Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-07-13

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All times shown according to UTC.

Time Nick Message
01:36 dnewkirk left #bioperl
05:58 bag joined #bioperl
10:21 deafferret :)   I meant no offense to anyone's chosen critters. My mentor was saying "wtf? where are all the comparitive assemblies? only one of each of these animals exist???"
10:22 deafferret I'm patiently waiting for someone to say: "here, download 122 different nemotode assemblies from this FTP site"
10:22 deafferret but apparently, there's no such thing, in any animal
10:26 * deafferret starts using the term 'lifeform' to avoid hurting anyone's feelings
10:26 deafferret and/or incurring their wrath
10:38 faceface deafferret: there are related species for fly
10:38 faceface 12 drosophila genomes
10:39 faceface deafferret: but the community doesn't tend to be happy when you turn round and say "hey, it's so important we assembled it twice!"
10:40 faceface also, there are like 1000 human assemblies
10:40 faceface so... why does Bio::FeatureIO::GFF have a new method, and my new module, Bio::FeatureIO::AGP not have one?
10:40 faceface anyone?
10:43 faceface is it lurking in Bio::FeatureIO?
10:44 faceface return "Bio::FeatureIO::$format"->new(@args);
10:59 faceface package Bio::FeatureIO::agp; # :-D
11:00 faceface deafferret: want a contributor listing :P
11:56 deafferret faceface: where can I get my hands on these 1000 human assemblies?
11:57 deafferret I would think new() would get inherited from somewhere
11:57 deafferret it certainly would in biome  :)
11:57 deafferret if you want I can stare at those classes specifically
12:12 faceface deafferret: my Bio/FeatureIO/agp.pm had "package Bio::FeatureIO::gff;" set (my bad)
12:12 faceface works now
12:14 faceface deafferret: 1000 genomes is here ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/
12:14 faceface but I'm not saying which one is me ;-)
12:14 deafferret RLY?
12:15 faceface I wish
12:15 faceface instead of downloading the data, its easier to run a kernel image on the cloud
12:15 faceface (where the data is)
12:16 * deafferret stares blankly at faceface
12:16 faceface just say the word 'cloud'
12:16 deafferret c...   clowd
12:17 * faceface gives deafferret a pay rise
12:17 deafferret there's a farm somewhere that lets me launch server instances?
12:17 deafferret with fiber to all that data?
12:17 * deafferret drools a little
12:17 faceface according to the hype, yes there is
12:18 faceface however, ... I'm not sure where it is really...
12:18 faceface clearly, downloading all that data is going to be a pain
12:18 faceface uploading your kernel is much more sensible
12:18 deafferret wget -r, walk away  :)
12:19 * deafferret seeks out a website containing this 'upload your kernel' rumor
12:19 faceface eta 3:45:9:10:30
12:19 faceface just google cloud
12:19 faceface amazon cloud
12:20 faceface literally.... the book seller!
12:20 * faceface implements torrentfs
12:20 deafferret uh... what? I'm familiar with Amazon EC2 and such. But I need specific information about hooking whatever cloud service has these 1000 genomes sitting wherever they're sitting
12:21 faceface ic
12:21 faceface not sure where that rumor started, but I'd email them if you can't find nuffin
12:22 faceface also, I'd download one to check if it's what you need ;-)
12:25 deafferret um... I've found 3 articles spreading the AWS (Amazon Web Services) rumor, but zero hard information about it
12:25 faceface deafferret: can you help me with testing?
12:26 faceface deafferret: you don't get pay rises for hard information
12:26 deafferret faceface: um sure? what's up?
12:26 deafferret pay? who gets paid in this field?
12:26 faceface I wrote a new Bio::FeatureIO format, and there are 3 'example' files on the website describing the format
12:26 faceface heheh
12:26 faceface where shoudl I put those files?
12:27 faceface (so I can test the parser on them)
12:27 faceface also, are you a git?
12:27 deafferret what website? sticking everything in github would be a huge boon to my productivity
12:27 faceface I mean, do you grok git?
12:27 deafferret yessir
12:28 deafferret sufficiently to do serious damage anyway
12:28 faceface OK, I forked bioperl-live, and I even seem to have 'pushed' a commit onto my fork...
12:28 faceface cool
12:28 faceface http://github.com/dbolser/bioperl-live
12:29 faceface deafferret: but that happened more as a result of me blindly pushing buttons rather than a coordinated attempt to get something specific done...
12:29 faceface deafferret: can you help me push my new file onto that site?
12:30 faceface or pull from the origin/master first?
12:30 deafferret um...   git add newfile; git commit; git push  ?
