Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-05-24

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All times shown according to UTC.

Time Nick Message
02:34 cawiss joined #bioperl
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04:13 barani joined #bioperl
04:14 barani I have firewall problem in bio::biblio . Can anyone help me
04:14 barani I have already posted this in mailing list. got no reply yet..Its quite urgent for me
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13:52 CIA-95 bioperl-live: Chris Fields lstein-seqfeature-store-summaries * rcbed980 / Bio/Tools/EUtilities/Link.pm : small doc fix, more to come - http://bit.ly/cy4DNQ
13:52 CIA-95 bioperl-live: Lincoln Stein lstein-seqfeature-store-summaries * r5539ba3 / (8 files in 4 dirs): Merge branch 'lstein-seqfeature-store-summaries' of git@github.com:bioperl/bioperl-live into lstein-seqfeature-store-summaries - http://bit.ly/angh6X
13:52 CIA-95 bioperl-live: Lincoln Stein lstein-seqfeature-store-summaries * r8095dc7 / (3 files in 2 dirs): Cleaned up summary generation. Can generate summary without doing a load. - http://bit.ly/drxV31
13:52 CIA-95 bioperl-live: Lincoln Stein lstein-seqfeature-store-summaries * re7e42c0 / (6 files in 4 dirs):
13:52 CIA-95 bioperl-live: The Berkeleydb adaptor is now building summary status indexes
13:52 CIA-95 bioperl-live: correctly, and retrieval of summary stats is close, but not
13:52 CIA-95 bioperl-live: quite right. - http://bit.ly/bNP9jN
13:55 CIA-95 bioperl-live: Lincoln Stein topic/lstein-seqfeature-store-summaries * re7e42c0 / (6 files in 4 dirs):
13:55 CIA-95 bioperl-live: The Berkeleydb adaptor is now building summary status indexes
13:55 CIA-95 bioperl-live: correctly, and retrieval of summary stats is close, but not
13:55 CIA-95 bioperl-live: quite right. - http://bit.ly/bNP9jN
14:37 cawiss joined #bioperl
15:31 deafferret ..o..v
15:45 rbuels joined #bioperl
16:14 JunY Hi rbuels
16:15 rbuels JunY: hello
16:17 rbuels JunY: did you add links to your blog?
16:17 JunY yep, I have added link in my blog
16:18 JunY but how can I add link of my blog in bioperl wiki?
16:18 rbuels JunY: same as any wiki.  create an account and edit the page.
16:18 rbuels JunY: this also goes for the open-bio.org wiki
16:19 JunY really? cool... I will try that
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17:09 CIA-95 bioperl-live: Lincoln Stein topic/lstein-seqfeature-store-summaries * r7470ac4 / (2 files in 2 dirs): berkeleydb adaptor generating summary statistics more-or-less correctly; still remain small puzzling discrepancies with output from mysql and sqlite adaptors - http://bit.ly/aXypJU
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21:05 kblin evening folks
21:05 kblin my perl-fu is clearly lacking, but is there a way to run only specified tests?
21:06 rbuels kblin: in bioperl-live?
21:06 kblin yeah
21:06 rbuels kblin: safest:   perl Build.PL; ./Build;  prove -b t/test_i_want.t
21:07 rbuels kblin: but i usually just do prove -I. t/test_i_want.t
21:07 rbuels the build business is only important for pieces of bioperl that need pokey configuration data that the build generates
21:08 rbuels and there are thankfully not too many of those pieces
21:08 kblin well, I've already built it before, now I want to extend the hmmer parser
21:09 kblin given that the guy who seems to have written one but not uploaded it so far doesn't reply and my boss wants me to support hmmer3
21:09 kblin so of course the obvious piece to start is to break the unit test
21:10 rbuels kblin: you know how to use git, and develop on branches?
21:10 rbuels http://www.bioperl.org/wiki/Using_Git if you don't
21:11 deafferret kblin++
21:11 deafferret that dude went poof?
21:11 rbuels which dood
21:12 rbuels and don't call him a poof it's not nice
21:12 deafferret the "here's hmmer3" from March dude
21:12 deafferret rbuels: YOU seem to be the one with a problem with his poof-ness
21:12 * rbuels looks in his list archives
21:12 deafferret rbuels: stop projecting your insecurities
21:12 rbuels no no, my best friend likes cheesy poofs
21:13 deafferret RIGHT, that concludes the reading of the rules.
21:13 deafferret RULE 6: There is NOOOOOOOOoooo....   rule 6.
21:13 deafferret kblin: do try to stay on topic
21:14 rbuels oh, thomas sharpton
