Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-06-15

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All times shown according to UTC.

Time Nick Message
00:09 brandi joined #bioperl
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01:38 deafferret :)
02:45 dnewkirk Is a week too long a time frame for script to run? :p
03:20 CIA-94 biome: Chris Fields cleanup_seqfeature * r580fce5 / (7 files in 5 dirs): first pass. pushing methods back into roles for possible use in SFs - http://bit.ly/9bbIpN
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08:30 vinnana joined #bioperl
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09:50 roibrodo I have a newbies question. I have downloaded some large RefSeq files (Genbank format, i.e. both sequence and annotations; e.g. http://www.ncbi.nlm.nih.gov/nuccore/NC_002945. I want to get a part of that sequence along with its annotations - exactly as I do online using the "Change region shown" window on the right - then dump this as a (smaller) Genbank file. Very simple... but I couldn't figure out how to do that.
09:51 XaeroOne joined #bioperl
10:16 vinnana roibrodo: I am not sure but you could try seqret from the emboss package
10:44 roibrodo vinnanaL thanks, but I think it only returns the sequence (without the features)
10:45 brandi joined #bioperl
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11:46 vinnana roibrodo: Nope - it works! try `seqret -sformat1 embl -sequence yourfile.embl -sbegin 10000 -send 50000 -feature -outseq out.embl -osformat2 embl`
11:58 brandi joined #bioperl
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12:47 roibrodo Thanks!
12:47 roibrodo vinnana: thanks! I missed th '-feature'
12:49 faceface Jason Stajich is now connected to C. Robin Buell ??
12:52 XaeroOne joined #bioperl
15:14 CIA-94 biome: Chris Fields cleanup_seqfeature * r70bed66 / (2 files in 2 dirs): type munging - http://bit.ly/9BqH4c
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16:04 nuba joined #bioperl
16:27 deafferret .oo.O.
16:39 * rbuels pokes deafferret to check if his irc connection is working
16:41 deafferret ow. quit it
16:43 deafferret rbuels: you like my Root clone()?
16:43 deafferret it's a spicy meatball
16:43 * rbuels just got back from "vacation", is not up to speed yet
16:43 * rbuels in other words has no idea what you are talking about
16:43 rbuels but here's a bunny with a pancake on its head.
16:44 deafferret where?
16:44 deafferret <.<     >.>
16:44 deafferret O_O
16:44 deafferret hareitic
16:47 rbuels omg.
16:47 * rbuels throws up a little
16:55 * deafferret sends his puke pup on a cleanup run
16:59 deafferret rbuels: excited for YAPC??   /me squeals like a tween at a Beatles concert
16:59 rbuels deafferret: i'm not going.  :-(
16:59 deafferret rbuels: we gonna cleave off some bio.........  what what what??!?
16:59 deafferret YOU LIED TO ME
17:00 rbuels well, i thought i was telling the truth at the time ...
17:00 deafferret http://bioperl.org/wiki/YAPC   !!!
17:00 * rbuels shifts uncomfortably in his seat
17:00 deafferret oh, damn. your fingerprints aren't on here   http://bioperl.org/w/index.php​?title=YAPC&amp;action=history
17:00 deafferret I was so gonna get you the chair
17:00 deafferret CSI FAIL
17:00 * rbuels covers his bases
17:01 * deafferret drinks rbuels' half of the Mexico trip tequila in a crying rage
17:02 * deafferret trashes the place
17:02 * deafferret has been watching too much 'Rescue Me'
17:03 deafferret http://bioperl.org/wiki/YAPC
17:11 rbuels :-(
17:19 deafferret you've forced me to forgo the bioperl hackathon and enslave myself to the moose hackathon
17:19 deafferret next time, think of the children
18:18 * perl_splut shoots all the children dead so he doesn't have to think about them *
18:18 CIA-94 biome: Chris Fields cleanup_seqfeature * r74f6946 / (6 files in 5 dirs):
18:18 CIA-94 biome: move Range to SimpleRange (same for role implementation). Class does
18:18 CIA-94 biome: abstract interface Does_Range - http://bit.ly/9UekPr
18:18 CIA-94 biome: Chris Fields cleanup_seqfeature * r6001b2f / (4 files in 2 dirs): add abstract roles - http://bit.ly/a8K28o
18:18 CIA-94 biome: Chris Fields cleanup_seqfeature * rb9ad89e / (28 files in 9 dirs):
18:18 CIA-94 biome: move older Location implementation to unimplemented, and Segment to
18:18 CIA-94 biome: Location - http://bit.ly/aA8Sl7
18:22 deafferret oh dear.