12:30 faceface or should I rebase? do I status my hub tag?
12:30 faceface gaaa!
12:30 * faceface opens a new terminal
12:30 deafferret step 1: deep breath
12:30 deafferret step 2: pick a question, ask it
12:31 faceface ok
12:31 faceface within the bioperl-live directory (under git) I hit 'git status' and itsays  On branch master
12:32 faceface ...
12:32 faceface but is that the bioperl bioperl, dbolser's bioperl, or my local repo?
12:32 deafferret git remote -v
12:32 faceface origin  git://github.com/bioperl/bioperl-live.git
12:33 deafferret so your local is your local, and 'origin' is bioperl/bioperl
12:33 faceface http://pastebin.com/Y8yQjjJ7
12:33 faceface IC
12:33 faceface so I want to 1) pull from bioperl/bioperl (so I'm up to date) then push to dbolser/bioperl, so you can see my work
12:34 * deafferret blinks
12:34 deafferret how out of date is dbolser/bioperl ?
12:34 faceface 1 day
12:35 faceface git add Bio/FeatureIO/agp.pm # ?
12:35 deafferret remote add dbolser git://github.com/dbolser/bioperl-live.git
12:35 deafferret git commit; git push dbolser master;
12:35 deafferret I think
12:35 faceface deafferret: that adds dbolser/bioperl to the list of things that I'm tracking in this local repo?
12:35 * deafferret blinks
12:36 faceface remote add dbolser ...
12:36 faceface Because I think I did that already
12:36 deafferret git remote -v lists it already?
12:37 faceface more .git/config
12:37 faceface no
12:37 deafferret so git add remote ...
12:37 faceface ty
12:38 faceface just trying to commit 'git remote -v' to memory...
12:38 deafferret you can have 20 remotes. git isn't really "tracking" any of it, they are just different spots for pull/push
12:38 deafferret each attempt to pull/push from any of those 20 will succeed or fail on it's own merits
12:39 faceface IC
12:39 faceface can't I have more?
12:39 faceface ;-)
12:39 faceface OK, so git commit is now going to add my recent changes to dbolser/bioperl?
12:40 faceface or is it going to commit them locally?
12:40 faceface and should I git add "Bio/FeatureIO/agp.pm"?
12:40 deafferret http://gist.github.com/473797
12:41 deafferret git commit is local
12:41 deafferret push / pull take changes to/from local to whatever remote you specify
12:41 deafferret commit is always local only
12:42 faceface mine just says ++
12:42 faceface sorry
12:42 faceface I meant to say "++"
12:42 deafferret git --version   should be 1.7.1
12:42 deafferret or higher
12:42 faceface mine just says http://pastebin.com/EYJSKCN6
12:42 faceface git version 1.5.5.6
12:42 faceface Yay!!
12:42 deafferret eww
12:42 faceface er...
12:43 faceface lets struggle on shall we... me hits git commit
12:43 faceface no changes added to commit (use "git add" and/or "git commit -a")
12:43 * deafferret strongly recommends a client update
12:43 deafferret yup
12:43 faceface because I didn't get these files ready to commit yet?
12:43 deafferret yup
12:43 faceface wait... what was the first yup for?
12:44 deafferret http://zrusin.blogspot.com/2​007/09/git-cheat-sheet.html
12:44 brandi joined #bioperl
12:45 brandi left #bioperl
12:45 faceface ty
12:45 deafferret hmm... the "commands sequence" doesn't show 'git add'
12:45 deafferret pretend it's there  :)
12:45 deafferret or   git commit -a    which says "commit all"
12:45 faceface how do I 'stage' a modified file?
12:46 faceface git add?
12:46 deafferret yup
12:46 deafferret or commit -a   which does add for you
12:46 faceface OK, looking for a different command when it wasn't really added
12:46 deafferret git is easy!     ;)
12:46 faceface yeah, I don't want to submit the changes I made to Bio/DB/SeqFeature/Store/DBI/mysql.pm
12:47 deafferret git commit --interactive
12:47 faceface what about 'git commit -a --interactive'?
12:47 deafferret "by using the --interactive switch with the commit command to decide one by one which files should be part of the commit, before finalizing the operation. Currently, this is done by invoking git add --interactive. "
12:48 faceface or does the latter imply the former
12:48 deafferret yes, it does
12:48 deafferret --interactive and -a are just short cuts to save you some time
12:48 deafferret I usually just copy/paste the ones I want and git add them all
12:48 deafferret -shrug-
12:49 faceface oops
12:49 faceface I have a modified version of a file that I think was patched by someone already
12:50 faceface I'm writing the commit message now...
