Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-11-22

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All times shown according to UTC.

Time Nick Message
04:59 CIA-101 bioperl-live: hyphaltip topic/tree_dbsqlite_memoryfix * rf93dbb4 / Bio/TreeIO/newick.pm : mild formatting - http://bit.ly/bE0rrE
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15:28 paul-in-pgh joined #bioperl
15:28 paul-in-pgh hi all
15:29 paul-in-pgh anybody around to help me fix a Git problem?
15:49 pyrimidine paul-in-pgh: what kind of git problem?
15:49 pyrimidine (only have a couple minutes, btw)
15:50 paul-in-pgh I get this when I do a git status: Your branch and 'origin/master' have diverged,
15:50 paul-in-pgh so when I do a git pull, I get this: fatal: You have not concluded your merge. (MERGE_HEAD exists)
15:51 paul-in-pgh I could just delete my whole 'bioperl-live' and reinstall but would like to learn about how git works
15:51 pyrimidine seems like you ran a 'git pull', which tried to merge remote changes locally
15:51 pyrimidine and it stalled somewhere during that
15:52 pyrimidine (presence of MERGE_HEAD)
15:53 pyrimidine paul-in-pgh: have you tried this? http://www.btaz.com/scm/git/git-fatal-you-hav​e-not-concluded-your-merge-merge_head-exists/
15:54 paul-in-pgh no, but i'll take a look ...ty
15:54 pyrimidine paul-in-pgh: of course, you may just need to commit any local changes (see comments on that page)
15:57 paul-in-pgh it didn't work for me ... oh well, no problem. ...I'm gonna just reinstall
15:57 paul-in-pgh I think I better learn how to make testing branches and do all my local changes there
15:57 paul-in-pgh instead of the master
17:30 dukeleto git pull --rebase is your friend
17:31 pyrimidine agreed
17:35 rbuels unless you don't know what --rebase does.
17:35 rbuels in which case not using --rebase is safer.
17:35 rbuels much safer.
17:40 pyrimidine rbuels: have you been hit by rebase issues?  We
17:40 pyrimidine * haven't
17:40 pyrimidine (knock on wood)
17:59 dukeleto ALL YOUR REBASE ARE BELONG TO US.
18:01 * dbolser is happy to outsource his db needs
18:01 * dbolser goes home
18:50 deafferret pyrimidine: rebase ate your cat?  ;)
18:51 pyrimidine deafferret: :)
18:51 pyrimidine deafferret: but we have more cats, so no prob
18:51 deafferret pyrimidine: do tell your sad, sad tale of woe
18:51 * deafferret grabs some popcorn
18:58 pyrimidine my sad tale of woe, by pyrimidine
18:58 pyrimidine we have lots of cats
18:59 pyrimidine fin
18:59 pyrimidine pulitzer material
18:59 * deafferret posts a scathing review on imdb.com
19:03 * pyrimidine wants his cut of the script payout, bitches
19:03 deafferret how did you know I'm genetically most similar to a female canus domesticus?
19:04 * deafferret rechecks the "privacy" settings on his 18 social networking (aka totally private memoir) services
19:05 pyrimidine hah: http://www.groklaw.net/articl​e.php?story=20101122130625952
19:05 pyrimidine quoting: "selling any patents to Microsoft is like selling your baby to a pedaphile in the limited sense that you can reasonably predict what it will do with the acquisition"
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19:12 deafferret profit?
19:12 deafferret :)
19:16 pyrimidine I don't think anything will come of it
19:17 pyrimidine but a little paranoia isn't bad in this case
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20:35 paul-in-pgh I wrote a 'seq' routine (http://pastebin.com/xmFWBwX8) for Bio::Seq::PrimaryQual.
20:36 paul-in-pgh it is nice to have one so that if you switch your SeqIO scripts to handling 'qual' files, then the 'seq' routine still works
20:36 paul-in-pgh should I send this to the bioperl-l list for comment?
20:44 rbuels paul-in-pgh: i could have sworn there was already something in existence like that ...
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20:44 * rbuels looks around
20:44 paul-in-pgh there is a sub qual but it returns a reference to an array
20:45 paul-in-pgh so I just put a 'seq' wrapper around that
20:47 rbuels paul-in-pgh: i'll just apply it.  no need to go round and round on the mailing list for a small thing like that.
20:48 paul-in-pgh great thanks!
20:52 deafferret rbuels++ # bein' all helpy
20:53 rbuels paul-in-pgh: you are paul cantalupo right?
20:53 * rbuels makes sure the IRC handle matches who he thinks it does
20:54 deafferret rbuels++ # cyber stalking
20:55 pyrimidine paul-in-pgh: pretty much if it's something that's documented to act one way but acts another, there might be a good reason for it
20:55 deafferret ?  isn't that the definition of "a bug" ?
20:55 rbuels heh, in theory
20:56 pyrimidine (e.g. there were implementation issues that weren't documented in the interfaces classes)
20:56 pyrimidine so, yes it's a bug
20:56 pyrimidine but would that be in the documentation or the implementation?
20:57 pyrimidine not sure in this case
20:57 pyrimidine but it's lon been my opinion there are design issues with all the Qual/PrimaryQual things anyway
20:57 pyrimidine *long
20:59 rbuels pyrimidine: basically the thing here is, should you get a space-separated qual string by calling ->seq on a primaryqual object
21:00 rbuels most people would probably expect that, and it's an addition, so ... eh.  apply.
21:00 paul-in-pgh rbuels, yes
21:00 pyrimidine makes sense to me
21:00 paul-in-pgh i'm Paul Cantalupo
21:00 CIA-101 bioperl-live: Robert Buels master * rac16962 / Bio/Seq/PrimaryQual.pm : add seq() method to PrimaryQual, which is similar to the Bio::Seq::Quality qual_text method. patch by Paul Cantalupo. - http://bit.ly/foPEr8
21:00 pyrimidine I also see why it wasn't implemented right away
21:00 rbuels there we go then.
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21:06 paul-in-pgh ty rbuels
21:06 rbuels np
21:19 pyrimidine paul-in-pgh: any reason you needed that implemented?  Serialization?  Just curious.
21:20 paul-in-pgh i have a SeqIO script that has a 'seq' routine so when I switched to reading a 'qual' file, it gave me an error on the 'seq' routine
21:20 paul-in-pgh I shook my head and said that cannot be
21:20 paul-in-pgh it is a "sequence" and therefore should return the sequence of quality values
21:21 paul-in-pgh i expected a seamless transition from one type of sequence file to the next
21:21 paul-in-pgh isn't this a design principle of BioPerl?
21:28 rbuels well, it's not a sequence.  it's actually metadata about a sequence.
21:28 rbuels so that's why, if you are going to be a stickler, you would not call it seq()
21:29 rbuels and that's probably why the seq() method was not originally put in there.
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23:41 pyrimidine yes, what rbuels said
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