Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-05-20

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All times shown according to UTC.

Time Nick Message
00:22 dnewkirk joined #bioperl
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00:22 JunY joined #bioperl
03:45 CIA-42 bioperl-live: Chris Fields master * rd4a0f3d / .shipit : add basic shipit file - http://bit.ly/aow90s
03:45 CIA-42 bioperl-live: Chris Fields master * r636d3cd / Build.PL : require, not use - http://bit.ly/cvmIRg
03:45 CIA-42 bioperl-live: Chris Fields master * r936ad3e / (6 files in 6 dirs): Merge branch 'master' of github.com:bioperl/bioperl-live - http://bit.ly/bzfpvF
03:57 bag_ joined #bioperl
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12:14 barni joined #bioperl
12:14 barni hi all
12:14 barni joined #bioperl
12:14 barni i have a query  on bio::biblio
12:14 barni can anyone help me
12:17 barni anybody there ?
12:18 vinnana yes, but I don't know bio::bioblio
12:21 barni ok
12:22 barni i am using bio::biblio in my  PERL CGI script
12:39 JunY Hi, Barni. You can post on bioperl-I mail list. I am sure there will be someone who can help u
12:41 barni ok
12:41 barni thanks
13:27 deafferret ah, PERL. There's the problem.  :)
14:34 gwo joined #bioperl
15:06 CIA-60 bioperl-live: Chris Fields master * rcbae795 / Bio/Range.pm : strand() is a set of fixed types, throw if invalid (perl 5.12 fix) - http://bit.ly/9v1HuP
15:06 CIA-60 bioperl-live: Chris Fields master * r13b9056 / Bio/Location/Split.pm : fix warning (perl 5.12) - http://bit.ly/deKDXJ
15:06 CIA-60 bioperl-live: Chris Fields master * r7ea9c9d / Bio/Perl.pm : fix warning (Replacement list is longer than search list) (perl 5.12) - http://bit.ly/cUDdl4
15:06 rbuels PERL.
15:06 * rbuels chuckles
15:27 CIA-60 bioperl-live: Chris Fields master * r0f972a1 / t/Align/SimpleAlign.t : remove debugging - http://bit.ly/9zza55
15:27 CIA-60 bioperl-live: Chris Fields master * r4fed083 / (Bio/DB/DBFetch.pm Bio/DB/SwissProt.pm): don't use lc/uc unless you have defined input (perl 5.12) - http://bit.ly/9pycGM
15:27 CIA-60 bioperl-live: Chris Fields master * r02ea7fe / Bio/Restriction/EnzymeCollection.pm : UNIVERSAL->import is deprecated (perl 5.12) - http://bit.ly/buXvgp
15:27 CIA-60 bioperl-live: Chris Fields master * rb364a9c / Bio/Tree/TreeFunctionsI.pm : UNIVERSAL->import is deprecated (perl 5.12) - http://bit.ly/c3Xxxx
15:27 CIA-60 bioperl-live: Chris Fields master * r94bc595 / Bio/Restriction/Analysis.pm : uc/lc must have defined input (perl 5.12) - http://bit.ly/98cNEq
15:37 rbuels damn, look at him go
15:53 CIA-60 bioperl-live: Chris Fields master * rb1c30f0 / Bio/DB/CUTG.pm : can't use uc/lc with possibly undefined variables (perl 5.12) - http://bit.ly/aRk1CW
15:53 CIA-60 bioperl-live: Chris Fields master * r28ec366 / Bio/SearchIO/Writer/ResultTableWriter.pm : Can't use uc/lc with undefined vars (perl 5.12) - http://bit.ly/9rruge
15:58 spekki01 im trying to use Bio:Align in my script, Bioperl is installed locally in my home directory i have all my environment variables pointing to it so the script knows where to look for bioperl modules but im getting this error http://codepad.org/rtBEn11b anyone know what it might mean?
16:00 rbuels spekki01: you are probably passing a filehandle as the -file argument to something in your code
16:00 rbuels spekki01: -file needs a filename
16:00 rbuels spekki01: if you are doing a filehandle, use -fh
16:00 spekki01 oh i see now
16:00 rbuels (not all modules support -fh but many do)
16:03 cawiss joined #bioperl
16:15 spekki01 hmmm maybe im just doing this wrong but i have a bunch of sequences in a file in fasta format, and i want to align them and have them in stockholm format, I'm assuming Bio::Align can do this ?
16:15 spekki01 or does it just do type conversion?