12:50 faceface what should I do?
12:50 deafferret that's fine, your change will merge into theirs
12:50 faceface I hope...
12:50 deafferret unless you both changed the same lines, in which case it'll conflict and you can fix it
12:51 deafferret I've heard git makes conflicts pretty easy
12:51 faceface I think they just applied my patch
12:51 faceface but IDK
12:51 deafferret git'll figure that out and do the right thing then
12:51 deafferret (the right thing being nothing)
12:52 faceface right, now it's time to "git push dbolser master" ... does that mean update the HEAD branch on remote dbolser?
12:54 faceface deafferret: you got me to set up a RO vsn of my remote repo :.....(
12:55 faceface git remote add git@github.com:dbolser/bioperl-live.git
12:56 faceface fail
12:57 faceface http://pastebin.com/KK7xBiL1
12:58 brandi joined #bioperl
12:59 deafferret git remote delete dbolser
12:59 deafferret then go to  http://github.com/dbolser/bioperl-live   and use whatever 'Git' URL is there (read/write)
13:00 deafferret then push again
13:00 deafferret git remote add git@github.com:dbolser/bioperl-live.git
13:00 deafferret sorry about that
13:01 deafferret it's whatever branch you're on (master)
13:02 Levi_ joined #bioperl
13:02 faceface I did that
13:02 faceface git remote rm dbolser
13:03 faceface git remote add dbolser git@github.com:dbolser/bioperl-live.git
13:03 deafferret ya, sorry. multitasking and failing
13:03 faceface np
13:03 deafferret FAILING!!!!
13:03 * deafferret sobs
13:03 faceface git push dbolser master ... wny not git push dbolser
13:03 deafferret I found your genome. it's the 743rd one
13:03 * faceface consoles
13:03 faceface nooooooooooooo
13:04 faceface master -> master (non-fast forward)
13:04 deafferret um, git has a jillion defaults that may or may not work depending on your config and what version of the client you're running
13:04 deafferret if you find a shortcut, great
13:04 faceface ahhh....
13:04 deafferret so if you don't say 'master' that probably defaults to whatever your current branch is
13:04 faceface ic
13:05 faceface git branch says * master
13:05 deafferret git branch -a    for fun
13:06 faceface are these local branches from the clone?
13:06 faceface I'm actually using this live via a symlink in my perl5/lib
13:07 faceface when did bioperl an gbrowse last actually work?
13:07 faceface origin/topic/update-1-6 ?
13:07 deafferret http://gist.github.com/473797
13:08 deafferret huh? My bioperl-live + GBrowse worked fine last week
13:08 faceface do you use mysql database?
13:08 deafferret not for gbrowse, no
13:08 deafferret we don't do any serious gbrowse, just fiddle with it
13:08 faceface that is the it that's broke
13:08 brandi left #bioperl
13:09 faceface is that list of branches... why is your list of branches bigger than mine?
13:09 deafferret from the gist above, all my branches are remotes/   except master    but if I branched locally it would say   mybranch
13:09 deafferret cause I have more remotes
13:09 faceface http://gist.github.com/473818
13:09 faceface IC
13:09 deafferret those are not local branches. they are a list of all branches
13:09 deafferret across all remotes
13:10 deafferret &   rollout   back in a bit
13:10 faceface so any idea why we have ! [rejected]
13:10 faceface tyanks
13:10 faceface for help
13:10 deafferret gist everything so I can see what's going on
13:12 faceface http://gist.github.com/473823
13:13 faceface hrm... I added a comment
13:14 deafferret you need to pull because you're out of date on that file
13:14 faceface right
13:14 faceface seem my comment
13:14 faceface need to merge... reading
13:14 faceface http://www.kernel.org/pub/software/scm/​git/docs/user-manual.html#how-to-merge
13:17 deafferret hmm? merges should just happen automatically...
13:17 faceface http://gist.github.com/473835
13:17 faceface what do conflict tags look like?
13:18 faceface I think I'm in a special state
13:19 deafferret <<<<<<<<<<<<<<<<<<< and >>>>>>>>>>>>>>>>>>>>>
13:19 faceface I don't se em
13:19 deafferret i think. haven't conflicted in git lately
13:19 faceface see em
13:19 faceface something is weirder than a conflict
13:19 faceface OK, I think i just need to revert
13:20 faceface I have a borked edit that I don't want to commit
13:21 faceface feck... I'm confused ;-) Half my edits go down the 'what was I doing' pan... I think this is my unpatched vsn
13:21 faceface lemmy work it out and get back to you
13:30 deafferret :)   this $work[0] rollout is hit and miss, with breaks to stare at your stuff, so whenever you want me to stare again, gist it
13:30 faceface deafferret: just reached a wall ;-)
13:33 faceface deafferret: http://gist.github.com/473865
13:34 deafferret so your local is also behind dbolser?  git pull dbolser?
