Camelia, the Perl 6 bug

IRC log for #bioperl, 2009-08-17

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Time Nick Message
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17:36 rbuels deafferret: all your base are belong to rbuels
17:36 deafferret AWOOOGA!! AWOOOGA!! rbuels spotted in BioPerl SVN! Battle stations!
17:36 was kicked by deafferret: deafferret
17:36 rbuels joined #bioperl
17:36 rbuels mwahahaha
17:36 deafferret lol
17:42 * deafferret would be deeply offended by the complete futility and worthlessness of this $day_job project if they weren't paying him so much to do it.
17:42 * deafferret dries his tears with piles of cash
17:43 rbuels lol
17:45 rezecib joined #bioperl
17:48 jonathan__ joined #bioperl
17:48 jonathan__ I have a question on my bioperl module
17:49 jonathan__ very simple - I want to have multiple pm's that are all under the same "use xxx".  how to split the files and have it work?
17:50 deafferret if you use X;  then X can use A,B, and C, and your program doesn't know or care
17:50 jonathan__ is that the only way?
17:51 deafferret This is Perl. There's a million ways to do anything.  :)
17:52 jonathan__ sure then what's way #2 lol
17:53 * rbuels is a little confused about what exactly jonathan__ is trying to do
17:53 deafferret Until I understand why you don't like my first suggestion I can't suggest something else
17:54 jonathan__ just want to refactor my "big"  x.pm that is used with "use Bio::X";  into separate files like x.pm and x-one.pm, x-two.pm, etc
17:54 deafferret what's the difference between one and two?
17:54 deafferret (on what basis does the split occur?)
17:55 jonathan__ arbitrary category split for the methods
17:55 jonathan__ I prefer smaller files when editing
17:55 rbuels Bio::X can use Bio::X2 inside it.
17:55 rbuels or you can just use Bio::X and Bio::X2 both in your scripts
17:56 deafferret Bio::X should probably use Bio::X::one;  use Bio::X::two;
17:56 rbuels you can do that too
17:56 deafferret if one and two are subtypes of X
17:56 rbuels jonathan__: does this make sense?
17:56 jonathan__ then I guess that means subdirs Bio/X, Bio/X/one, Bio/X/two
17:56 deafferret do, Bio/X is a subdir containing one.pm and two.pm
17:57 deafferret s/^do/no/
17:57 jonathan__ Ok I will do that.   user does "use Bio::X" and internally it does "use Bio::X::one / two /three"
17:57 deafferret ya.
17:58 jonathan__ thanks
17:58 jonathan__ to all
17:58 deafferret except rbuels
17:58 jonathan__ uh wait
17:58 rbuels lol
17:59 * rbuels smacks deafferret
17:59 rbuels (with a fish)
17:59 * deafferret lools
17:59 rbuels woopwooopwoop
17:59 * rbuels pulls deafferret's nose
17:59 rbuels nyuck nyuck nyuck
17:59 rbuels jonathan__: this is just tomfoolery, don't worry about it
18:04 jonathan__ how does the POD work in this case?
18:05 jonathan__ does all the POD somehow get created from the internal one/two/three.pm 's
18:05 deafferret same as always. Every package should have a NAME, SYNOPSIS, etc.
18:05 deafferret nope. you have to slap all that stuff in there for every package
18:05 rbuels jonathan__: no, there is no automatic magic that happens with the POD
18:06 jonathan__ from that perspective it is better to have 1 big file then
18:06 rbuels jonathan__: since POD is intended for your users, usually people put all the POD in Bio::X
18:06 jonathan__ i guess I like to put my POD right above my sub's
18:07 rbuels jonathan__: different people have different opinions about that
18:07 deafferret I organize my source code by concept, not worrying so much about the size. When things get too big I split them if I can come up with sensible subcats.
18:07 jonathan__ so it sounds like the main X.pm will just be several "use"s and a huge POD
18:07 deafferret ick. inline POD for the win
18:07 deafferret =head2 foo =cut sub foo {}  =head2 bar =cut sub bar {}
18:07 rbuels jonathan__: lots of people seem to be coming around to the "put all your POD below an __END__ in your module" camp
18:07 deafferret everyone else is wrong.  :)
18:08 * deafferret boos loudly
18:08 deafferret heretics
18:08 rbuels jonathan__: see?
