:03 was kicked by rbuels: no no!
16:03 deafferret joined #bioperl
16:04 * rbuels giggles
16:04 deafferret I didn't tell anybody to do anything.   :)   I stated a fact about what *I* do
16:04 deafferret this isn't #bioperl-help  :)
16:04 rbuels yannickw: yes, the most recent *release* is 1.6.1
16:05 rbuels yannickw: which is 1.006001 in decimal
16:05 rbuels yannickw: and 1.0069 is what is in SVN
16:05 rbuels yannickw: because it is getting ready for the 1.7 release
16:05 yannickw okay that makes sense
16:06 yannickw thanks very much for the clarification
16:06 * deafferret prefers 0.16_03
16:06 rbuels no problem.
16:07 rbuels heh.
16:08 deafferret huh. moose is still 0.99
16:08 yannickw (was a bit confused because in older versions it would simply say "1.4" )
16:08 yannickw thanks & have a great day
16:09 yannickw \exit
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16:09 deafferret I withdraw my M.mm_cc > M.mmmccc numbering scheme comment
16:10 deafferret they both suck, for different reasons
16:39 space_agent @rbuels Thank you, I think this is it, I will try out with my own blast were I know the parameters to verify.
16:40 rbuels space_agent: no problem, happy to help.  best of luck in your galactic travels.
16:42 deafferret http://headrattle.blogspot.com/2010/03/f​irefly-shot-me-51-days-into-future.html
16:45 deafferret what the...?  this job has been running on the cluster for 21551 hours? 2.5 years??
16:46 deafferret oh... one job on 50 nodes simultaneously... interesting
16:46 * deafferret rubs rbuels' chin
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16:51 driveby_bot /home/svn-repositories/bioperl: r16924 (jason) : bug #3032 - no whitespace between Gene: and number
16:51 driveby_bot Diff: http://tinyurl.com/ylylomh
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18:34 pyrimidine buelsbot, is that like buel's cuels?
19:24 deafferret cruella buelsville
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21:16 pyrimidine hmm, interesting off-list discussion going on about bioperl/git/github...
21:17 pyrimidine we may have more on board with a git migration that I thought...
21:21 driley joined #bioperl
21:22 rbuels i wonder why hilmar is so git-resistant
21:25 deafferret maybe git molested him as a child?
21:25 * deafferret wouldn't be surprised
21:25 driley joined #bioperl
21:25 * deafferret feels a bit "bad touchy" due to git sometimes
21:26 rbuels lol
21:26 rbuels git is sometimes a little too familiar with me as well
21:26 deafferret git feels 5X harder to learn than svn to me... -shrug-
21:27 rbuels yes it's definitely harder to learn
21:28 deafferret thank god irc.perl.org #moose is so #git-help'y  :)
21:28 deafferret Sartak: wtf does this mean??? *nopaste*
21:33 pyrimidine git isn't for newbies, but I don't think (within the core devs) we have anyone falling in that category
21:33 * deafferret votes rbuels for core
21:33 * rbuels votes no on the motion
21:34 deafferret referendum! draft him!
21:34 pyrimidine and hilmar has a github account: http://github.com/hlapp
21:34 * rbuels follows him
21:36 deafferret pyrimidine: rbuels said he wants to coordinate BioPerl 1.8
21:36 was kicked by deafferret: shh
21:36 rbuels joined #bioperl
21:36 * rbuels said no such thing, whatever that means
21:36 deafferret rbuels: congrats!!
21:37 * pyrimidine okay, rbuels is now in charge of biope... um, I mean....
21:37 * pyrimidine whistling...
21:37 * deafferret is so proud of rbuels
21:37 * deafferret sighs
21:37 deafferret (adoringly)
21:37 * pyrimidine gives rbuels a gold star
21:37 rbuels bioperl will be free to slowly morph into something less infuriating once we break it up
21:38 pyrimidine yup, until then it continues to infuriate
21:38 * rbuels nods
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