13:35 faceface sounds hard to believe... but I did make it rw
13:35 faceface http://gist.github.com/473865
13:36 faceface git pull dbolser master
13:36 faceface Merge made by recursive. scripts/bioperl_netinstall.pl |    4 ++-- 1 files changed, 2 insertions(+), 2 deletions(-)
13:37 faceface I see... I modified scripts/bioperl_netinstall.pl and pushed it onto my remote, it was additionally modified in bioperl, and I pulled it locally
13:37 faceface not sure how it didn't get changed locally...
13:38 faceface deafferret: how do I compare a local file to a remote vsn?
13:38 faceface push worked! http://gist.github.com/473877
13:40 faceface heh... someone didn't like my comments on
13:41 faceface bp_seqfeature_load.PLS
13:41 faceface sooo....
13:42 faceface I want to write tests to check the performance of my module against these files http://www.ncbi.nlm.nih.gov/projects/genome/as​sembly/agp/AGP_Specification.shtml#VALIDATION
13:42 faceface where should I put the files in the BP tree, and where should I put the testes?
13:42 faceface tests I mean
13:50 faceface push push
13:50 faceface does this mean that my random hacking will live forever?
13:50 deafferret push it REAL good!
13:51 deafferret amen!
13:54 faceface let me know when you have written tests / refactored my code / written a write method. I'll add you as a contributor ;-)
13:54 * faceface practices being a group leader
14:25 deafferret faceface: git diff origin/master
14:25 deafferret so when I do    git diff dbolser/master    I see your stuff
14:26 deafferret hmm... I prefer   git diff master dbolser/master    actually -- so mine is "left" and yours is "right"
14:28 deafferret ooo   I like git diff --stat
14:29 deafferret http://gist.github.com/473797
14:30 faceface does that mean we are both working on Bio/DB/SeqFeature/Store/DBI/mysql.pm?
14:30 deafferret find t -iname "*gff*"     gives you a feel for what's already out there
14:30 faceface cus I haven't touched Bio/DB/GFF/Adaptor/dbi.pm
14:30 deafferret so your data all goes in t/data and your tests... um
14:31 deafferret i'm probably out of date w/ bioperl/bioperl-live
14:31 faceface oic
14:31 faceface Bioperl is really great on paper
14:32 deafferret http://gist.github.com/473797
14:32 * deafferret slaps faceface
14:32 deafferret GET AHOLD OF YOURSELF MAN
14:32 faceface lol
14:32 deafferret BioPerl is GREAT EVERYWHERE!
14:32 faceface I'm just trying to handle a shed load of featuers
14:33 faceface starting to wish I had just done it not the bioperl way
14:33 deafferret nonononononono
14:33 deafferret don't take the easy way out! suck it up!  :D
14:33 faceface deafferret: but ...
14:33 deafferret did you only change   scripts/bioperl_netinstall.pl    ?
14:33 deafferret or have I screwed something up now?
14:33 deafferret git is easy!
14:33 deafferret :o)
14:34 faceface deafferret: just wondering the same thing
14:34 faceface I have changed a few different things
14:34 deafferret actually bioperl sucks, biome rules
14:34 faceface deafferret: latest 'culture clash' with bioperl :
14:34 faceface http://bioperl.pastebin.com/naQR1MEL
14:34 faceface like... WTF?
14:34 deafferret faceface: you've changes several files?
14:34 faceface JSUT SOTRE MY FETURES!
14:34 faceface deafferret: yes
14:35 deafferret oh? hmm
14:35 faceface building a feature collection from the AGP file
14:35 deafferret have you pushed crap back to bioperl/bioperl-live?
14:35 faceface actually loading a Bio::DB::SeqFeature::Store from the AGP file
14:35 deafferret and by 'crap' I mean your super awesome code
14:35 faceface deafferret: I'm afraid I can't do that dave
14:35 faceface RO
14:35 deafferret oh.. I wonder why my git diff doesn't show those other files then...
14:36 faceface afaikt, all my changes have been pushed to dbolser
14:36 faceface however... netinstall was one thing I changed and pushed yesterday...
14:36 faceface perhaps I haven't pushed what I thought I had?
14:37 deafferret hmm... not sure what this means    # Your branch is ahead of 'origin/master' by 9 commits.