18:08 rbuels lol
18:08 jonathan__ the only benefit of putting below __END__ is not having to do a lot of =cut right
18:08 deafferret wanna see who's right? I can kickban rbuels, then you can ask your question again  :D
18:09 deafferret jonathan__: no, you need well-formed POD regardless
18:09 deafferret __END__ is just a lazy way of saying "don't bother looking at this, perl compiler"
18:09 deafferret podchecker checks your POD for well-formedness
18:09 jonathan__ If POD is below __END__ then it's just 100% POD.   so no =cut to go back to code
18:10 deafferret uh... ya, I guess
18:10 rbuels jonathan__: well yes that's true
18:10 * deafferret wonders if podchecker will complain about that
18:11 deafferret huh. podchecker is happy w/o a final =cut, so I'm happy
18:11 jonathan__ my smaller one.pm two.pm three.pm are meant as templates for abstraction though so hmmm
18:12 deafferret umm... usually abstractions of X live elsewhere, not inside X/
18:12 deafferret "plugins" of X might live in X/
18:12 * deafferret shuts up now, since every project is different
18:12 deafferret perhaps you want Xx::one  :)
18:13 deafferret like DBIx::Class
18:13 deafferret and MooseX::Workers
18:14 jonathan__ hm
18:15 balin Hi guys. Is there a way to get a MSA from Bio::Tools::Run::StandAloneBlast?
18:16 deafferret balin: blast doesn't do alignments, does it?
18:16 deafferret not multiple sequence alignments, anyway?
18:16 balin -m6 looks good to me
18:16 * deafferret lools
18:17 rbuels jeez
18:17 balin what?
18:17 rbuels (about deafferret's lool)
18:17 deafferret balin: do you have an -m6 output sample handy? pastebin.com ?
18:19 deafferret http://gist.github.com/ looks ok too.  :)
18:19 balin http://pastebin.com/m717f32d
18:20 deafferret well, I'll be damned
18:20 deafferret why am I using clustalw?
18:20 rbuels well, I'll be damned
18:21 rbuels deafferret: how do you get perl syntax highlighting in a gist
18:21 deafferret pick perl from the drop-list?
18:23 deafferret balin: I didn't know BLAST did MSAs. Thanks for showing me that.  :)   So what's your question? How to run with Bio::Tools::Run::StandAloneBlast? Or how to read the output (Bio::AlignIO)?  (I don't use StandAloneBlast, I just run my own system("blastall ..."))
18:25 balin I'm just wandering if Bio::Tools::Run::StandAloneBlast can parse out the alignment.
18:25 rbuels doubt it.
18:26 rbuels but i don't really know
18:26 erimar77 joined #bioperl
18:26 deafferret balin: no. StandAloneBlast runs blastall for you. Bio::AlignIO is how you read and write MSAs
18:27 rbuels doesn't standaloneblast call searchio?
18:27 * rbuels thought it did...
18:27 erimar77 trying to install Bio::Root::Utilities via cpan, it trys to redownload and install bioperl even though it's already there
18:27 deafferret oh, it might. I don't use it.
18:28 balin StandAloneBlast returns a report as SearchIO.
18:28 rbuels erimar77: what does "already there" mean?  already installed in wherever cpan is trying to install stuff?  or already downloaded to your hard drive?
18:28 deafferret erimar77: I don't user CPAN for BioPerl, I just grab bioperl-live out of SVN
18:28 rbuels deafferret: what????
18:28 erimar77 installed via ubuntu repo version 1.6.0-2ubuntu1
18:28 deafferret rbuels: indeed!
18:29 rbuels erimar77:  bio::root::utilities is part of the regular bioperl, so you should already have it
18:29 rbuels erimar77: if you have it from ubuntu's .deb package
18:30 rezecib left #bioperl
18:30 rbuels as for why cpan does not think that you already have it....