18:26 CIA-94 biome: Chris Fields cleanup_seqfeature * r0c29b2c / (3 files in 3 dirs): move simple Range implementation into similar base path as for the role - http://bit.ly/cCp21Q
18:32 deafferret CIA-94: knock it off with the r already
18:37 pyrimidine joined #bioperl
18:56 pyrimidine now I'm a superop
19:28 dave_messina joined #bioperl
19:29 dave_messina hola amigos
19:30 * deafferret waves
19:30 CIA-94 biome: Chris Fields cleanup_seqfeature * r0a944bd / (6 files in 3 dirs): move types Segment->Location - http://bit.ly/8YsncS
19:31 CIA-94 biome: Chris Fields cleanup_seqfeature * r097c83b / (8 files in 5 dirs): get Simple locations working again - http://bit.ly/aJL6PH
19:31 pyrimidine kaboom
19:31 deafferret hmm... should I merge my topic/jhannah-seqfeature-clone  ?
19:31 deafferret to master?
19:32 deafferret before rbuels reads it and destroys me?
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19:32 dave_messina if'n you ran the test suite and nothing broke, I think you can go for it
19:32 pyrimidine sure, why not?
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19:33 deafferret I was just being cautious since it's Root.pm. No additional tests broke anywhere after my changes, according to my laptop
19:33 pyrimidine meh.  If it breaks we can revert.
19:33 deafferret branches are for sissies
19:34 pyrimidine exactly
19:34 dave_messina Yeah, but you're adding a new method to Root, not changing an existing one, so it should be a-ok.
19:34 deafferret oh... so that's how git svn info works.  boo.
19:35 pyrimidine and, if anyone needs to override it just reimplement clone in that class
19:36 deafferret ya. <ghetto attitude>if ya dont like my clone(), use your own, sucka!</>
19:37 dave_messina or I'll bust a cap in yo class.
19:37 deafferret word
19:38 dave_messina suh-weeT!
19:38 dave_messina :)
19:38 pyrimidine :)
19:38 deafferret dave_messina: keep it real
19:38 deafferret oh, snap!
19:39 was kicked by deafferret: pyrimidine
19:39 pyrimidine joined #bioperl
19:39 deafferret :)
19:39 pyrimidine :-D
19:39 * deafferret flashes gang signs to ChanServ
19:42 CIA-94 bioperl-live: Jay Hannah master * rea368af / (Bio/Root/Root.pm t/SeqFeature/Clone.t):
19:42 CIA-94 bioperl-live: Added Bio::Root::Root clone() (which uses Storable dclone()) so
19:42 CIA-94 bioperl-live: I can clone Bio::SeqFeature::Generic objects. Or anything else,
19:42 CIA-94 bioperl-live: for that matter(?). t/SeqFeature/Clone.t seems happy so far. - http://bit.ly/coZIlE
19:45 deafferret huh. I gotta learn to relax and love the git
19:45 deafferret it freaks me out that I delete remote branches and that's not an event in history
19:45 deafferret i assume it's in a github server log somewhere that we don't have access to  :(
19:45 deafferret svn++
19:45 perl_splut heheh
19:46 perl_splut I really should spend a bit of time and learn it
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19:47 deafferret huh. gitX doesn't show my branch at all, it looks like everything I did was master  :/
19:47 deafferret voodoo
20:00 deafferret oh! git tracks Date vs. Commit Date
20:00 deafferret wow
20:00 deafferret naama most recent patch was date: may 23, commit date: yesterday
20:00 * deafferret boggles
20:07 pyrimidine did you rebase your commit?  Would explain it.
20:10 pyrimidine BTW, before I go: http://www.bioperl.org/wiki/Usin​g_Git#Processing_a_Pull_Request
20:12 deafferret rebasing explains an entire branch not showing up in history at all?
20:12 deafferret cause it makes parent HEAD^ ?
20:13 pyrimidine I think so.
20:13 pyrimidine Still wrapping my head around it, though.
20:13 * deafferret is still failing that wrap
20:14 rbuels pyrimidine: i would have merged naama's commit a while ago, but i was being a fascist and asked her to add a test or two.  but she never did.
20:15 rbuels pyrimidine: so i hit her with a ball-peen hammer, and i guess that made her mad and she went to you.
20:15 * rbuels shrugs
20:15 rbuels some people.
20:15 deafferret naama++ # calling rbuels' bluff
20:16 deafferret how hard is it to add   pass("make rbuels happy");   ??
20:16 pyrimidine gotta go.  rbuels, we can revert that if needed, didn't wvwn realize there weren't tests attached.