21:14 rbuels kblin: he put his stuff in a branch of bioperl-dev
21:14 rbuels wow, now that's conservative.
21:15 deafferret :)
21:15 deafferret are we going to kill bioperl-dev?
21:15 rbuels kblin: http://github.com/bioperl/bio​perl-dev/tree/bioperl-hmmer3
21:15 rbuels deafferret: i iwsh
21:16 deafferret py<TAB> seemed on board with "those should just be branches of bioperl-live"
21:16 rbuels kblin: if you want to build off of that, please move it into a topic/hmmer3 branch of bioperl-live
21:16 kblin sure
21:16 rbuels kblin: if you want to start the hmmer3 stuff from scratch, that's fine too (same branch name)
21:16 deafferret rbuels: how'd you find that?
21:17 rbuels deafferret: i looked in the bioperl-guts commit emails
21:17 rbuels deafferret: searched for 'sharpton' in my thunderbird
21:17 rbuels deafferret: and saw the modified paths
21:17 rbuels deafferret: and then boggled that he put it both in bioperl-dev and in a branch thereof
21:17 deafferret snark snark
21:18 kblin rbuels: I'll have a look at the existing code first
21:19 rbuels kblin: sounds good.  let me know if you have any questions
21:20 kblin sure.
21:21 kblin hm, I wonder, should this be a separate format (as the current hmmer3 parser handles it) or should this be integrated into the hmmer.pm parser?
21:22 rbuels kblin: i don't know anything about hmmer and its formats, but in general if the format is very similar, it should go into hmmer.pm
21:22 deafferret is hmmer3 backwards compatible?
21:22 rbuels kblin: but if it's a big departure from the original format, probably a hmmer3.pm is ok
21:22 kblin I'm just cloning the repo to see the diff of the two files
21:22 kblin they sure look similar
21:23 kblin deafferret: I doubt it
21:24 kblin deafferret: but the parsers for hmmpfam and hmmsearch are in the same module, and those two formats seem to differ more than hmmsearch between hmmer2 and hmmer3
21:24 deafferret if hmmer3 is just hmmer + some stuff, then great, add the code the hmmer.pm. If it's in conflict, then it has to be separate.
21:24 rbuels kblin: sounds a lot like it should just go in hmmer.pm
21:25 deafferret rbuels: not if it conflicts with old files...
21:25 rbuels kblin: if it turns out too hard to shoehorn it in there, can always split it out again
21:25 rbuels deafferret: well of course it needs to still be compatible with the old formats
21:27 kblin sure, but there's tests for that, right? :)
21:27 rbuels kblin: should be ...
21:27 rbuels kblin: i hope.
21:27 * rbuels looks
21:27 kblin there is, I checked :)
21:27 deafferret did sharpton write tests?
21:27 kblin t/SearchIO/hmmer.t has some 116 tests
21:28 kblin yeah, but not integrated into the test architecture for all I can see
21:28 kblin cd ..
21:28 kblin ls
21:28 kblin er
21:29 * rbuels chuckles
21:29 kblin I need focus-follows-brain
21:29 rbuels alias s='cd ..'
21:29 rbuels alias ss='cd ../..'
21:29 rbuels alias sss='cd ../../..'
21:30 rbuels some of my favorite aliases
21:30 rbuels oh, that and alias realias='$EDITOR ~/.bash_aliases; source ~/.bash_aliases'
21:31 * kblin shrugs
21:32 kblin I'd be happy to hit the correct terminal when I click
21:33 kblin anyway, thanks for the pointers, I'll have a closer look when I'm at work tomorrow
21:33 rbuels kblin: no problem, thanks for your work on this
21:34 kblin no problem. I'm happy that I only need to write a parser once in a while instead all of the time :)
21:35 kblin night folks :)
21:35 rbuels kblin: night
21:35 rbuels kblin++
22:51 CIA-95 bioperl-live: Lincoln Stein topic/lstein-seqfeature-store-summaries * rcd7b828 / (2 files in 2 dirs): don't add :bins to summary feature type; it confuses gbrowse2 - http://bit.ly/b7oSTu
22:51 CIA-95 bioperl-live: Lincoln Stein topic/lstein-seqfeature-store-summaries * r6a6f0ac / (4 files in 3 dirs): memory adaptor produces summary stats; ready to merge into master - http://bit.ly/9kZEQZ
23:08 deafferret s/^r//
23:08 rbuels deafferret: you'll need to inform the folks at Langley
23:09 deafferret space center?
23:09 rbuels oh wait, they already know
23:09 deafferret oh, i get jokes.
23:10 deafferret Culinary Institute of America
23:12 deafferret me++ # encapsulation
23:13 rbuels truly a tour de force.
23:16 * deafferret suppresses rbuels' rates

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