18:30 rbuels not sure about that
18:31 erimar77 roger, checking a few things
18:32 rbuels erimar77: when using cpan, it's always a wonderful idea to use local::lib
18:32 rbuels saves a lot of guessing and pain
18:32 erimar77 will do, thanks
18:33 rbuels actually, what i've found to be frickin wonderful is using local::lib, AND version my local lib dir with git
18:37 erimar77 now when I try to install Bio::Tools::Run::TigrAssembler, it's wanting to grab bioperl 1.6.1, uugh, this never ends
18:38 rbuels there is no 1.6.1 released yet!
18:38 erimar77 er, sorry
18:39 erimar77 BioPerl-run-1.6.1.tar.gz
18:39 rbuels ?
18:39 rbuels ah.
18:39 rbuels yes, apparently run is at 1.6.1 now
18:40 rbuels run is another set of modules, so that's not surprising
18:40 rbuels bioperl-run is not the same as bioperl
18:40 erimar77 i would imagine that's an intensive install, this is all for a user to run one application, i'd prefer it all to come out of his homedir
18:41 rbuels wonderful command:  perl -MCPAN -Mlocal::lib=--self-contained,/home/someguy/perl5 -e shell
18:42 rbuels or just:  perl -MCPAN -Mlocal::lib=/home/someguy/perl5 -e shell
18:42 rbuels to have it use the stuff that's already on the system in addition
19:18 deafferret rbuels: I'm a movement by myself, but I'm a force when we're together.
19:19 deafferret you make me better
19:19 rbuels what song is that from
19:19 deafferret song?
19:19 rbuels movie?
19:19 rbuels shakespeare play?
19:19 * deafferret feels so rejected
19:19 rbuels awwwww
19:20 deafferret Fabolous ft. Ne-Yo - [Make Me Better]
19:20 * rbuels hugs deafferret
19:20 rbuels oh yeah, that's the original singer from Ace Hood right?
19:20 deafferret http://www.lyricsondemand.com/f/fab​olouslyrics/makemebetterlyrics.html
19:20 deafferret dunno. I just SOC my iPod. Have you heard the one about the boy who moved into the henhouse to sleep?
19:21 rbuels heh no
19:21 deafferret http://www.sing365.com/music/lyric.nsf/Th​e-Humour-Of-The-Situation-lyrics-Barenake​d-Ladies/568EF29F5383422B48256962000C05C9
19:21 rbuels lol
19:22 deafferret the problem with iPods nowadays is hundreds of songs get in the way of my loco and my cake
19:55 rbuels deafferret: could you grab the new Bio-Tools-HMM and make sure it builds cleanly for you?
19:55 rbuels svn+ssh://rbuels@dev.open-bio.org/home/svn-repo​sitories/bioperl/Bio-Tools-HMM
19:56 rbuels replacing rbuels with your login of course
19:56 deafferret word
19:57 deafferret MySQL says "kaboom!"
19:57 rbuels ...mysql??
19:58 deafferret I thought you asked how my day was going?
20:00 rbuels no i asked you to try building the hmm thing you knucklehead
20:00 * rbuels bops deafferret on the head
20:00 rbuels nyuck nyuck
20:02 deafferret sigh... $boss at $work is even punchier than rbuels right now, making it hard for me to help rbuels
20:03 rbuels that's fine, do what you need to do
20:03 deafferret definately the 3 stooges if he came in here
20:03 deafferret rbuels: ignoring him, working for my true master
20:04 rbuels the tests won't pass, just checking that it builds.
20:05 deafferret - ERROR: Couldn't find a $VERSION in prerequisite Bio::Root::Root
20:05 rbuels cause the tests are fucked
20:05 rbuels yeah that's fine
20:05 deafferret perl Build.PL  ?
20:05 rbuels yeah
20:05 rbuels and then ./Build
20:05 deafferret - ERROR: Couldn't find a $VERSION in prerequisite Bio::Matrix::Scoring
20:05 rbuels and make sure the compiles are OK
20:05 rbuels yeah ignore the version stuff
20:05 deafferret um... looks like it worked? how do I check?