16:22 spekki01 nm i figured it out
16:39 CIA-60 bioperl-live: Chris Fields master * r9709584 / Bio/SeqIO.pm :
16:39 CIA-60 bioperl-live: var must be defined when using in a string or with uc/lc or "\L" (perl
16:39 CIA-60 bioperl-live: 5.12) - http://bit.ly/c58FC7
16:39 CIA-60 bioperl-live: Chris Fields master * r820a841 / t/Assembly/Assembly.t : remove redeclared vars (perl 5.12) - http://bit.ly/9kAD1D
16:39 CIA-60 bioperl-live: Chris Fields master * r14a4ee6 / Bio/Assembly/IO/sam.pm : Latest Bio::DB::Sam needs -autoindex on to work - http://bit.ly/cIcSUX
16:39 CIA-60 bioperl-live: Chris Fields master * r7882c7a / t/Assembly/Assembly.t :
16:39 CIA-60 bioperl-live: (re)fix assembly to cleanup up files, make skipping tests more
16:39 CIA-60 bioperl-live: consistent - http://bit.ly/dokV13
16:43 deafferret spekki01: what was the answer
16:43 deafferret ?
16:45 spekki01 sry was afk, it only does type conversion
16:46 spekki01 i ended up using some program called MUSCLE to make an allignment out of my seqences, then converted that fasta allignment to stockholm alignment via alignIO
16:46 * deafferret nods
16:47 rbuels 'some program called muscle', lol
16:47 rbuels that's a very widely used thing
16:48 deafferret /kick rbuels /join #snoot
16:48 deafferret hey!
16:48 deafferret that's better
16:48 deafferret /kick rbuels /join #snoot
16:48 rbuels at wur.nl in the netherlands, they have a machine called kokosnoot
16:49 rbuels which i find highly amusing.  even though it's just dutch for coconut
16:49 deafferret is that a Gentlemen Broncos reference?
16:49 * rbuels hasn't seen it
16:49 deafferret rbuels cam: http://www.imdb.com/media/rm1950779648/tt1161418
16:52 CIA-60 bioperl-live: Chris Fields master * rc0c0f62 / Bio/Assembly/Contig.pm : uc/lc must have defined var (perl 5.12) - http://bit.ly/b1y8Ns
17:04 CIA-60 bioperl-live: Chris Fields master * r4b74f5a / t/Microarray/Tools/ReseqChip.t :
17:04 CIA-60 bioperl-live: fix brittle test based (possibly changing) file size, close the correct
17:04 CIA-60 bioperl-live: fh - http://bit.ly/bx6CDs
17:06 CIA-60 bioperl-live: Robert Buels master * racb58ba / Bio/DB/Taxonomy/entrez.pm : if Bio::DB::Taxonomy::entrez cannot load XML::Twig, it should include the perl error (that has @INC for diagnosis) - http://bit.ly/91rHfT
17:14 deafferret how do I know which branch this is  http://github.com/bioperl/bioperl-live/comm​it/c0c0f6248784f1a1d14651b73d75fa461c3c4088   ?
17:18 deafferret (the first CIA-60 bit.ly above)
17:20 rbuels deafferret: well, gitk tells you that ...
17:20 * rbuels sees where github might have that info ...
17:20 deafferret gitk.com not found
17:20 rbuels deafferret: it's a command
17:20 deafferret :)
17:20 * rbuels kicks deafferret in the shin
17:21 deafferret :D
17:21 * rbuels pulls deafferret's nose
17:21 rbuels woopwoopwoop
17:21 rbuels nyuck nyuck
17:26 deafferret huh. i find that very odd. github says tree: COMMIT#
17:26 deafferret instead of branch: X
17:26 deafferret but then below it says tree: DIFFERENTCOMMIT#
17:27 * deafferret fears this may be the final sign of the end of the world
17:27 * deafferret raptures
17:37 CIA-60 bioperl-live: Chris Fields master * r8c86821 / Bio/Nexml/Factory.pm : fix odd use of isa, popping up with latest Bio::Phylo - http://bit.ly/9OXoLf
17:37 CIA-60 bioperl-live: Chris Fields master * r81e9e77 / Bio/DB/Taxonomy/entrez.pm : Merge branch 'master' of github.com:bioperl/bioperl-live - http://bit.ly/b1DpH6
18:04 CIA-60 bioperl-live: Chris Fields master * rcf8909f / (t/AlignIO/nexml.t t/data/characters.nexml.xml): update files, expected test data for nexml (AlignIO) - http://bit.ly/aFd2fo
18:07 CIA-60 bioperl-live: Chris Fields master * r96523fb / t/SeqIO/nexml.t : updated expected test data for updated nexml file - http://bit.ly/dqoIvK
18:47 CIA-60 bioperl-live: Chris Fields master * r4e610bb / (3 files): add updated tree nexml files, old files for comparison - http://bit.ly/bOclUS
18:47 CIA-60 bioperl-live: Chris Fields master * r58fa5ec / t/data/characters+trees.nexml.xml : updated nexml file - http://bit.ly/cv18E0
19:13 BerndBauer joined #bioperl
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20:13 CIA-60 bioperl-live: Chris Fields master * r99f57c4 / Bio/Tools/Run/WrapperBase/CommandExts.pm : can't lookup an undefined value as an executable - http://bit.ly/dziJkd
20:36 spekki01 dumb question and not related but anyone on osx ever use curl?
