Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-06-28

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All times shown according to UTC.

Time Nick Message
11:33 * kai waits for pyr[tab] to wake up
13:12 brandi joined #bioperl
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15:40 deafferret py[tab] WAKEY WAKEY!
15:41 deafferret 12:20 <@pyrimidine> deafferret: email defamer
15:41 deafferret :)
15:45 kblin hehe
15:45 kblin still at yapc?
15:48 deafferret nah, back on thr   :)
16:12 XaeroOne joined #bioperl
16:29 wizi joined #bioperl
16:30 wizi hello?
16:41 wizi joined #bioperl
16:41 wizi hello?
16:47 wizi anyone here?
16:47 XaeroOne they are here but will have to wait
16:52 wizi thanks
16:54 kblin and also ask whatever you want to ask
16:54 kblin apart from "anybody here?"
16:55 wizi sorry i am new here
16:55 wizi i just want to ask if Bioperl suppose BLAT?
16:55 wizi and where can I find the examples?
17:04 flu http://doc.bioperl.org/biope​rl-live/Bio/Tools/Blat.html
17:09 wizi my $obj = Bio::Tools::Blat->new(-fh=>$filehandle);  (what is filehandle, my database or my queries?)
17:10 wizi and what is the differnet between filehandle and filename?
17:10 wizi different*
17:19 rbuels wizi: a filename is a string with the name of the file, a filehandle is a filehandle.  you should read a book about programming perl.
17:20 deafferret rbuels should too
17:21 deafferret :)  rbuels: did you miss me?
17:23 wizi there are 2 paras for Blat-> new: filename and filehandler, i am just wondering which is my query file and which is my database. Sorry i am new to bioperl
17:25 deafferret looks like you use one or the other. give it a filename, or give it a filehandle (where you've already opened that filename for read)
17:25 deafferret your choice
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17:39 * deafferret does a silly dance trying to get rbuels' attention
17:39 rbuels eh what
17:40 deafferret you coming to YAPC::NA::2011?
17:40 rbuels oh stop it!  i have to get the new repeats set into the ITAG pipeline and get the new tomato release going through it
17:40 rbuels i don't know yet, too far away
17:40 deafferret Ah, the Pittsburgh Heinz goons are threatening you?
17:40 rbuels lol
17:41 rbuels no heinz is so far down the food chain, they are not involved
17:41 rbuels we just happen to be using the Heinz 1706 tomato as our reference
17:41 rbuels that's the one they use in their ketchup.
17:41 deafferret wut? aren't they like the largest corporate interest in tomatoes on the planet?
17:42 dnewkirk they use tomatoes in the ketchup?
17:42 deafferret dnewkirk: they flavor the corn syrup with real tomatoes, yes
17:43 deafferret YAPC::NA::2009 toured Heinz field in Pittsburgh  :)
17:43 deafferret with the crazy 50 foot long celebratory ketchup-pouring thing when they score
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18:01 deafferret wizi: no, they're not the same  :)
18:01 deafferret read the POD of each, they describe what they do
18:01 deafferret Bio::Tools::Blat parses BLAT files.  those other things run things
18:02 deafferret (I assume)
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18:22 CIA-95 bioperl-live: Chris Fields topic/species_proxy * r1687dce / Bio/Species.pm : Bio::Species delegates to Bio::Taxon and Bio::Tree::Tree; this removes the need for weaken() as Bio::Species just acts as a proxy class. Needs further testing to ensure no mem leaks persist - http://bit.ly/bV8s77
18:22 deafferret purl: rbuels is also King of the Veggie Tales
18:22 rbuels web services and data federation!
18:22 deafferret that's what I said
18:24 deafferret purl: rbuels also services The Federation
18:24 rbuels right.
18:53 CIA-95 bioperl-live: Chris Fields topic/species_proxy * r5cba9a6 / Bio/Species.pm : remove code refs for index tests, a few doc changes and comments - http://bit.ly/c0Ms5u
19:02 pyrimidine joined #bioperl
19:07 CIA-95 bioperl-live: Chris Fields topic/species_proxy * r9ca1de9 / (t/SeqIO/Handler.t t/SeqIO/swiss.t): bit premature to check for this (API indicates this should be the more general Bio::Species until we deprecate it) - http://bit.ly/b91Ur5
19:48 kblin pyrimidine: hey there
19:48 pyrimidine o/
19:49 kblin pyrimidine: tom's tests still print out results fine, so I figure they're covered
19:49 kblin so from my point of view bioperl-hmmer3 can be removed
19:49 pyrimidine ok
19:49 deafferret py[tab]!! hi!  :)
19:49 pyrimidine will post to the list on that
19:50 pyrimidine deafferret: hi right back at ya
19:50 * deafferret swoons
20:05 * kblin sighs
20:05 kblin #bioinformatics is lots and lots of off-topic chatter
20:07 deafferret kblin: did you see the US vs. Ghana game? hoo-doggies!
