Camelia, the Perl 6 bug

IRC log for #bioperl, 2011-02-03

| Channels | #bioperl index | Today | | Search | Google Search | Plain-Text | summary

All times shown according to UTC.

Time Nick Message
00:38 deejoe left #bioperl
00:39 deejoe joined #bioperl
00:44 deejoe left #bioperl
00:45 deejoe joined #bioperl
02:42 Vutral left #bioperl
02:53 Vutral joined #bioperl
03:29 mzgrideng joined #bioperl
05:04 Vutral left #bioperl
05:07 Vutral joined #bioperl
05:53 mzgrideng left #bioperl
07:36 bag__ joined #bioperl
08:14 rbuels left #bioperl
09:24 bag__ left #bioperl
09:42 bag__ joined #bioperl
09:43 bag__ left #bioperl
10:57 dbolser my rant about sf::store was unfounded
10:57 dbolser user error
11:28 dbolser is this canonical, or crappy code:
11:28 dbolser my $clone_id = ($clone_end->get_tag_values('parent_id'))[0];
11:28 dbolser or can I just grab the parent feature using some foo?
12:10 Vutral left #bioperl
12:29 Vutral joined #bioperl
12:36 Vutral left #bioperl
14:58 Vutral joined #bioperl
15:02 dbolser hrm hrm hrm
15:04 dbolser when I call $feat->desc(), it seems to pick up $feat->attributes->{'Note'}, however when I set $feat->desc('some such'), it seems to create a new 'desc' feature field (like for score, phase, etc).
15:04 dbolser so when I come to read $feat->desc(), it says undef
15:08 dbolser so I'm writing this: "$clone_end->add_tag_value( 'Note' => ($clone->get_tag_values('Note'))[0] )"
15:08 dbolser when I'd rather write: "$clone_end->desc( $clone->desc )"
15:11 dbolser the problem with refactoring code is that you discover how crap it is in the first place, which triggers a new round of refactoring
15:12 dbolser by the time you break out of the loop, you forgot what the code was supposed to be doing in the first place
15:27 mzgrideng joined #bioperl
15:48 rbuels joined #bioperl
17:24 Vutral left #bioperl
17:26 Vutral joined #bioperl
17:51 dukeleto left #bioperl
17:52 dukeleto joined #bioperl
18:08 Vutral left #bioperl
18:27 Vutral joined #bioperl
19:19 spoust joined #bioperl
19:20 spoust May I ask a question about using  Bio::Tools::Run::Alignment::Clustalw; in BioPerl?
19:20 spoust I'm running this code EGIN { $ENV{CLUSTALDIR} = '/Users/spoust/clustalw/' } use Bio::Tools::Run::Alignment::Clustalw; at the beginning of my program
19:21 spoust and I'm getting this error: an't locate Bio/Tools/Run/Alignment/Clustalw.pm in @INC (@INC contains: /fink/lib/perl5/5.10.0/darwin-thread-multi-2level /fink/lib/perl5/5.10.0 /fink/lib/perl5/darwin-thread-multi-2level /fink/lib/perl5 /fink/lib/perl5/darwin /Library/Perl/Updates/5.10.0​/darwin-thread-multi-2level /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0​/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl
19:21 spoust What am I doing wrong?
19:26 deafferret spoust: how did you install BioPerl?   (I tend to clone from git)
19:26 spoust I used fink
19:26 spoust I am running it on a mac
19:27 deafferret fink will install BioPerl? wow    :)   what version?
19:27 deafferret (I use Macs and Linux)
19:27 spoust spoust-m:desktop spoust$ fink list bio Information about 4433 packages read in 1 seconds.  i   bioperl-pm5100                           1.6.1-3                        Perl module for molecular biology      bioperl-pm588                            1.6.1-3                        Perl module for molecular biology      libaubio2                                0.3.2-1                        Library for audio labelling      libaubio2-bin
19:27 spoust 1.6.1-3  i suppose
19:29 deafferret looks like the package you're looking for is in bioperl-run, not bioperl itself
19:29 deafferret https://github.com/bioperl/bioperl-run/​tree/master/lib/Bio/Tools/Run/Alignment
19:29 deafferret does fink have an "install bioperl-run" ?
19:30 deafferret (me, i'd just git clone it)
19:33 spoust How do you do that?
19:33 spoust Is there a tutorial online?
19:35 deafferret hmm
19:35 deafferret http://www.bioperl.org/wiki/Using_Git
19:41 deafferret I just updated that wiki page with a far easier OSX install link
19:41 deafferret should only take 2 minutes
19:42 deafferret spoust: ^
19:49 spoust So git got the bioperl run package
19:49 spoust But how do I install it to perl?
19:59 bag__ joined #bioperl
20:04 spoust Is there a tutorial for that?
20:11 deafferret export PERL5LIB=/wherever/you/put/bioperl-run
20:17 spoust I ran that
20:17 spoust but it still can't find the module
20:18 deafferret use gist.github.com to show me what you type and what happens
20:18 deafferret (or whatever paste service you want)