14:37 deafferret since I haven't coded anything
14:38 * faceface slaps deafferret
14:39 faceface http://bioperl.pastebin.com/fBiUEr1K
14:40 faceface stored 59400 features
14:40 deafferret http://gist.github.com/473797
14:41 faceface there are changes there I haven't touched... and I thought I pulled from origin before I pushed to dbolser...
14:41 deafferret huh... well, i re-branched origin/master as master...
14:42 faceface oh rly... er...
14:42 faceface OK, lets agree git is weird and go back to svn?
14:42 deafferret :)
14:42 deafferret DVCS CANNOT BE DENIED
14:43 * deafferret welcomes his new DVCS overlords
14:43 faceface so how do I get a feature by ID?
14:43 deafferret BioRuby?
14:43 faceface get_feature_by_id said I was stupid
14:43 faceface ah, good idea
14:44 * faceface takes a vacation
14:44 deafferret unfortunately, they're in github too. nm
14:44 faceface gitfs
14:44 deafferret *telecommute fail*   need whiteboard and vulcan mind meld to help you
14:44 * deafferret wanders back to $workp0[
14:44 deafferret $work[0]
14:44 faceface gl
14:45 * faceface uses a hash O.O
14:45 Topic for #bioperlis now git is easy!
14:45 Topic for #bioperlis now http://bioperl.org/wiki/IRC#Getting_help | http://www.bioperl.org/wiki/Using_Git
14:45 faceface /topic USE A HASH!
14:46 deafferret NONONONONO  use Moose::Meta::Attribute::Native::Trait::Hash;
14:46 deafferret Moose is easy!
14:46 * faceface wimpers
14:47 deafferret rofl
14:47 * deafferret watches biome growl at faceface
14:48 faceface I had such good intentions
14:49 deafferret "the road to hell..."
14:49 faceface the road to bioperl..."
14:50 faceface can we have a tweet bot in here please?
14:50 deafferret if you've got your stuff up to dbolser then I can clone that and poke around if you're getting stuck
14:50 deafferret faceface: well volunteered!
14:55 bp_tweet_bot_PLS joined #bioperl
14:55 faceface rot13 I don't really work
14:55 bp_tweet_bot_PLS faceface: V qba'g ernyyl jbex
14:56 faceface deafferret: I hope you're happy!
15:01 deafferret if faceface ain't happy, ain't nobody happy
15:12 faceface believe
15:12 faceface rot13 if faceface ain't happy, ain't nobody happy
15:12 bp_tweet_bot_PLS faceface: vs snprsnpr nva'g unccl, nva'g abobql unccl
15:13 faceface seriously though, thanks for gitty help
15:22 ank joined #bioperl
16:57 faceface given two sets of positions and two strands, how do I create an alignment?
16:59 deafferret clustalw?
17:10 faceface sorry, I mean some kind of perl alignment object... basically I want a coordinate converter
17:11 faceface id x, pos 1, pos 2 -> id y, pos 3, pos 4
17:11 * faceface tries bpml
17:16 deafferret well, Bio::AlignIO parses/writes alignments. but it doesn't actually align anything
17:16 faceface where is the sequence name of a feature?
17:16 faceface deafferret: right, thinking I can just create an alignment object and use it's methods
17:16 deafferret "sequence name"  ?? like $seq->description  ?
17:16 deafferret $feat->seq->description?
17:17 deafferret if you create alignments from scratch in pure bioperl please add that to the wiki -- i haven't seen that done
17:17 deafferret (not sure why I'd want that, but...)
17:17 faceface $feat->seq_id(
17:17 faceface deafferret: I did that at one point, but I forget where the code is
17:18 faceface I don't know why I'm so idiotic
17:18 * faceface breaths ;-)
17:18 deafferret nature? nurture?
17:19 faceface hehe
17:19 faceface peer group?
17:20 deafferret ya, you have been hanging out with me *all day*. That can't be good for your IQ
17:24 faceface and you
17:24 faceface we are a bad infludence on each other
17:27 deafferret together, our ignorance and apathy are invincible!
17:34 faceface there has to be a better word than invincible
17:43 deafferret incorrigible?
17:57 pyrimidine joined #bioperl
18:01 faceface how does this look?
18:01 faceface http://bioperl.pastebin.com/enFKkHLb
18:02 faceface line 23 to 32 - coordinate conversion
18:03 pyrimidine what's this for?
