Camelia, the Perl 6 bug

IRC log for #bioperl, 2009-08-05

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All times shown according to UTC.

Time Nick Message
00:18 asjo joined #bioperl
00:19 asjo` joined #bioperl
00:47 biomoose joined #bioperl
00:47 biomoose biome: Christopher Fields master SHA1-c52d537
00:47 biomoose * fix length(), implement a validate_seq() (this may become lazily called in the future)
00:47 biomoose http://bit.ly/18MKUV
00:47 biomoose biome: Christopher Fields master SHA1-56bd8bc
00:47 biomoose * move into specific subdirectory tree
00:47 biomoose http://bit.ly/roH5A
00:47 biomoose left #bioperl
07:09 faceface where do I get a commit bit?
08:54 rbuels faceface: heh.  that's a good question.
08:55 rbuels faceface: i got one by asking pyrimidine for it
10:46 faceface cool
10:47 faceface how is it going? up early or late?
10:47 faceface guess late and now your in bed?
13:38 deafferret I got one from pyrimidine and have thus far failed to earn my keep  :(
14:19 gwo joined #bioperl
15:29 deafferret He removed my last really good excuse for not patching things a lot...  -sigh-
15:29 deafferret jerk
15:30 deafferret now it's on me.  ME!! Can you imagine that? oh, the humanity
15:40 * rbuels hands deafferret a hankie
15:52 * deafferret grumbles something about 'stupid open source' and 'dont have time to solve my own problems'
15:53 * deafferret and 'my Oracle VAR doesn't pull this stupid 'patches welcome' crap'
15:53 deafferret </acting>
16:01 faceface anyone know the status of GFF3 code review?
16:01 faceface I remember banging my head against this
16:01 faceface but I forgot my conclusions
16:02 rbuels faceface: heh.
16:02 rbuels i think the status of gff3 code review is 'stalled'
16:03 rbuels both me and chris are interested in fixing it
16:03 rbuels and it sounds like you are too
16:03 faceface yup
16:03 faceface how are you?
16:04 rbuels heh fine.  karaoke last night, was pretty fun.
16:04 * rbuels is a karaoke fiend
16:04 faceface nice
16:05 rbuels with the gff3 stuff, i think there are some bioperl bugs, and a few wiki pages that chris wrote
16:05 rbuels but nothing much has been done
16:05 faceface iirc the problem was the variety of different modules that output gff2/3
16:06 rbuels well, that, and the fact that Bio::SeqFeature::Annotated is yucky
16:06 rbuels i don't remember all the details
16:06 * rbuels looks
16:06 faceface I'll look over chris's pages... and his pages' comments... <- did I do that right?
16:07 * faceface lools
16:07 rbuels yeah i think that's right.  but the lool part is not right.  lol
16:07 faceface awesome!
16:08 rbuels although, deafferret sometime lools.
16:08 rbuels i saw him do it once.  not a pretty site.
16:08 * rbuels shudders
16:08 faceface I think its just cool with extral  ool
16:09 rbuels chris had a good idea for the refactor...
16:09 rbuels i'm trying to find what it was
16:12 rbuels http://www.bioperl.org/wiki/GFF_Refactor seems to be a good hub page for this, it has links to everything i remember
16:13 faceface yup
16:13 faceface I'm really missing a nice summary diagram of the class inheritance hierarcy in BioPerl
16:14 rbuels i'm not sure if one could draw one and have it be useful
16:14 rbuels it's such a mess
16:14 rbuels there are a couple of scripts in maintenance/ that try to i think
16:15 faceface yeah, but that's info overload... I just want the 'core' modules
16:15 faceface ;-)
16:15 faceface but you can guess what I mean
16:15 rbuels yeah
16:17 rbuels i need about 3 more of me, i think
16:17 faceface me too, and me
16:17 faceface I mean 3 more you + 3 more me
16:18 faceface for synteny, I've just been using blast, but I get the feeling I should be using blat or similar, and/or 'diagonalizing' the HSPs somehow
16:18 rbuels does maj's tiling thing have anything to offer there?