20:19 spoust Can't locate Bio/Tools/Run/Alignment/Clustalw.pm in @INC (@INC contains: /fink/lib/perl5/5.10.0/darwin-thread-multi-2level /fink/lib/perl5/5.10.0 /fink/lib/perl5/darwin-thread-multi-2level /fink/lib/perl5 /fink/lib/perl5/darwin /Library/Perl/Updates/5.10.0​/darwin-thread-multi-2level /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0​/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi
20:19 deafferret don't paste in channel
20:19 deafferret where did you put bioperl-run?
20:20 spoust https://gist.github.com/ad0efe15a1fa82f67cc2
20:21 deafferret show me (1) you running that export (2) the error occuring (3) perl -V   all in one paste
20:23 spoust https://gist.github.com/810121
20:24 deafferret oops   you need lib at the end   export PERL5LIB=/Users/spoust/Desktop/bioperl-run/lib
20:26 spoust still getting the same error
20:28 deafferret show me
20:30 spoust https://gist.github.com/810128
20:31 kyanardag_ joined #bioperl
20:32 deafferret spoust: now it's not finding BioPerl. where did you put bioperl?
20:33 deafferret spoust: it's finding that ::Run:: thing from earlier, but not Bio::Seq which is bioperl-live, which should be in what you did in fink
20:33 deafferret so git clone bioperl-live next to bioperl-run then
20:34 deafferret export PERL5LIB=/Users/spoust/Desktop/bioperl-li​ve:/Users/spoust/Desktop/bioperl-run/lib
20:35 deafferret (bioperl-live doesn't have a lib/ but bioperl-run does. go figure)
20:35 spoust But I've gotten other modules from Bioperl to work
20:35 deafferret rbuels: I thought you fixed that last year?  ^
20:35 deafferret spoust: um... "Can't locate Bio::Seq" says you're wrong  :)
20:35 deafferret perldoc -l Bio::Seq
20:37 rbuels deafferret: i didn't fix that.
20:37 deafferret sudo rbuels git mv Bio lib/
20:37 rbuels deafferret, spoust: feel free
20:37 deafferret rbuels: NOU
20:38 rbuels sudo: rbuels: command not found
20:38 spoust Here's the error I'm getting https://gist.github.com/810128
20:39 spoust WHen I comment out the reference to the ::run::tools, my code runs fine
20:39 deafferret hahaha... apparently "ho jo's" is "Howard Johnson's"
20:39 deafferret spoust: you didn't do the export in that window
20:40 deafferret spoust: do you understand environmental variables, in general?
20:40 deafferret what they are, how they work?
20:40 kyanardag_ left #bioperl
20:40 spoust I think so
20:40 deafferret do you see how  /Users/spoust/... wasn't in your @INC ?  that means you didn't export PERL5LIB
20:41 deafferret alternatively to PERL5LIB, you can stick these lines in the top of your program:
20:41 deafferret use lib "/Users/spoust/Desktop/bioperl-run/lib";
20:41 deafferret etc
20:45 spoust So if I use use lib "/Users/spoust/Desktop/bioperl-run/lib"
20:45 spoust my code runs, but how do I get the exporter to work?
20:45 deafferret define "the exporter"
20:46 spoust the line of code export PERL5LIB=/Users/spoust/Desktop/bioperl-run/lib didn't add bioperl-run to my @INC
20:46 deafferret export is not "a line of code"  you have to do that on the command line
20:47 deafferret if you want "a line of code" you do   use lib "...";
20:47 spoust Right, I did it on the command line
20:47 deafferret spoust: well, then you're mistaken and you have to show me anything so I can tell you what mistake you made
20:48 deafferret (1) (2) (3) above
20:48 deafferret my psychic powers are weak  :)
20:50 spoust https://gist.github.com/810165
20:50 spoust So your right
20:51 spoust it can't locate bioperl now
20:54 deafferret spoust: yup. so you could now take my advice from above about git cloning bioperl-live
20:54 deafferret i have no idea what fink did or didn't do for you
20:54 deafferret i don't use fink, don't know how to debug it for you
20:54 deafferret not quickly anyway  :)
21:04 spoust Thanks for your help
21:04 spoust I really appreciate you being patient with me
21:04 spoust ;)
21:09 spoust left #bioperl
21:21 dnewkirk deafferret++
21:28 sl33v3_ joined #bioperl
21:30 sl33v3 left #bioperl
21:31 sl33v3_ is now known as sl33v3
21:45 deafferret hey -- where'd he go?
21:45 * deafferret looks and lools
21:46 deafferret rbuels: fetch spoust
21:46 rbuels fetch: command not found
21:47 * deafferret re-installs rbuels
21:48 dnewkirk you might want to do git clone rbuels-live instead... ;)
21:49 deafferret merge failure: local changes to YAPC-attendence.log conflict
21:49 deafferret :(
21:50 mzgrideng left #bioperl
22:03 kyanardag_ joined #bioperl
23:35 bag__ left #bioperl

| Channels | #bioperl index | Today | | Search | Google Search | Plain-Text | summary