18:03 faceface pyrimidine: for some reason I decided to blast against contigs rather than the pseudo-chromosome
18:04 faceface the contig to chr 'mapping' is described in an AGP file:
18:04 faceface http://www.ncbi.nlm.nih.gov/projects/gen​ome/assembly/agp/AGP_Specification.shtml
18:04 pyrimidine right, I'll be peripherally working with those soon
18:04 faceface I've written a new FeatureIO to parse the AGP, which gives me the 'contig' features  on line 6
18:05 pyrimidine but I have an assembled genome that suits my purposes
18:05 pyrimidine oh, ok
18:05 pyrimidine well, you do know that FeatureIO is pretty muched to be scrapped
18:05 pyrimidine *much
18:05 deafferret faceface++ # assembly coordinate systems always fascinate me
18:05 pyrimidine maybe 'scrapped' is too harsh
18:05 faceface so I use the position and strand of the contig to get the HSP in teh context of the chr
18:06 faceface pyrimidine: yeah, but what should I do in the meantime ;-)
18:06 pyrimidine generic parser
18:06 faceface OIC
18:06 pyrimidine Bio::Tools::AGP or somesuch
18:06 faceface but creating features should be ++?
18:07 pyrimidine many of those modules create features
18:07 pyrimidine tRNAscan, etc.
18:07 faceface actually, I want a feature set that supports coordinate conversion methiods
18:07 pyrimidine Bio::Coordinate
18:08 pyrimidine Though I haven't used it much myself, but many use it
18:08 faceface Cool
18:08 faceface ty
18:08 faceface http://www.bioperl.org/wiki/Module:Bio::Coordinate
18:08 deafferret Bio::Coordinate::Socks::Color
18:09 pyrimidine Look in the Bio::Coordinate::* namespace
18:11 faceface pyrimidine: Bio::Coordinate::Utils can be made from a Bio::SimpleAlign
18:11 faceface how would I construct a Bio::SimpleAlign from two sets of coordinates ?
18:12 faceface query_start, query_end, hit_start, hit_end, hit_strand
18:12 pyrimidine If using SearchIO, you can do this via the HSP
18:12 pyrimidine $hsp->get_aln
18:13 faceface sorry, my example was a bit misleading
18:13 faceface my actual coordinates come from an AGP file
18:13 pyrimidine ok
18:13 faceface is Bio::Tools::AGP a good choice for my parser?
18:13 faceface I feel I want to put it in something like SearchIO
18:14 faceface (or FeatureIO)
18:14 pyrimidine FeatureIO isn't a really good choice, IMHO.  AGP describes an assembly (mapping from one coordinate system to another)
18:14 faceface deafferret: I saw that
18:15 faceface right
18:15 pyrimidine so maybe Bio::Assembly::IO
18:15 faceface nice idea
18:15 faceface indeed, it's an assembly format
18:15 pyrimidine have ace, bowtie, tigr, etc there
18:16 faceface cool
18:16 faceface should I make Bio::Coordinate objects within that, or should I build them outside of the 'assemblyu'
18:17 pyrimidine you could possibly use the Bio::Coordinate tools as a helper set of modules to map the coordinates, or do it de novo
18:17 pyrimidine (from scratch)
18:17 faceface I'll do it in-silico
18:17 pyrimidine :)
18:17 faceface ab-initio
18:18 pyrimidine ad hoc
18:18 faceface on the fly
18:18 * pyrimidine waiting for deafferret's response...
18:18 faceface It's only a few lines of code, but in general, coordinate systems are really important, so I want to make it flexible
18:19 pyrimidine the format is pretty simple
18:19 faceface i.e. I think GBrowse should support non-reference coordinate systems
18:19 faceface AGP you mean?
18:19 pyrimidine yes
18:19 faceface here is my parser: http://github.com/dbolser/bioperl-li​ve/blob/master/Bio/FeatureIO/agp.pm
18:19 deafferret pyrimidine: MAKE IT SO!   I mean... what? reponse to what?
18:19 deafferret YELLOW!
18:20 pyrimidine our latin catch-phrase bit above ^^^
18:21 deafferret Catapultam habeo. Nisi pecuniam omnem mihi dabris, ad caput tuum saxum immane mittam.
18:21 faceface pyrimidine: which reminds me, I have one more question: did you see my post to the bp-ml earlier today about Bio/DB/SeqFeature/Store/DBI/mysql.pm
18:21 pyrimidine yes
18:21 deafferret Warnocked!
18:21 faceface any clue why it's borked?
18:21 pyrimidine actually was hoping GMOD crew would anser that
18:21 pyrimidine *answer
18:22 faceface lol
18:22 deafferret rbuels: ^^
18:22 faceface I've had that dilema many times
18:22 faceface I was pretty explicit about it on the bio* list recently
18:22 pyrimidine faceface: let me run local tests here on that to see what happens...