20:16 pyrimidine *even
20:16 * deafferret revoked pyrimidine's commit bit
20:16 deafferret s
20:16 deafferret damn
20:19 CIA-94 biome: Chris Fields cleanup_seqfeature * r7b32fb4 / (4 files in 3 dirs): some last-minute fixes for the day - http://bit.ly/cGZvsL
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20:53 pgc joined #bioperl
20:53 pgc hi
20:53 pgc my first time here
20:53 * deafferret waves
20:57 dave_messina kblin: you there?
21:02 kblin dave_messina: yeah
21:02 kblin just got back :)
21:02 dave_messina ah good timing! :)
21:02 dave_messina so, we were trying to "get" rebasing.
21:03 dave_messina does rebasing hide or remove a branch because you're replaying the branches commit on the master?
21:03 kblin not quite
21:03 deafferret rebase makes the parent of my branch HEAD^ ?
21:05 kblin hang on...
21:07 * kblin draws some ascii art
21:13 kblin http://gist.github.com/439745
21:16 deafferret oh...wow
21:16 deafferret kblin++
21:17 kblin the second step is in brackets because it's actually not necessary. it just helps me to pretend that's how the fast-forward works
21:17 deafferret straight line, right?  -------------A-----------B--------X
21:17 * deafferret did not realize it was that history-rewritey
21:17 kblin yeah, technically in the last step you could draw it as a straight line
21:18 kblin it rewrites the history, so all the sha1s change
21:18 deafferret git seems cavelier about history munging  :)
21:18 deafferret "nope, that was never a branch. stop asking"  :)
21:19 deafferret the sha1 is a checksum of all files + the parent?
21:19 deafferret (why do all the sha1s change?)
21:19 deafferret YOU CAN'T HANDLE THE TRUTH
21:21 kblin deafferret: I think it's a bit more complicated than that
21:21 kblin it's the current tree, the parent tree and the commit message
21:22 kblin and if you rebase, the parent tree changes
21:23 kblin anyway, the really cool part about the rebae is the following scenario...
21:23 * kblin draws some more ascii art
21:24 * deafferret boggles
21:29 kblin http://gist.github.com/439745​#file_git_rebase_cherry_pick.txt
21:31 kblin note that this assumes Y wasn't changed during the cherry pick, or the rebase might stop and ask you to resolve conflicts manually
21:31 kblin but if you do a plain cherry-pick, this just works
21:31 kblin even though the sha1sums of the two Y commits are different
21:32 deafferret wow
21:33 kblin and again, technically the history is linear after the rebase
21:53 kblin ok, hope that helps, just caught a SIGGF :)
21:53 kblin see you tomorrow.
21:53 deafferret kblin++
21:53 deafferret haha
22:00 deafferret oh. I thought kblin was leaving so would immediately lose his +o  :)
22:00 dave_messina heh :)
22:00 dave_messina kblin: sorry to go quiet — had a local distraction.
22:01 dave_messina kblin: thanks so much for the explanation! that helps a lot.
22:01 dave_messina damn, he's away.
22:01 dave_messina ah well, I'll ask it anyway:
22:03 dave_messina kblin: I though one of the purposes of branching was to keep a group of commits together, so that even after merging they could be reverted as a unit
22:03 deafferret dave_messina++
22:03 dave_messina but if we're replaying commits ont he branch, and out of order, then aren't we losing that 'branch as a unit' ??
22:03 dave_messina oops, lemme try that again.
22:04 dave_messina but if we're replaying commits on the master, and potentially out of order if we've cherry-picked, then aren't we losing that 'branch as a unit' ?
22:05 * dave_messina will tune in tomorrow night for the exciting conclusion
22:16 * rbuels branches deafferret's unit
22:17 dave_messina ha!
22:17 * dave_messina giggles
22:53 deafferret rbuels: you sir, have lost "deafferret's unit" priviledges on account of your hareisy
22:53 * rbuels slaps his forehead
22:54 deafferret git checkout -b topic/large-wooden-badger
22:54 * deafferret already forgot how rabbits got connected to YAPC-FAIL, but I know they are somehow
22:54 deafferret tradition++
22:55 deafferret oh yes, noidea.jpg
22:55 deafferret + what what what ?!?!?!
22:55 * deafferret recalls totally
22:55 rbuels no, it was + some kind of root cloning claptrap
22:55 rbuels and you asked me what i was talking about
22:55 rbuels but, you did call it hareisy.
22:55 rbuels because of noidea.jpg.
22:55 rbuels or something
22:56 * rbuels wonders why he is spending time on this
22:56 deafferret rbuels: your silly little opinion has been noted.
22:56 rbuels lol
22:56 * deafferret wonders who's going to fall out of his chair repeatedly in Columbus
22:56 * deafferret sighs
22:58 deafferret ha! one less op to interfere with my dastardly plans
23:05 * deafferret plans additional dastardidlies

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