Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-07-26

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All times shown according to UTC.

Time Nick Message
05:40 bag_ joined #bioperl
08:00 dbolser genehack: right
08:00 dbolser however, I think it should be
08:00 dbolser I think "$contig_object->start" is totally reasonable
08:01 dbolser otherwise its something like "$contig_object->get_feature_collecti​on->get_feature_by_id("_main_contig_f​eature:".$contig_object->id)->start
08:02 dbolser "
08:02 dbolser (untested ;-)
08:34 BioHisham joined #bioperl
08:34 BioHisham hello folks
08:35 BioHisham anybody's in for a very basic answer to a question for I have lost directions  a little bit
08:36 BioHisham hello
08:36 BioHisham .......
08:44 dbolser hi
11:19 CIA-94 bioperl-live: Lincoln Stein master * rf638961 / Bio/DB/SeqFeature/Store/DBI/Pg.pm : added interval stats support to pg - untested - http://bit.ly/dgSdNl
11:28 ank joined #bioperl
12:59 genehack BioHisham: just go ahead and ask your question...
13:00 dbolser would he could hear us
13:01 genehack dbolser: i think you've got an argument that there should be; it's probably going to be a lot easier to do that in something like Biome (i.e., BioPerl in Moose)
13:01 dbolser BioHisham: wait more than 120 seconds?
13:01 dbolser oh
13:01 genehack where you can delegate methods to attributes that are objects
13:01 dbolser so ... moose eh?
13:01 genehack (but again, I'm pretty newb-ish around these parts and this is all IMO)
13:02 * genehack got into work today to find out his office is being moved -- the day just got a lot more complicated.
13:02 dbolser so, once I commit to learning biome, you're not going to say 'do this in Elk on the road' biopelk-on-tarmac
13:03 genehack heh -- depends on how long it takes you to learn biome. 8^p
13:04 brandi joined #bioperl
13:04 brandi left #bioperl
13:05 dbolser ;-)
13:06 dbolser thanks for the idea genehack
13:06 genehack biome is at http://github.com/cjfields/biome, BTW -- haven't had a chance to look at it as much as I'd like to.
13:07 dbolser I'm surprised he isn't using Perl 6
13:13 genehack there's a bioperl-in-perl6 project somewhere too
13:14 genehack http://github.com/cjfields/bioperl6
13:19 * dbolser hides
13:57 * deafferret waves
14:01 * genehack waves back
14:35 kyanardag joined #bioperl
16:11 Jun joined #bioperl
16:50 pyrimidine joined #bioperl
17:54 pyrimidine wtf kinda spam is this? http://www.bioperl.org/wiki/Mac_Cleanup
17:55 pyrimidine ah, there's the prog link... out, damn spam!
17:55 * pyrimidine brings down the wiki hammer of doom
18:04 pyrimidine dbolser: re: your question on the wiki about making changes to bioperl code, the best way to do this (if you aren't a dev with direct commit rights) is to fork the code
18:04 pyrimidine http://help.github.com/forking/
18:04 pyrimidine hack, hack, hack
18:04 pyrimidine then submit a pull request
18:43 buelsbot joined #bioperl
19:18 pyrimidine For those interested, started a section on creating a fork on the bioperl git page:
19:18 pyrimidine http://www.bioperl.org/wiki​/Using_Git#Creating_a_Fork
20:54 pyrimidine left #bioperl
21:31 dukeleto t/Tools/Run/StandAloneBlast.t is failing for me on master
21:32 rbuels me too.
21:34 * rbuels bisects
21:34 rbuels 2bfc2c93e13edc560d1e156d2b278404eb6d9006 is the first bad one
21:36 CIA-94 bioperl-live: Robert Buels master * rfb68a05 / Bio/Tools/Run/WrapperBase.pm : whitespace cleanup in WrapperBase.pm code - http://bit.ly/bfXios
21:38 rbuels <3 git bisect
21:39 rbuels _setparams strikes me as a really stupid function.
21:42 CIA-94 bioperl-live: Robert Buels master * r3997d70 / t/Tools/Run/StandAloneBlast.t : StandAloneBlast.t should allow different types of quoting - http://bit.ly/dAy8Ud
22:14 rbuels dukeleto: should be fixed now
22:23 dnewkirk joined #bioperl
22:27 dukeleto rbuels: danke
22:32 CIA-94 bioperl-live: Jonathan "Duke" Leto topic/leto_interpro_cite * r95f860a / t/Ontology/IO/interpro.t : Add a failing test for <cite> elements in term definitions - http://bit.ly/cHdhm5
22:34 dukeleto rbuels: look at the most recent commit, tell me if that is a bug or not
22:34 rbuels dukeleto: i don't know.
22:34 rbuels dukeleto: kind of seems like there should not be snippets of XML floating around
22:35 rbuels dukeleto: but i don't really know enough about this to think of a better alternative
22:35 rbuels dukeleto: maybe pyrimidine will have a better idea
22:38 dukeleto rbuels: yes, i will ask him
22:39 bag_ joined #bioperl
22:44 rbuels dukeleto: i can't write $blah->create({}) in my bcs tests, the second run fails.
22:44 rbuels dukeleto: cause the database sticks around.
22:45 rbuels oh wait, this is probably not the right channel
23:00 spekki0 joined #bioperl
23:53 CIA-94 bioperl-live: Chris Fields master * rffb03eb / t/data/PX1CG.gb : phiX174 sequence, for is_circular SF tests - http://bit.ly/cuRkmn
23:53 CIA-94 bioperl-live: Chris Fields master * r6213d4a / Bio/SeqIO/genbank.pm : ss-DNA is legit - http://bit.ly/8ZeXiv
23:59 dnewkirk OT: anyone ever run into an issue where a perl script is unable to open an output file and output data, but doesn't flag an error? THe script worked but moments ago on another file, and there is no notable difference between the two? It's very strange...

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