Camelia, the Perl 6 bug

IRC log for #bioperl, 2009-11-02

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All times shown according to UTC.

Time Nick Message
02:57 phaedrus441 joined #bioperl
02:58 phaedrus441 hi guys, anybody up?
03:03 kyanardag_ joined #bioperl
03:05 phaedrus441 I'm 100% new to molecular biology, etc. BUT, can BioPerl help me search through a chromosome for certain regex expressions?
03:07 phaedrus441 Here's what I want to do: input AFLP recognition site templates (eg. gattctc and ttaacat) plus a certain number of base pairs that could be between them (eg. 110 +/- a few percent) and find everywhere in chromose that pattern resides
04:21 rbuels phaedrus441: depending on the size of your input sets (how many chromosomes and how many AFLP markers), you can do a number of thigns
04:21 phaedrus441 really?
04:21 phaedrus441 I'm just working with arabidopsis right now, and only need to search for one set of inputs at a time
04:22 rbuels phaedrus441: bioperl is mostly stuff for reading in and writing out various formats
04:22 rbuels phaedrus441: also some stuff to help with running various analysis tools
04:22 phaedrus441 rbuels: right now I've just been playing with regular perl, trying to learn how to write a simple program to slurp in the .fas file and run a regex on it. Should I just continue down that road?
04:23 rbuels if you just have one set of AFLP recognition sequences to search against a set of ATH chrs at a time, i'd say read in the chrs with Bio::SeqIO (cause they are probably in fasta format), and then use a regex to match the aflp recognition seqs
04:23 rbuels use Bio::SeqIO to read in a .fas
04:23 rbuels do perldoc Bio::SeqIO and Bio::PrimarySeq
04:24 rbuels phaedrus441: what programming language are you heretofore most familiar with?
04:24 phaedrus441 rbuels: Thanks! one more quick question. I'm doing this coding to help a professor out, and he seems to think that python would be the way to go rather than perl. I know you're probably biased (haha), but what do you think?
04:24 rbuels whatever.  if he wants python use python.
04:24 phaedrus441 rbuels; just a little bit of c and java from university days, and vb
04:24 rbuels there's a biopython too
04:24 phaedrus441 I'm really a beginner
04:28 phaedrus441 rbuels: any advice on where I should begin? :-/
04:28 rbuels well, step 1 is choose whether to do it in perl, python, or java
04:28 rbuels all 3 have bio* libraries that can do this
04:29 rbuels lol
04:29 phaedrus441 is there any difference in terms of speed, etc.?
04:29 rbuels i don't really know, i don't know much about java or python
04:29 phaedrus441 ahhh
04:30 phaedrus441 is bioperl more developed than the others?
04:30 rbuels probably.
04:30 rbuels i get the impression it's a bit older
04:30 rbuels but as i said, i don't really know much about the others, lol
04:30 phaedrus441 haha, yeah
04:31 phaedrus441 do people just leave their IRC clients open all the time?
04:31 phaedrus441 (sorry, random)
04:31 rbuels yes, that's the usual procedure
04:31 rbuels usually people run a command-line client inside of screen on a server somewhere
04:32 phaedrus441 ahhh, of course
04:32 rbuels either that, or they run an irc proxy
04:32 rbuels (that's what i do)
04:32 rbuels which is a program that sits on a server and holds open your chat sessions
04:32 phaedrus441 what's the name of the software you use?
04:32 phaedrus441 or is it some hosted thing?
04:32 rbuels i use dircproxy, which has a nice convenient ubuntu/debian pacakge
04:32 phaedrus441 awesome
04:32 rbuels i use Konversation (the kde irc client) to connect to it
04:33 * rbuels runs kubuntu
04:33 phaedrus441 ahhh, I'm in OS X, so I'm giving colloquy a try
04:33 * rbuels has heard good things about colloquy
04:33 phaedrus441 any special etiquette I should know? I picked up the "name:" thing, I suppose
04:34 phaedrus441 I'm amazed how helpful people are here... I thought I'd just be a nuisance
04:35 rbuels most IRC clients do tab-completion on people's names
04:35 rbuels rb<tab>
04:35 rbuels try that
04:36 phaedrus441 whew, that's nice
04:36 phaedrus441 how'd you do the action about?
04:36 phaedrus441 "rbuels has heard..."
04:37 rbuels type '/me something'
04:37 * rbuels instructs phaedrus441 on the ins and outs of gratuitous third-person
04:37 * phaedrus441 can't figure this out
04:37 phaedrus441 haha
04:37 phaedrus441 this reminds me of connecting to a bbs or something
04:38 rbuels well it depends a lot on which client you're using, lol
04:39 rbuels if it's not Web Squared enough for you, you could maybe run your irc proxy on EC2
04:39 rbuels lol
04:40 phaedrus441 hahaha
04:40 phaedrus441 hey now, I built a ton of stuff on ec2
04:40 phaedrus441 a ton being one ubuntu image with sugarcrm, but still...
04:41 rbuels in open source development, irc and mailing lists are pretty much the primary way things get done