20:06 rbuels heh you can't.  if the compiles went by without error, that's all i'm looking for right now
20:06 deafferret http://gist.github.com/169342
20:06 rbuels i'll send it back to the list and tell yee man to fix his tests
20:06 rbuels hmmmmmm
20:07 rbuels the -lm thing is worrisome
20:07 deafferret is it? I grok not dat juju
20:07 deafferret It didn't call me a chucklehead, so I thought that was PASS   :)
20:09 rbuels yeah i dunno
20:09 rbuels it's better than it was though
22:00 ptl joined #bioperl
22:40 * rbuels slaps forehead
22:41 rbuels "I noticed that Bio/Tools/HMM.pm was removed from the trunk. So I added it back in."
22:41 deafferret who?
22:41 rbuels not the swiftest
22:41 rbuels yee man
22:41 deafferret who?
22:41 rbuels yee man chan
22:42 rbuels on bioperl-l
22:42 deafferret didn't he take the "do no harm" oath?
22:43 deafferret http://images.google.com/images?q=wee+man&amp​;oe=utf-8&rls=org.mozilla:en-US:official&​amp;client=firefox-a&um=1&ie=UTF-8&am​p;ei=89yJSoCiGI66Nfjo5N0E&sa=X&oi=ima​ge_result_group&ct=title&resnum=1
22:43 rbuels wasn't he in "in bruges"?
22:44 rbuels maybe it was a different dwarf
22:44 deafferret laugh   http://www.tmz.com/2008/12/08/wee-m​an-sued-by-two-chicks-he-arrested/
22:44 deafferret tsk tsk. they prefer "shorties"
22:45 * rbuels cannot win
22:45 deafferret that'd be like me calling yeti 'sasquatch'.  tsk tsk
22:46 deafferret or ogres 'oafs', etc
22:48 * deafferret growls at his stupid merge_dics()
22:48 deafferret PNAS!
22:49 * deafferret goes loco with the cake. I shit you not.
22:49 deafferret how can I count my chickens while simultaneously not bothering to count them if their count exceeds $max_variance ?
22:55 deafferret damn .... I need to strip a specific file out of $merged_dict->{$word}->{$file} = 1;  ... preferably in 0 lines of code
22:58 deafferret http://pastebin.com/m47ac6489
23:09 rbuels um, delete $_->{$file_to_delete} for values %$merged_dict; ?
23:10 deafferret oh. u r genyus
23:10 deafferret geen yus
23:10 deafferret o
23:11 rbuels i didn't quite hit the 0 lines of code
23:11 rbuels alternatively, you could never put it in there in the first place
23:11 deafferret std dev was +- 1200 lines, so you're fine
23:12 deafferret delete $merged_dict->{$_}->{$file} for values %$merged_dict;
23:13 rbuels no, that would be for keys
23:14 deafferret delete $merged_dict->{$_}->{$file} for keys %$merged_dict;   # rbuels++
23:14 rbuels why don't you just use values
23:14 rbuels because values is gives you the hashrefs that are in there anyway
23:14 rbuels see my original code
23:15 deafferret delete $_->{$file} for values %$merged_dict;   # rbuels++
23:15 rbuels yarp.
23:17 deafferret o u r geen yus
23:19 rbuels my god.  google for perl help and look at the first hits
23:19 deafferret is this bad? http://johnbokma.com/perl/
23:21 rbuels what's a general mailing list where complete non-programmers can get help with their stupid scripts.
23:22 * rbuels wants to refer abishek pratap to this list
23:22 * rbuels is feeling mean right now, abishek's script is probably not actually stupid and abishek is probably not a complete non-programmer
23:22 deafferret NNTP  http://www.nntp.perl.org/group/perl.beginners/  ?
23:23 deafferret http://www.perlfoundation.org/​perl5/index.cgi?perl_beginners
23:23 deafferret laugh dead  http://beginners.perl.org/
23:24 rbuels perl-beginner@yahoo.com?
23:24 deafferret dunno. does it have traffic?  http://perl-begin.org/ ?