20:42 rbuels spekki01: curl is not just osx
20:42 rbuels spekki01: but no i've never used it on osx
20:47 rbuels (but i've used it on linux, which should not be any different)
20:49 spekki01 ok well i never used it before and wasnt sure of the syntax when dling a file i used this command curl ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz > progress.txt  i made the assumption it would just put the file in the current directory i think i was wrong, is my progress.txt the file i want or did i do this completely wrong?
20:51 rbuels spekki01: yes by default curl fetches to sdout, so progress.txt should probably be the gzipped nr.
20:51 rbuels spekki01: wget, in contrast, would fetch a url like that to nr.gz in the current directory
20:51 spekki01 oh thank god, i though i just wasted 2 hours
20:51 rbuels only 2 hours to waste? lol.
20:51 rbuels that's nothin.
20:51 dnewkirk joined #bioperl
20:51 rbuels this is bioinformatics, son.
20:51 spekki01 lol
20:51 rbuels we waste *days*
20:52 spekki01 tell me about it, ive been trying to get sequences --> allignments --> hmmer3 profiles --> hmmer searches going all week
20:53 dnewkirk wasting days? is that like running meme on 10k sequences?
20:53 perl_splut wasting days sounds like a normal work day for me
20:53 rbuels yup.
20:54 spekki01 its a pretty steep learning curve i have to admin, i hadn't really done any bioinformatics stuff untill i started it last month for my job at my university
20:54 spekki01 admit*
20:54 rbuels i gathered.  :-)
20:54 rbuels well you've gone down the rabbit hole now.
20:55 spekki01 *someone let me out lol*
20:55 perl_splut here's a drink
21:19 dnewkirk lab tech spekki01?
21:19 dnewkirk post doc?
21:52 spekki01 undergrad summer job
21:52 deafferret *days*? this is my fifth *year*  (part time)
21:53 spekki01 thats a long time
21:53 deafferret perl_splut: how do you waste days in a single day?
21:54 deafferret apparently I've been slacking off
21:56 dnewkirk use more processors. The more processing time wasted, the more time wasted in a day...
21:56 spekki01 lol
21:57 spekki01 so an hour wasted using 16 processors is longer than an hour wasted using 4?
21:57 deafferret jaded: made dull, apathetic, or cynical by experience or by surfeit
21:58 dnewkirk or you can program in Java, that's just a waste in general...
21:58 deafferret Rationing had put an end to a surfeit of biscuits long ago.
21:58 spekki01 lol awwwe i dont mind java
22:00 dnewkirk Java isn't bad, it's just the running joke in our lab
22:16 rbuels hmmm, a surfeit of biscuits.
22:18 rbuels guys:  seems like finding the longest ORF in a protein sequence is a very common thing, right?
22:18 rbuels there's a script for this in examples/
22:18 rbuels but it kind of seems like there should be a method for this on Bio::PrimarySeq or someplace like this
22:19 * rbuels loves him some git branches
22:19 * rbuels grabs them and jiggles them
22:23 rbuels lord, lots of the PrimarySeqI code is written indented *8 spaces*
22:23 rbuels a bit ...excessive
22:25 CIA-60 bioperl-live: Florent Angly master * re71c10c / Bio/Assembly/IO/ace.pm : Change in Bio::Assembly::IO::ace logic to remove warnings that can occur sometimes - http://bit.ly/cLuBbY
22:25 CIA-60 bioperl-live: Florent Angly master * rd3ca4dd / (28 files in 18 dirs): Merge branch 'master' of git@github.com:bioperl/bioperl-live - http://bit.ly/aY4lMS
22:25 CIA-60 bioperl-live: Florent Angly master * r81df066 / (8 files in 5 dirs): Writing assembly files (ace, tigr) at once or a contig by contig - http://bit.ly/bYDwR0
22:47 deafferret oh dear. e71c10 looks errant
22:48 deafferret "Change in Bio::Assembly::IO::ace logic to remove warnings that can occur sometimes" should probably not change 30 files?