20:10 kblin deafferret: nope, I didn't even see England vs. Germany
20:11 deafferret kblin: that was an "off topic" joke   :)
20:11 kblin yeah, I realized
20:11 kblin about at the moment when I hit enter
20:11 * deafferret moves kblin's jaw to simulate laughter
20:11 * deafferret laughs along with kblin
20:12 kblin by just moving your jaw? I'd love to see _that_
20:12 kblin :D
20:13 deafferret centuries of ventriliquism
21:05 flu rbuels, any idea what is going on with this simple shipwright import?  http://pastebin.com/Bzd6mR4j
21:06 * rbuels looks
21:06 rbuels that's not shipwright, it's your cpan that's borking.
21:06 rbuels perhaps it doesn't like running under shipwright.
21:07 flu hrmm
21:07 rbuels i'd recommend disabling CPAN::SQLite
21:07 rbuels it's always been very questionable for me.
21:08 rbuels flu: cpan[1]> o conf use_sqlite  0
21:09 flu that did it
21:09 * flu tips his hat to rbuels once again
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21:16 summatusmentis hi all, I have some... conceptual questions about how this all works
21:16 pyrimidine 42
21:17 summatusmentis I'm wondering about using BioPerl in a context that isn't biology, but what my problem amounts to is I've got sequences of numbers
21:17 summatusmentis that I'm looking to compare, and either show that they're similar, or show where the differences are
21:17 pyrimidine Array::Compare?
21:18 summatusmentis umm... I have no idea? Is that perl?
21:18 kblin yeah
21:18 kblin check CPAN :)
21:18 summatusmentis I have a rough working knowledge of perl, so...
21:18 summatusmentis hah, right
21:18 pyrimidine List::Compare as well
21:19 summatusmentis oh, that's simple comparison. unfortunately my life isn't that easy
21:19 * pyrimidine is sad no one got the '42' joke
21:19 pyrimidine summatusmentis: code example? (use gist.github.com)
21:20 summatusmentis pyrimidine: I haven't started coding with bioperl yet, I'm kinda trying to figure out if it's worth my time to try and get it to fit my problem
21:21 pyrimidine saying this as a perl prog and a bioperl core dev, if it isn't biologically relevant it probably not isnworth using bioperl
21:21 pyrimidine *isn't worth
21:22 pyrimidine an explanation of the problem might help, though
21:22 summatusmentis sure, I can do that
21:22 summatusmentis my "full traces" are lists of chunk requests, from startup to login of VMs
21:23 summatusmentis the overall goal is to show that on the block level, chunk requests for boot time (for the time being) are fairly consistent and ordered
21:24 summatusmentis so what this means is either "traces are the same" (which they aren't) or "traces have subsequences that are the same)
21:24 summatusmentis which manually comparing seems to suggest there are subsequences that are consistent
21:25 summatusmentis based on the reading I've done, it looks like bioperl is pretty biologically based, but might be able to be wrangled to fit this problem, given that (again, as I understand it), the abstract problem is the same?
21:28 pyrimidine this almost seems like something you would use a B-Tree or R-Tree for
21:29 summatusmentis so then, can I ask, what is it bioperl gets the biologically inclined?
21:30 pyrimidine the only thing within bioperl that would probably fit something like this is Bio::Range, but I'm pretty sure (99.99%) this isn't what you want
21:31 pyrimidine summatusmentis: 'biologically inclined?'  It's bioperl, the name is pretty self-explanatory.
21:31 summatusmentis let me rephrase that
21:31 summatusmentis I know it's bioperl
21:32 summatusmentis but is the purpose "help find sequences" or is the purpose "expose data in a way that's useful to perl" ?
21:33 pyrimidine For bioperl, that should be qualified as 'biological sequences', but it's not just that.
21:33 dnewkirk It's "format data in a useful manner to use in downstream analysis," more or less...