16:19 faceface no, not if I understand correctly what we discussed on the issue
16:19 rbuels i've never had to do large-scale synteny
16:19 faceface me either... I'm hoping that looking at the HSPs will be enough in the first instance
16:20 rbuels there's probably a lot of tweaking of the params that can be done to get bigger, longer alignments
16:20 rbuels a big word size comes to mind
16:20 rbuels if you're doing blast
16:21 faceface right
16:21 rbuels but that's about as far as my tweaking-alignment-tools prowess goes
16:21 rbuels heh
16:21 faceface I asked the list and they said 'use those in the orily blast book'... I bet that's around here somewhere
16:21 rbuels hmmmm
16:22 rbuels if you want to start poking at gff3-related things, you don't have to wait for a commit bit
16:23 * deafferret lools
16:23 rbuels eeewww
16:23 faceface Gah!
16:23 rbuels we could do a git mirror of bp again or something
16:23 faceface right.
16:24 faceface I'll need to look at the code before I can work out if I can do anything constructive though
16:24 * deafferret chuckles, loolily
16:30 rbuels hmm well here's a new git of the repos: http://github.com/rbuels/bioperl-live/tree/master
16:30 rbuels feel free to play and piggyback on my commit bit
16:30 faceface I see
16:31 rbuels oh, it's still uploading
16:31 rbuels it'll be done in a sec
16:31 faceface don't worry, I'm not that quick!
16:32 faceface also, I only just started to feel confident with svn...
16:32 rbuels lol
16:32 faceface now I need to git myself up to speed
16:32 rbuels git is great.  so much rope.
16:33 rbuels i hang myself regularly
16:33 faceface I love rope
16:34 deafferret mmmm distributed rope w/ rebasing grease
16:34 deafferret s/grease/spikes/
16:34 rbuels well if you feel like cloning and playing with that git repo, feel free, and anything you do can be percolated into the bioperl svn when it's ready
16:34 faceface thanks rbuels
16:35 rbuels i'm gonna go get some food
16:35 faceface I'm wondering now if I should create GFF after tiling, so it may be that I start playing
16:35 rbuels food &
16:36 faceface I still think that should mean your not gone
16:36 faceface food > /dev/canteen
16:36 faceface then we know your away ;-)
16:36 deafferret -bash: food: command not found
16:36 deafferret [1]+  Exit 127                food
16:37 faceface /usr/local/bin.food ?
17:11 faceface rbuels: for the time being I'm using bp_seqfeature_load.pl
17:11 faceface it needs some better defaults, but it can be fixed using the command line
17:12 faceface btw, about your git hub... will you check it out to directory blah, svn update on that version, then check in the latest svn version? Just tring to immagine how the two systems will be combined
17:12 faceface or is bioperl-live already in git?
17:13 faceface if these are some basic git concepts, just slap me
17:13 rbuels well, github uses git, not svn
17:13 deafferret rbuels has ... oh, nm. he's back
17:13 deafferret quick eater
17:13 deafferret num num num
17:14 rbuels i'm actually on the wireless at the pizza place
17:14 rbuels lol
17:14 deafferret really??   NERD!!!
17:14 faceface nice!
17:14 rbuels if you 'check out' the github repo, and do stuff in it
17:14 rbuels and then check things in,
17:14 faceface .. chomp ..
17:14 rbuels i can get those changes pretty easily and put them into the bioperl svn
17:14 rbuels lol
17:14 * deafferret chokes on the wrong lingo usage
17:15 * rbuels wipes grease off of his keyboard
17:15 faceface ok, but if the SVN changes while I'm changing the git ...
17:15 rbuels scott cain is _really_ bad about eating at the computer
17:15 rbuels faceface: if somebody does something in svn that conflicts with what you're doing, it may need to be resolved
17:15 faceface er... like how will those svn changes get synced with your git repo?
17:15 rbuels but there are tools that help with resolving
17:16 rbuels faceface: i wasn't planning on pulling any of the changes into it, unless it becomes clear that it's really needed
17:16 faceface rbuels: right, thats standard repo stuff, but the repo I'm working against isn't the repo that is 'live' right?
17:16 rbuels no it's not
17:16 rbuels it's a mirror
17:16 rbuels i made it using a tool called git-svn
17:16 faceface but how is it mirrored?
17:16 faceface ahh
17:16 rbuels git svn clone svn+ssh://....
17:17 rbuels makes a git repo that has the same contents as the bioperl svn
17:17 rbuels and it can pull in changes from the svn too
17:17 rbuels and push them out
17:17 faceface so that manages keeping the git repo in step with the primary svn repo?