18:22 faceface is this a) too boring, b) too hard, or c) too dumb
18:23 faceface pyrimidine: ty
18:23 rbuels faceface: gbrowse stuff is supposed to go to the gbrowse list?
18:23 rbuels faceface: gmod-gbrowse@lists.sourceforge.net
18:23 rbuels faceface: and then scott will answer you
18:23 deafferret rbuels: YOU are the email gateway dammit!
18:23 faceface rbuels: right, I sent it to bioperl and gbrowse too
18:23 deafferret and lolcatz!
18:23 faceface rbuels: are you going to send me to the naughyt corner in a minute?
18:23 faceface I mean #gmod
18:24 deafferret #mmmmgod
18:24 faceface #gmod-the-god
18:24 rbuels oh.  i bet scott is traveling.
18:24 rbuels which is why he hasn't been hitting the gmod-gbrowse list
18:24 pyrimidine he's at ISMB
18:24 rbuels yep.
18:24 * deafferret grows disillusioned by deafferret's constant failure to take anything seriously in IRC
18:24 pyrimidine just saw him and Lincoln at BOSC
18:24 faceface IC
18:25 pyrimidine there is a GMOD meeting there, I think
18:25 pyrimidine http://gmod.org/wiki/GMOD_News#GMOD_.40_ISMB_2010
18:25 rbuels oh, i had my dates wrong
18:26 faceface rbuels: title 'Difference between "-adaptor memory" and "-adaptor DBI::mysql"' gmod-gbrowse@
18:26 pyrimidine ending today, it seems
18:26 pyrimidine BTW, next year's BOSC is...
18:27 * deafferret submits $work[0] for Most Worthless VC Commit Messages Award
18:27 * pyrimidine makes sound of a drumroll......
18:27 deafferret "bug fix"
18:27 pyrimidine Vienna!
18:27 deafferret "development"
18:27 deafferret "stuff"
18:27 faceface wuh?
18:27 dnewkirk joined #bioperl
18:28 pyrimidine deafferret's rambling, hit the reset button!
18:28 faceface pyrimidine: are you using latest git?
18:28 * faceface does a hard reboot on pyrimidine
18:29 faceface pyrimidine: I'd be really interested to know if it works for you because I kind of need to drive GB from the Mysql
18:29 pyrimidine faceface: are your local SeqFeature::Store MySQL tests passing?
18:29 pyrimidine mine are (latest master branch)
18:29 faceface I didn't run them because last time I tried it refused to believe my host was not localhost
18:29 faceface let me try
18:31 * rbuels is sorry to not be more helpful, but is slammed right now
18:31 faceface rbuels: np, tomato is hard!
18:31 rbuels not as hard as corn, just ask deafferret
18:31 deafferret :)
18:31 pyrimidine just make sure you always chew your corn... oh, sorry TMI
18:32 pyrimidine :)
18:32 deafferret (Korn - Y'all Want A Single?)++
18:32 pyrimidine I can say that 'cause I live in Illinois
18:32 deafferret they should *definately* sequence Korn
18:32 rbuels deafferret: dude, i was cuing you for 'corn is a fucker'
18:32 rbuels deafferret: you are slipping.
18:32 deafferret rbuels: I retired that joke due to YAPC no-show
18:32 pyrimidine cornholio
18:33 rbuels gah.
18:33 pyrimidine hmm, PodSyntax test is failing with Scott's bioperl_install script... investigating
18:34 faceface pyrimidine: Fail http://bioperl.pastebin.com/XgaPUj5W
18:34 pyrimidine ah, but that's BioDBGFF, not Bio::SeqFeature::Store
18:34 faceface still running
18:35 faceface yeah, same testing bug I think:
18:35 faceface i.e. the tests don't work
18:35 faceface not that they fail
18:36 faceface http://bioperl.pastebin.com/FYp2xTbn
18:36 faceface I tried to debug that once, and I'm fairly sure I logged my findings somewhere, but I guess it never got resolved
18:37 deafferret is mysql running?
18:37 faceface sh: -user: command not found
18:37 * faceface slaps deafferret
18:37 faceface yup, its running fine
18:37 faceface on a different server!
18:37 deafferret woop! woop! woop!
18:38 faceface ;-)
18:38 faceface I'll start it locally
18:38 * deafferret poke pyrimidine in the eyeballs
18:38 deafferret s
18:42 faceface seems I can't start mysql locally
18:43 faceface well... I can, but I don't have bioperl installed locally
18:47 faceface deafferret: yup, tests pass fine locally
18:47 faceface of course, I'm not running GB on this install...
