Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2015-04-09

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01:49 Topic for #opentreeoflife is now Open Tree Of Life | opentreeoflife.org | github.com/opentreeoflife | http://irclog.perlgeek.de/opentreeoflife/today
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03:16 travis-ci Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/81da2fffad99...cc719ada0447
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14:38 travis-ci OpenTreeOfLife/phylesystem-api#713 (support-tree-collections - 0189744 : Jim Allman): The build passed.
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18:02 jar286 https://github.com/OpenTreeOfLife/phylesystem-api/pull/147
18:02 jar286 I say merge
18:02 pmidford2 sure
18:03 jar286 done.
18:03 jar286 re https://github.com/OpenTreeOfLife/reference-taxonomy/pull/131 , we’re waiting for comments i think
18:03 pmidford2 Did you look at what I added Tuesday evening?
18:04 jar286 no, just now saw you added a commit
18:04 jar286 will look now
18:04 kcranstn much better, thanks!
18:04 pmidford2 Pretty much what jar suggested
18:05 pmidford2 (at least for the comments)
18:05 kcranstn I still, in general, like to see comments for each method  (but won’t hold this up for that)
18:06 pmidford2 agree, - may come back to that, but jar wanted general comments so that's what I addressed first
18:06 jar286 I think the method names are fairly self explanatory…
18:07 jar286 anyhow, looks good to me, i’ll merge
18:07 kcranstn agreed on merge
18:08 jar286 forgot ‘confirm merge’ for the other PR… I’ve done that all too often
18:09 * jimallman has done that once or twice
18:09 jar286 I think we’re done with PR review
18:09 kcranstn wow, that was very little
18:09 kcranstn maybe it would be good to do a code walk-through next week of the peyotl changes
18:09 jimallman yeah, i’ve got a lot of work bottled up in support-tree-collections branches in multiple repos
18:10 kcranstn if there are again so few PRs
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18:10 travis-ci OpenTreeOfLife/phylesystem-api#714 (master - 08a77e3 : Jonathan A Rees): The build passed.
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18:11 jimallman that (code review in peyotl) would be great. i’m planning to deploy it on devtree shortly. hopefully that will flush out any bugs in study management. (in addition to our unit tests, i mean)
18:12 kcranstn might also be good to do the same with synthesis
18:14 * jimallman nods
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20:03 jar286 pmidford2, I’m still struggling with what to do
20:04 pmidford2 jar286 - how so?
20:04 jar286 seems there are two choices, and both are painful:
20:04 jar286 1. enhance your python code to do the full membership-based merge of ANT and silva
20:05 jar286 2. enhance smasher to be able to do membership-based merges (so it would take trees with genbank ids as inputs)
20:05 jar286 #1 would mean doing the polytomy refinement thing I wrote up
20:06 pmidford2 does smasher already do the polytomy refinement thng?
20:06 jar286 yes
20:07 jar286 looking for the code now...
20:09 jar286 https://github.com/OpenTreeOfLife/reference-taxonomy/blob/master/org/opentreeoflife/smasher/Taxon.java#L461
20:09 pmidford2 looking at it
20:10 jar286 umm… there’s also the code that gathers oldChildren and newChildren
20:11 jar286 hmm, it’s not as general as what I wrote up.
20:11 jar286 it only deals with the case where m’s children (mapped) are a subset of n’s
20:12 jar286 it’s awful code
20:12 jar286 well, so it would probably have to be rewritten anyway
20:13 pmidford2 so either option would require (re)writing
20:14 jar286 yes… that’s what I mean by painful
20:14 jar286 I’m guessing java will perform better than python
20:15 jar286 I was halfway through a rewrite of the alignment code, so had already started down this path
20:16 pmidford2 yes, even faster than pypy which is what I've been using to test this (about 4x faster than c-python)
20:16 jar286 but this is a lot to do.  I have two days on the train coming up…
20:17 jar286 how big would trees be that added genbank ids to ncbi and silva?…
20:17 jar286 the silva-only ids, I guess
20:17 pmidford2 That doesn't sound that bad
20:17 jar286 that’s 400k, yes?  so if they got added to ncbi, that would be…
20:18 jar286 (looking at size of ncbi)
20:19 jar286 drop in the bucket.  1.1M + .4M = 1.5M which is still much smaller than GBIF
20:19 pmidford2 sounds about right
20:22 jar286 ok. I will look into it when i’m on the train tomorrow and Sunday.
20:23 jar286 I wonder if you could email me any stats you have gathered on how the two taxomonomies relate
20:24 jar286 basically counts of all 5 rcc-5 articulations between ant tips and silva clusters
20:25 pmidford2 I don't have that immediately (73k non-empty intersections - I can get the other relations easily enough).
20:25 jar286 # compatible pairs, # tips contained in clusters, # clusters contained in tips, some kind of count of incompatibility
20:26 jar286 wow, only 73k.  i guess we talked about this before
20:26 pmidford2 Got it
20:27 jar286 remind me how this works… where are the other 327k clusters in ncbi? not in ncbi taxonomy, or in ‘buckets’ like environmental samples, or some combination?
20:27 jar286 that is, if every genbank accession were in ncbi taxonomy, you’d have 100% overlap
20:28 jar286 or was that 73k ncbi taxa?
20:28 jar286 i.e. 400k clusters fit inside of 73k taxa?
20:28 pmidford2 probably most in non taxonomic buckets, and yes, 73k taxa
20:30 jar286 you were going to give me two scripts, right?  you gave me the NCBI one, but what’s the state of the SILVA taxonomy with clusters?
20:31 pmidford2 Yes, I need to commit that - I'll make sure there's documentation like the NCBI script
20:31 jar286 thanks
20:32 jar286 I don’t know how the internet is going to be on the train
20:32 pmidford2 I'll get that by tomorrow - and mail you the stats.  I should be available most of Saturday (wife has to work)
20:33 jar286 hmm. if you have something that works it would be nice if you could put it on github tonight (maybe in a branch) even if without comments
20:34 jar286 I’m going to load up the laptop tonight. train is early tomorrow
20:34 pmidford2 got it - I'll commit what I have
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22:27 travis-ci OpenTreeOfLife/phylesystem-api#715 (support-tree-collections - 8c0420a : Jim Allman): The build passed.
22:27 travis-ci Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/01897444c43f...8c0420a222c3
22:27 travis-ci Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/57876209
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22:28 jimallman_ fyi - i’ve temporarily borked devapi… should have it back up shorty
22:28 jimallman_ shortly
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