Camelia, the Perl 6 bug

IRC log for #bioperl, 2012-03-22

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

All times shown according to UTC.

Time Nick Message
00:10 Sheena joined #bioperl
00:59 dnewkirk while $in_grad_school == 'True' { my $coffee = $massive_quantities; drink($coffee); }
01:00 leont That's where I go wrong, I don't drink coffee :-p
01:01 dnewkirk You prefer the non water based liquids? ;)
01:14 gtuckerkellogg joined #bioperl
02:39 Sheena joined #bioperl
02:39 leprevost joined #bioperl
03:09 scottcain joined #bioperl
03:25 gtuckerkellogg joined #bioperl
03:28 sizz_ joined #bioperl
05:30 dnewkirk joined #bioperl
07:19 ank joined #bioperl
08:27 sl33v3 joined #bioperl
08:31 daube joined #bioperl
09:20 leont joined #bioperl
11:33 carandraug joined #bioperl
11:36 daube joined #bioperl
12:06 daube joined #bioperl
12:43 theZenman joined #bioperl
12:53 kai joined #bioperl
12:53 kai joined #bioperl
14:27 leont joined #bioperl
14:51 audy how to install a perl module from a tar file?
14:52 scottcain joined #bioperl
15:01 audy I'm trying to install the SEED annotation server perl module
18:47 scottcain_ joined #bioperl
18:54 carandraug joined #bioperl
20:13 scottcain_ joined #bioperl
20:28 N0s3n joined #bioperl
20:32 N0s3n Hello! I got a Bio:TreeIO object. How do you convert it to a string? Me and my buddy have tried for hours with lots different commands. $tree->as_string,  $tree->as_text etc.
20:33 leont What do you mean, a string?
20:34 leont Trees very much don't look like strings, and vice versa
20:35 leont The only thing I can think of is 'as the content of a file would be', but I'm not sure why you'd want to do that
20:35 N0s3n I want to convert the tree object to a regular string looking something like this: "(A,(B,C));"
20:35 scottcain Zero experience with TreeIO, but with a 15 second look at the code, perhaps you are looking for "write_tree"?
20:36 N0s3n write_tree writes the tree directly to the standard output which isn't what i want
20:37 leont You could just recurse through the tree, and generate the string yourself
20:38 rbuels N0s3n: (A,(B,C)) looks like newick format
20:38 rbuels N0s3n: is that what you want?
20:38 rbuels N0s3n: i'm sure there's a treeIO that will print newick
20:38 N0s3n Yes it is :)
20:39 rbuels N0s3n: although, the cool kids say these days that newick sucks
20:39 leont It's close to newick, but not quite the same
20:39 rbuels just what i heard on the street
20:39 leont newick has more information, usually
20:39 leont (distances and such)
20:39 * rbuels discusses tree format down on the corner with the boys
20:39 scottcain Hmm, and what's the name of the method that would print newick? :-)
20:40 * rbuels sighs and goes to read the POD for people
20:40 leont There is no method specifically for it
20:41 leont But writing it to a string-filehandle should do the trick
20:41 rbuels N0s3n: try something like Bio::TreeIO->new( -format => 'newick', -fh => \*STDOUT )->write_tree( $your_tree )
20:41 rbuels yeah, a string filehandle would probably do
20:41 rbuels N0s3n: the tree object itself has no as_string or as_text, because there is no one-true-format for printing trees
20:41 rbuels N0s3n: which is why TreeIO exists
20:42 rbuels N0s3n: if you want your newick in a string, you could make an IO::String like
20:42 rbuels N0s3n: try something like Bio::TreeIO->new( -format => 'newick', -fh => IO::String->new(\$string_I_want_my_newick_in)  )->write_tree( $your_tree )
20:43 N0s3n Will try!
20:43 leont IO::String is useless
20:43 leont You can open a string filehandle as «open my $fh, '>', \$string»
20:45 rbuels leont: ah, yes that's probably better
20:45 N0s3n It worked! Thank you my lovely street friend!
20:45 N0s3n And also thanks to you other guys :- )
20:46 leont IO::String uses tie, and ties are evil
20:48 N0s3n See you around! bye
20:48 N0s3n left #bioperl
20:48 bull_serg joined #bioperl
20:48 * rbuels just realizes that we probably did that guy's homework for him
20:49 * rbuels will traceroute anybody else who asks questions to make sure they're not swedish
20:49 * rbuels chuckles
20:54 leont Actually, it may be a good idea to tear all use of IO::String out of BioPerl
20:54 leont It should deliver a speed increase, though I'm not sure it's all that big
20:54 leont Only thing you need it for is perl 5.6 compatibility, which you really don't want to care about
21:38 pyrimidine leont: agree
21:39 pyrimidine I would rather not support perl 5.6.x
21:40 pyrimidine and ties are evil (ask Damian Conway.  he's evil)
21:41 leont Actually, it appears BioPerl doesn't work on 5.6 anyway http://matrix.cpantesters.org/?dist=BioPer​l%201.6.901;reports=1;os=linux;perl=5.6.2
21:42 pyrimidine \o/
21:42 pyrimidine i mean
21:42 pyrimidine :(
21:42 pyrimidine heh
21:43 pyrimidine wow, those are some pretty massive test fails
21:45 leont It seems to be just one small parsing difference, and a subtle one at that
21:46 pyrimidine odd
21:46 pyrimidine oh well, if it makes users upgrade I'm okay with that
21:47 leont No one seems to have complained so far, so probably they've left 5.6 behind them, or they don't upgrade
21:47 deafferret my lovely street friend? lol
21:47 pyrimidine We *could* sneak in a 5.8 requirement
21:47 pyrimidine see what happens
21:48 leont We could. or we could fix it and see what happens.
21:48 leont I wouldn't do any meaningful work to fix it on 5.6, but this seems trivial
21:49 deafferret http://media.englishrussia​.com/carmagedon/1_019.jpg
21:50 pyrimidine leont: want to tackle it?
21:50 pyrimidine easy enough to add you as a dev
21:50 pyrimidine :)
21:51 leont I suppose
21:55 * pyrimidine decommuting
21:55 leont At least I can explain that to my supervisor as useful non-thesis work ;-)
21:56 pyrimidine and you can say (with some modicum of truth) that you are a bioperl developer
21:56 pyrimidine (with all the stigma that comes along with it)
21:56 * pyrimidine really decommuting
22:00 sizz joined #bioperl
23:21 scottcain joined #bioperl
23:22 leont Blergh, a working 5.6 setup is harder than I thought
23:27 leont Got it working, finally. Turns out it shipped without a cpan command…
23:36 leont left #bioperl
23:36 leont joined #bioperl
23:36 leont pyrimidine: I see Build.PL is executable and has a shebang path set, this is considered a bad thing.
23:37 leont One shouldn't assume that that perl is the one the user wants, or even that perl is located there.

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