21:33 pyrimidine dnewkirk++
21:33 summatusmentis ah
21:34 summatusmentis then yes, you're probably right that bioperl won't help me a whole lot
21:34 pyrimidine I'm thinking what you describe would fit within the B-Tree/R-Tree type of search
21:34 summatusmentis I think I'm at the downstream analysis stage, and given that I'm not using biological data, it's sorta moot
21:35 summatusmentis I'll definitely look into those, thanks
21:35 summatusmentis manual comparison bites, so, you know :)
21:36 pyrimidine perl implementations are on CPAN.  But it's probably worth looking into the various DB implementations (SQLite, mysql, Pg, BDB, etc)
21:38 CIA-95 bioperl-live: Chris Fields topic/species_proxy * r04253fe / t/Species.t : add test for mem leak (may have to be modified) - http://bit.ly/dB8AVl
21:38 summatusmentis the reason I ended up here is when googling things like "sequence analysis" and "sequence comparison" bioinformatics seemed to be where all this work was being done
21:39 summatusmentis but I really appreciate the help, and I'll checkout the B-Tree/R-Tree stuff
21:39 pyrimidine ok
21:40 summatusmentis thanks again. tah
21:40 summatusmentis .wc
21:40 summatusmentis left #bioperl
21:41 CIA-95 bioperl-live: Chris Fields topic/species_proxy * r457ad89 / (4 files in 2 dirs): clean up cleaning up (e.g. DESTROY properly) - http://bit.ly/bagP2G
21:42 wizi joined #bioperl
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21:59 newtobioperl why dont we support BLAT?
21:59 pyrimidine we do
22:00 pyrimidine at least, last I heard we did
22:00 newtobioperl you mean this http://doc.bioperl.org/bioperl-l​ive/Bio/Tools/Blat.html#SYNOPSIS
22:00 newtobioperl its just a parser
22:00 pyrimidine right
22:00 pyrimidine do you mean a wrapper?
22:00 newtobioperl No Bio::Tools::Blat - parser for Blat program
22:01 newtobioperl do we have a wrapper?
22:01 newtobioperl for Blat?
22:01 pyrimidine have you tried Bio::SearchIO
22:01 pyrimidine (as the parser)?
22:03 newtobioperl do you have any document or guide showing you how to use SearchIO Blat?
22:03 pyrimidine Looks like the wrapper is Bio::Tools::Run::Alignment::Blat
22:04 newtobioperl I just check it on CPAN, Bio::Tools::Run::Alignment::Blat is not there anymore
22:04 pyrimidine it's not in BioPerl, it's in BioPerl-run
22:04 newtobioperl oh
22:04 pyrimidine http://search.cpan.org/dist/BioPerl-Ru​n/lib/Bio/Tools/Run/Alignment/Blat.pm
22:05 newtobioperl oh i didnt install that package, thats why
22:05 pyrimidine The SearchIO format 'blast' will parse BLAT according to the POD
22:05 pyrimidine there is also 'axt' and 'psl' parsers
22:05 pyrimidine gotta go
22:06 pyrimidine left #bioperl
22:13 newtobioperl How can I install BioPerl-Run 1.6.1 using Perl Package Manager. I am running window 7 and using ActivePerl
22:17 rbuels newtobioperl: you might consider using strawberry perl, i think it comes with bioperl included.  but, see http://www.bioperl.org/wiki/I​nstalling_Bioperl_on_Windows
22:17 rbuels newtobioperl: in general, there are a lot of questions that will be answered on the wiki
22:18 rbuels newtobioperl: that wiki page has instructions for ppm installs
22:18 newtobioperl i followed the ppm installs
22:18 newtobioperl and i was able to install Bioperl
22:18 newtobioperl on Cppan
22:19 newtobioperl but Bioperl-run is not there
22:19 newtobioperl I am looking for the Repository of BioPerl-Run
22:21 rbuels newtobioperl: i'm not sure, i have never used perl on windows, you might try looking at the Beyond the Core section on that page: http://www.bioperl.org/wiki/Installin​g_Bioperl_on_Windows#Beyond_the_Core
22:22 rbuels newtobioperl: probably you could infer something from the instructions for installing bioperl-db (which is similar to bioperl-run)
22:22 rbuels newtobioperl: beyond that, i don't know anything, the mailing list would be the place to go.
22:23 newtobioperl thanks rbuels
22:35 dnewkirk either strawberry perl or cygwin would work
22:40 newtobioperl i am trying to install it manually
22:40 newtobioperl using CPAN
22:50 dnewkirk If something doesn't work in the way you need it to, you can use git on windows to grab the live version
22:51 dnewkirk strawberry should be able to install it from a local dir and you'd be good to go.