17:17 faceface cool
17:17 rbuels it can.  i wasn't planning on doing it, but it can, yes
17:17 rbuels in practice, keeping in step and conflicts and all that are not really a problem
17:17 faceface I was wondering if you git repo would have some uber-committer called 'svn changed' or somethign weird like that
17:17 faceface rbuels: right
17:18 faceface np, I was just curious
17:18 faceface btw, bad as in won't eat, or bad as in, eats all the time?
17:18 deafferret as in, accidentally bites his laptop
17:19 rbuels eats all the time.  not bites his laptop.  lol
17:19 faceface we've all been there
17:19 rbuels don't use his keyboard.  lol
17:19 faceface I'd love a kbd I could sponge down!
17:19 deafferret I like smearing some honey on my lappie so it tastes better when I absent mindedly take a nibble of it
17:19 rbuels nom nom
17:19 faceface or put in the washing mahchine...
17:20 * faceface looks at the engraned filth
17:21 * rbuels laughs at faceface's computer's enormous electrical plug
17:32 faceface heh
17:32 faceface is the bioperl wiki working for you guys?
17:33 faceface try an edit
17:33 faceface nm
17:33 faceface works now
17:34 deafferret darn. I was seconds too slow
17:42 faceface sorry
17:42 faceface I checked twice before asking...
17:42 * faceface hides in shame
17:43 perl_splut murphy struck again
17:43 perl_splut asked for help and then it worked before you got an answer
17:43 perl_splut :)
17:44 faceface is module a real namespace on the wiki or just a prefix?
17:44 faceface perl_splut: yup
17:44 faceface like bugs that dissapear once you set up all the debugging code you can think of...
17:45 faceface IT JUST CAN@T NOT BE WORKING... oh ... its working
17:45 faceface seems to be a real namesapce
17:45 faceface space
17:48 faceface rbuels: for the time being I'm using bp_seqfeature_load.pl * correction - I'm using bp_search2gff.pl ! bleah
17:49 rbuels faceface: does that thing actually make good gff3?
18:21 faceface rbuels: I think so
18:21 faceface C04SLm0040B16.1 BLASTN  match_part      57372   58777   1739    -       0       Target=GB028J20 21749 23193;score=1739
18:22 faceface there is one small tidy up required, perl -pi -e 's/Target=Sequence:/Target=/'
18:22 faceface and you need to set --method match_part in order to get the correct method term
18:23 faceface the default is 'similarity', which isn't SO complient
18:23 faceface I'll send you the GFF if you want to play...
18:23 faceface the only other relevant setting is --version 3
18:24 rbuels faceface: not necessary, just idle curiousity
18:24 * faceface idly slaps rbuels about the face
18:24 faceface ;-)
18:24 rbuels lol
18:24 * rbuels pulls deafferret's nose
18:25 rbuels woop woop woop
18:25 rbuels nyuck nyuck
18:25 faceface the --comp feature seems broken
18:25 faceface flag: whether to print a component feature
18:25 faceface generate GFF component fields (chromosome)
18:26 faceface but the result with or without --component is the same
18:26 faceface I'd debug, but I'm lying.
18:34 deafferret If you github'd a little ball of software, complete w/ a little input data, deafferret might clone that and play
18:34 deafferret or I might just work for The Man instead
18:34 deafferret The Man is always keepin' me down!! When they gonna let us white males have a shot at running things?
20:33 faceface tru that
20:33 faceface how do I quit a shell script?
20:33 faceface exit?
20:36 faceface ok, confused by the effect of exit when you source a shell script
20:36 faceface exit is the way to go
20:39 deafferret shutdown -h now         ?
22:28 gwo left #bioperl
22:31 faceface runlevel 3
22:32 deafferret but if you're already at runlevel 3 that won't quit your shell script (I don't think)
22:32 faceface oh... tried to pick a non-existent run level at random...
22:32 faceface runlevel 2?
22:33 gwo joined #bioperl
22:33 * deafferret shrugs. depends on the dist
22:33 * faceface sets 'un-graphical' login
22:43 faceface l8r
22:43 * faceface goes to Gmod conference
22:44 faceface left #bioperl
22:44 deafferret lucky
22:48 gwo joined #bioperl

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