18:48 * deafferret needs the bigger GB
18:48 faceface sorry, pyrimidine: yup, tests pass fine locally
18:48 pyrimidine ok
18:48 faceface I can install apache and do the same test as described in the email - my hunch is it will fail teh same
18:49 deafferret HILARIOUS: http://www.entertonement.com/clips/​xtbbzmznjb--Bigger-screen-internet-​faster-iPhone4-iPhone4-vs-HTC-Evo
18:50 faceface have you seen the adds ' you already know how to use it ... its awesome ... its amazingly powerfull ...'
18:51 faceface I want to add ' its a product ... we sell it for money ... '
18:51 deafferret oops... bigger GBs one is this one  http://www.entertonement.com/clips/​xtbbzmznjb--Bigger-screen-internet-​faster-iPhone4-iPhone4-vs-HTC-Evo
18:51 deafferret in-year-ism
18:52 deafferret ah, here's all 03:28  http://www.youtube.com/watch?v=FL7y​D-0pqZg&amp;feature=player_embedded
18:53 faceface is GB in git?
18:55 deafferret GB?
18:55 faceface GBrowse
18:55 faceface svn IC
18:55 faceface I heard scott talking about Git one time
18:56 pyrimidine probably not in a nice way ;-)
18:56 faceface I think he was just asking, 'what can it do and why do I want to do that'
18:56 deafferret http://gmod.org/wiki/GBrowse#SVN
18:57 deafferret sourceforge? wow
18:57 faceface http://gmod.org/wiki/GBrowse_2.0_Install_HOWTO ?
19:01 rbuels yes, gmod will be ditching sourceforge and going to github soon.
19:01 rbuels for certain values of soon.
19:02 faceface bounded?
19:02 rbuels max 1 year.
19:02 rbuels min 3 months
19:03 faceface I once heard about calculation that bounded a certain numerical proof
19:03 faceface the value of the maximum bound was so large, no notation existed that allowed it to be written down
19:03 faceface in physical space
19:03 faceface so the guy had to invent a new notation
19:04 faceface just to write the number down
19:04 faceface later the theorum was solved exactly
19:04 faceface the upper limit was 6
19:04 faceface now I need to configure apache...
19:07 deafferret git is SO easy! ask faceface!
19:09 nuba joined #bioperl
19:26 faceface deafferret: did you work out why my repo was showing no changes wrt origin/master?
19:26 faceface (git) ;-)
19:27 deafferret faceface: nope... want to pinpoint something that you think for sure you have done?
19:28 faceface added a script and this agp parser
19:28 deafferret does your    git diff origin/master master --stat   look how you expect?
19:28 deafferret and/or    git diff dbolser/master origin/master --stat     ?
19:29 deafferret and/or is git status clean?
19:29 deafferret are you on branch 'master' locally?
19:29 deafferret you have several things I don't know  :)
19:29 faceface http://gist.github.com/474367
19:29 faceface yup
19:30 faceface actually... thought scripts/bioperl_netinstall.pl should be the saem
19:30 deafferret if your diff looks like you expect I wouldn't worry about mine -- I'm probably out of date to origin and/or dbolser
19:30 faceface modified:   Bio/FeatureHolderI.pm
19:30 deafferret so diff that one file w/o --stat
19:30 faceface what?
19:31 faceface git -stat diff Bio/FeatureHolderI.pm
19:31 faceface or similar ;-)
19:31 faceface "are you on branch 'master' locally?"
19:31 faceface how do I test?
19:32 faceface how do I find out
19:33 faceface night
19:36 deafferret git branch -a
19:36 deafferret the one with the * is the one you're on
19:36 deafferret oh... or just    git branch    tells you which one you're on
19:37 deafferret git is easy! let's switch it mercurial
19:37 deafferret mercurialhub.com has blinking text!
19:46 dnewkirk you could always use git/murcurial, and whatever else together, with different data in each, and write a bioperl wrapper to pull out the relevent code ;)
19:46 dnewkirk course, then you'd need bioperl first to get bioperl
19:46 dnewkirk :P
19:47 * dnewkirk thinks work has driven him to the state of silly
20:16 deafferret Bio::VCIO is born!
20:22 pyrimidine left #bioperl
21:02 mrek joined #bioperl
21:02 mrek left #bioperl
22:40 bag joined #bioperl
22:40 CIA-95 bioperl-live: Jason Stajich master * r39652b0 / scripts/bioperl_netinstall.pl : fix POD - http://bit.ly/9mIEAd
22:40 CIA-95 bioperl-live: Jason Stajich master * rec09eb3 / scripts/bioperl_netinstall.pl : removed the leading typo - http://bit.ly/b7VJIW

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