22:48 rbuels deafferret: yes, i was thinking about making a stink about that as well
22:48 spekki01 for anyone who has used hmmer3 and searched the protein db off off ncbi (local download 2.4gigs in fasta format) say you have an average profile based off of 11 alligned sequences. Best guess as to how long it would take to do hmmrsearch of a small profile file on the entire protein database? Reason i ask is i cant tell if my script is broken and hanging or it just takes a long time :(
22:48 deafferret rbuels: go forth and stink
22:48 deafferret core dev
22:48 deafferret :)
22:49 rbuels deafferret: stinking is my specialty
22:49 deafferret you have RESPONSIBILITIES, mister
22:49 rbuels spekki01: i have no idea how long that should take.  deafferret, do you?
22:49 dnewkirk depends on the machine, but that can take quite a while
22:49 * deafferret was hoping he could stall until spekki01 said "oh, there it finished"
22:50 spekki01 lol no its still running
22:50 spekki01 30 min + atm
22:50 deafferret wait for it...  wait for it....!
22:50 spekki01 well i think its running anyway
22:50 deafferret if it's running go home and have some tequila
22:50 rbuels lol
22:51 rbuels spekki01: do not listen to deafferret, work on something else while it's running
22:51 * rbuels gives deafferret 2 demerits
22:51 spekki01 well if it works then I know my script works and i can que up the other 10 profiles that i need to search, and go home and have a beer and hopefully it'll be done when i come in tomorrow morning lol
22:52 deafferret spekki01: he's joking. prankster.  incorregible, that one
22:52 spekki01 lol
22:52 * deafferret tussles rbuels hair, hands him the bottle
22:52 rbuels spekki01: well, if it's quitting time you could just queue them up and go home, and let the computers break overnight if they want
22:52 deafferret "hair"    :)
22:52 * rbuels takes a swig
22:52 rbuels deafferret: 1 more demerit!
22:52 * deafferret sighs, remembers the days when there was a "quitting time"
22:52 spekki01 i hope it don't break the computers lol, its the university servers im running this on
22:53 rbuels oh, it's all in good fun.
22:53 rbuels the university sysadmins love it.
22:53 rbuels plus, you're a summer student, you're untouchable
22:53 rbuels lol
22:54 spekki01 I dont think the admin likes me my first week i made all these requests and had issues with permissions that i had to keep bugging him about,... now he ignores my emails i swear
22:55 dnewkirk sys admins don't like anyone. It's in the job description...
22:55 spekki01 lol
22:55 rbuels dnewkirk: that's very true.
22:56 rbuels i can't blame them either
22:56 perl_splut I like people... especially those that bribe me with goodies :)
22:56 rbuels perl_splut: you're a sysadmin?
22:56 perl_splut that's one of my roles
22:56 rbuels perl_splut: you just wait, mr. fresh face.  we'll see how your attitude is in 15 years
22:57 perl_splut fresh? been in IT for a decade
22:57 rbuels 15 *more* years then!
22:57 dnewkirk Sys admins hate people. Perl_splut likes people. Therefore, perl_splut is not a (real) sys admin
22:57 * rbuels is starting to think perl_splut is too cheerful
22:57 dnewkirk :P
22:58 rbuels dnewkirk: possibly.
22:58 rbuels perl_splut: start hating people.
22:58 perl_splut life isn't worth living if you're not happy
22:58 perl_splut which is why so many depressed people kill themselves
22:59 rbuels um, *downer*!
23:00 * rbuels hands perl_splut the bottle of tequila
23:00 perl_splut on that note tis time to head home, pay some bills and meet up with some friends
23:01 rbuels heh, night
23:01 rbuels deafferret: fangly's commit isn't so bad, the modified files in the merged commit are modified relative to him pulling from *his* branch
23:02 * rbuels needs to write about rebasing on the using git page
23:03 rbuels er, into his branch i mean
23:03 rbuels but he probably should really be doing this assembly work on a topic branch ...
23:15 rbuels anybody familiar with CodonTable.pm?

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