| Time |
S |
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/200[…]-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 gitgithub.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 gitgithub.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/soft[…]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/pr[…].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 |
| 14:56 |
|
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 |
| 15:13 |
|
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/pr[…]ecification.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/Mo[…]e: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/biop[…]/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-gbrowselists.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/c[…]Phone4-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/c[…]Phone4-vs-HTC-Evo |
| 18:51 |
|
deafferret |
in-year-ism |
| 18:52 |
|
deafferret |
ah, here's all 03:28 http://www.youtube.com/watch?v[…]e=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 |
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faceface |
http://gmod.org/wiki/GBrowse_2.0_Install_HOWTO ? |
| 19:01 |
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rbuels |
yes, gmod will be ditching sourceforge and going to github soon. |
| 19:01 |
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rbuels |
for certain values of soon. |
| 19:02 |
|
faceface |
bounded? |
| 19:02 |
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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 |
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deafferret |
git is SO easy! ask faceface! |
| 19:09 |
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| 19:26 |
|
faceface |
deafferret: did you work out why my repo was showing no changes wrt origin/master? |
| 19:26 |
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faceface |
(git) ;-) |
| 19:27 |
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deafferret |
faceface: nope... want to pinpoint something that you think for sure you have done? |
| 19:28 |
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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 |
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| 22:40 |
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| 22:40 |
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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 |