22:55 newtobioperl hi dnewkirk, it doesnt work
22:55 newtobioperl test failed for CPAN installer
22:55 dnewkirk hmm
22:56 newtobioperl ill try Git
22:56 dnewkirk which version of strawberry are you using, just out of curiosity?
22:57 newtobioperl i am using Activeperl
22:57 newtobioperl on window 7
22:57 dnewkirk ahhh, right, sorry
22:58 newtobioperl I installed BioPerl using Perl Package Manager
22:58 newtobioperl (very easy)
22:58 dnewkirk yep
22:58 newtobioperl but Bioperl-run is not there
22:58 dnewkirk That was a nice addition they made recently
22:58 newtobioperl do you know how I can run GIT on window
22:58 newtobioperl ?
22:59 newtobioperl all I want to do is BLAT
23:00 dnewkirk lemme get on a windows box and check a couple things
23:10 dnewkirk are you building it in the command prompt from cpan directly?
23:12 newtobioperl yes
23:12 newtobioperl but it failed
23:12 newtobioperl i just installed GIT
23:12 newtobioperl but i still dont understand the whole Git thing
23:12 newtobioperl i am running GIt Gui -->clone "http://github.com/bioperl/bioperl-run.git"
23:13 dnewkirk ok, so that dumps everything into a directory, and you'll build from that directory similar n downloading a file from cpan
23:14 newtobioperl yes i see all the file in the target directory
23:15 newtobioperl now what?
23:16 newtobioperl so I have to do the whole CPAN installation again?
23:16 dnewkirk no, use "perl Build.PL"
23:16 dnewkirk assuming that n/dmake is in your path
23:18 dnewkirk then make with dmake, make test, etc.
23:18 newtobioperl dmake?
23:19 dnewkirk part of mingw
23:20 newtobioperl fail
23:20 newtobioperl i typed "perl
23:20 newtobioperl "perl Build.pl"
23:20 dnewkirk what is the error returned?
23:20 newtobioperl got "Possible Missing or corrupt "MANIFEST" file
23:21 newtobioperl "Nothing to enter for 'provides' field in metafile"
23:21 newtobioperl "creating new 'Build' script for Bioperl-Run version 1.006900
23:22 newtobioperl OH THIS IS the error I got right after I typed "perl Build.pl"
23:23 newtobioperl Bio::Root::Version (1.006001) is installed, but we need version >= 1.006900
23:24 newtobioperl where can I get Bio::Root?
23:25 dnewkirk you may need to install the latest version of Bioperl to get the Bioperl-run to work then
23:25 dnewkirk Didn't think of that, my apologies
23:25 dnewkirk Did the original fail to compile when you tried to install it from CPAN?
23:25 dnewkirk Or was it some sort of other error?
23:26 newtobioperl I used Perl Manager to Install Bioperl
23:26 newtobioperl and the Bioperl version is 1.6.1
23:26 newtobioperl I believe it is the lastest one
23:26 newtobioperl right?
23:27 deafferret that's the latest official release, yes
23:27 dnewkirk its the latest full release. The live (git) version has updated code that the live (git) version of the bioperl-run module may require
23:28 newtobioperl I am trying to install Bioperl-live
23:28 newtobioperl using git
23:28 newtobioperl lets see what happen
23:36 dnewkirk dmake isn't playing nice with installing one of the prereqs for bioperl on my xp machine
23:36 dnewkirk You may be having a similar problem
23:38 newtobioperl hopefully, ill get it working
23:38 newtobioperl sigh
23:38 newtobioperl i haven been spending all day to install this bio-run
23:39 newtobioperl if its not working, do you think I should uninstall Active perl and go to Strawberry instead?
23:43 dnewkirk The DB_FIle-1.820 requirement can't be compiled properly, nor can it find a checksum for it (and this is what causes everything to fail)
23:43 dnewkirk hmm
23:45 dnewkirk give me ten minutes to test it out and I'll let you know before you waste your time
23:48 deafferret switch to linux. works great  :)
23:52 newtobioperl thank you so much dnewkirk
23:54 newtobioperl lol what is the best software that allows you to run dual OS: window and linux?
23:54 deafferret no clue. I'm addicted to OSX as my desktop and linux servers
23:59 dnewkirk you can run a vm of linux in windows, if you need windows for most of your work
23:59 newtobioperl but vm of linux is prob very slow to do Blast, blat

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