23:25 rbuels http://perl-begin.org/mailing-lists/
23:25 rbuels i'll point him at that
23:29 deafferret woot! 30 lines merged.dict!
23:29 deafferret PNAS!!
23:36 rbuels wow, you're going to get a PNAS paper?
23:36 deafferret PNASs make paper now?
23:37 rbuels well they publish them anyway
23:37 rbuels what's so funny?  why are you grinning like that?
23:37 rbuels i fail to understand the humor.
23:37 deafferret if I'm ever published you need to move to your south american bomb shelter immediately
23:38 * deafferret eats him a rain forest moneky
23:38 deafferret key even
23:38 rbuels unfortunately, construction is not finished on my secret lair
23:38 rbuels although the cladding on the shark moat is almost done
23:38 rbuels and i'm taking delivery of the sharks next week
23:39 deafferret I'm thinking southern Cnile should be fairly radiation free, and it has tasty monkeys
23:39 deafferret Chile
23:39 rbuels southern chile does not have monkeys.
23:39 deafferret says you
23:39 rbuels southern chile has pine trees and elk and shit
23:39 deafferret tasty elk and shit?
23:40 rbuels the elk are probably fairly yummy, anyway
23:40 rbuels might be a little tough.
23:40 rbuels probably want to either stew or braise.
23:41 rbuels ugh
23:46 deafferret holy frak. I'm building my secret lair THERE   http://upload.wikimedia.org/wikipedia/commons/4​/49/Cuernos_del_Paine_from_Lake_Peho%C3%A9.jpg
23:47 deafferret http://en.wikipedia.org/wiki/T​orres_del_Paine_National_Park
23:49 rbuels kalmia's former PI lives in Valparaiso, we're planning to go down there in the next year or two and use them for a staging area to do some backpacking and such
23:50 rbuels it's not that far south though
23:51 deafferret need a shitty shurpa?  :)
23:51 rbuels heh.  i could fit you with a sedan chair on your back.
23:51 deafferret I'm like a reverse shurpa -- I can't climb anything, but I can eat all your food for you
23:51 rbuels hahahahaa
23:52 rbuels i cooked with a guy who used to be a sherpa
23:52 rbuels on everest
23:53 rbuels he never went above the everest base camp though
23:53 deafferret wow. still.
23:53 rbuels now he has a nepalese food cart in portland
23:53 deafferret I wonder if I could make it up to base camp.  :)
23:53 rbuels makes really great chai
23:53 deafferret I quit smoking 6 years ago, so perhaps
23:53 rbuels actually, the biggest determinant is not so much fitness
23:54 rbuels it's kind of genetic
23:54 deafferret THANKS GOD
23:54 rbuels have you ever been above 13000 feet?
23:54 deafferret sure, I flew to PITT
23:54 rbuels well, what's the highest you've ever been
23:54 deafferret 40K?
23:54 rbuels well, what's the highest you've ever been *unpressurized*
23:54 deafferret like bp 0 ?
23:55 deafferret you're not making any sense
23:55 deafferret like in Total Recall?
23:55 deafferret :D
23:55 rbuels bp 0?
23:56 deafferret Shakira is wooing me. I'm wood.
23:56 deafferret blood pressure zero
23:56 * rbuels does not remember total recall
23:56 deafferret woo'd
23:56 * deafferret checks the Longs Peak trail topo map
23:56 rbuels anyway, one of the biggest determinants is actually how easily you get altitude sickness
23:56 rbuels some people are really susceptible
23:56 rbuels and some people aren't
23:57 rbuels some people just get nauseous and incoherent as soon as they get about like 12 or 13 thousand feet
23:58 rbuels thankfully, i'm fine.  but i've seen what happens to people that get it.  it's not pretty
23:58 rbuels puking all over the place........
23:59 rbuels ok, i've got to work some more
23:59 deafferret looks like I can claim 11,600 feet
23:59 rbuels not bad
23:59 rbuels pretty much have to go to colorado to get any higher than that in the us
23:59 deafferret google maps added a bunch of non-existant glaciers to Longs Peak.  :(

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