04:43 phaedrus441 excellent
04:45 phaedrus441 rbuels: anyway, thanks for the help. I might be back tomorrow :-p
04:48 rbuels phaedrus441: ok, good luck
10:40 ptl joined #bioperl
13:19 deafferret phaedrus441: What everyone uses is listed here: http://bioperl.org/wiki/IRC
15:15 deafferret heh. under-engineering FAIL
18:10 deafferret ptl: lol http://bioperl.org/wiki/User:Patola
18:10 * deafferret sets a reminder in his calendar for 2011
18:50 driveby_bot joined #bioperl
18:50 driveby_bot /home/svn-repositories/bioperl 16313 ...one more time
18:52 * deafferret laughs
18:52 rbuels driveby_bot, lol
18:52 deafferret rbuels: ^^
18:52 deafferret too slow
18:52 driveby_bot joined #bioperl
18:52 driveby_bot /home/svn-repositories/bioperl 16314 cjfields Add USER to IRC commit hook
18:52 deafferret i had dibs on laughter
18:53 deafferret cj<TAB>: you're a loose cannon
18:53 rbuels who was that masked man?
18:53 deafferret he doesn't even sit in channel while creating havok in here?
18:53 * deafferret boos
18:53 rbuels i know, seriously
18:53 deafferret ser<TAB>
18:53 rbuels but he reads the logs from a webpage
18:53 rbuels cause he's cagey like that
18:53 deafferret HI CJFIELDS FIREFOX!
18:53 * deafferret waves
18:53 * rbuels waves his hands around and ducks his head to demonstrate how cagey pyrimidine is
18:54 * rbuels waves
18:54 rbuels hello up there!
18:54 deafferret oh, right
18:54 deafferret py<TAB>
18:54 rbuels lol
18:54 deafferret Content-type: text/silly
18:54 rbuels you never know *where* he is
18:54 rbuels he's *here*
18:54 * deafferret lools
18:54 rbuels and then he's *there*
18:54 * deafferret lools there
18:54 rbuels *huh*?
18:54 rbuels *what*?
18:55 rbuels *where is he*?
18:55 * deafferret hides
18:56 deafferret who knew that 1500 lines of system("cd x;blastall y") code would be unstable to input variation?
18:56 rbuels hahahahahaah
18:56 * deafferret raises his hand, slowly
18:56 rbuels bioinformatics ftw
18:56 deafferret perl -d *pl
18:57 rbuels o.O
18:57 deafferret I wish that worked  :)
18:57 rbuels perl --auto-debug *.pl
18:57 rbuels all done!
18:57 deafferret perl -pi -e 's/$SUCK//g'
18:58 deafferret *.pl
18:58 rbuels lol
18:58 BioPerl joined #bioperl
18:58 BioPerl /home/svn-repositories/bioperl 16315 maj update PPM command line instructions
18:58 deafferret maj: spammer
18:58 rbuels lol
18:58 deafferret who uses ppm?
18:58 rbuels bioinformaticists.
18:58 deafferret I wonder if the update was "don't use this"
18:59 * rbuels hunts and pecks at a keyboard like an orangutan to demonstate
18:59 deafferret lol
18:59 rbuels ok enough shenanigans i have to finish this shit
18:59 rbuels &
18:59 deafferret WHO DOES NUMBER TWO WORK FOR!!??!
19:00 rbuels shut up i'm working
19:00 * rbuels closes the damn window
19:00 deafferret ya, right
19:05 driveby_bot joined #bioperl
19:05 driveby_bot /home/svn-repositories/bioperl 16318 cjfields ..yet another: r () :
19:07 driveby_bot joined #bioperl
19:07 driveby_bot /home/svn-repositories/bioperl: r16319 (cjfields) : Test
19:09 driveby_bot joined #bioperl
19:09 driveby_bot /home/svn-repositories/bioperl: r16320 (cjfields) : Final one; was chopping commit msgs at first ws
19:09 pyrimidine joined #bioperl
19:10 ende joined #bioperl
19:11 pyrimidine Sorry about spamage
19:11 deafferret :)
19:12 * deafferret hugs all spammers  :D
19:13 pyrimidine I'm wondering if we can get a dalek-bot running here (I think those on #perl6/#parrot are running off feather)
19:13 pyrimidine May look into it, but for now this works.
19:14 deafferret cool.  :)   any movement on the svn server decompress problem?
19:16 driveby_bot joined #bioperl
19:16 driveby_bot /home/svn-repositories/bioperl: r16321 (maj) : full delegation of Bio::AnnotationCollectionI
19:18 driveby_bot joined #bioperl
19:18 driveby_bot /home/svn-repositories/bioperl: r16322 (maj) : pod: alias
19:27 pyrimidine deafferret: nope, not as far as I know.  Chris D. was looking into it.  I'll see if there's been any progress.
19:27 deafferret pyrimidine: thank you sir
19:32 driveby_bot joined #bioperl
19:32 driveby_bot /home/svn-repositories/bioperl: r16323 (fangly) : Made Bio::Tools::Run::TigrAssembler take in a FASTA file in addition to sequence objects
20:31 driveby_bot joined #bioperl
20:31 driveby_bot /home/svn-repositories/bioperl: r16324 (cjfields) : add infernal data file
20:33 ptl joined #bioperl
20:49 deafferret infernal?
20:50 * deafferret wonders if he can ignore join/part from driveby_bot only
21:02 ptl deafferret: on irssi, /ignore driveby_bot JOINS PARTS
21:08 deafferret ptl++
21:50 jhannah joined #bioperl
22:02 jhannah joined #bioperl
22:28 jhannah crap. svn problems spreading into my repo now  :(
22:29 * jhannah blames open-bio for all his troubles

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