Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-08-27

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All times shown according to UTC.

Time Nick Message
01:47 jimallman for the record: yes, pushdb does restart neo4j
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19:41 jorrit hey y'all - question about newick file "draftversion1.tre" - does this contain most tips?
19:42 kcranstn Downloaded from here: http://files.opentreeoflife.org/trees/?
19:42 jorrit yep
19:42 kcranstn It should contain all tips (noting that some OTUs from the taxonomy don’t make it into synthesis for various reasons)
19:43 kcranstn why - what seems strange?
19:43 jorrit just making sure . . . am about to use it to grab all ott ids for integation with GloBI
19:44 jorrit file looks pretty good to
19:44 jorrit me
19:44 kcranstn if you want all OTT ids, you might want the taxonomy instead
19:44 kcranstn http://files.opentreeoflife.org/ott/
19:44 jorrit ok. I counted over 3M taxa in ott and about 200k tips in newick
19:45 jorrit are there ott ids without tip?
19:45 kcranstn yes there are
19:47 jorrit ok, thanks!
19:47 kcranstn that newick should have ~ the same number of tips as OTT
19:47 kcranstn i.e. >2 millino
19:48 jorrit tail draftversion1.tre | tr  ")" "\n" | wc -l
19:48 jorrit give me: 219185
19:48 kcranstn polytomies
19:49 towodo try counting the commas
19:49 jorrit oops. thanks!
19:50 jorrit I'll probably use the ott as you suggested
19:50 kcranstn towodo - simple way to identify tips in taxonomy.tsv?
19:51 towodo you have to check to see if they’re the parent of any other node, sorry
19:52 jorrit ok. on second thought, I'll probably write a little script to merge newick file with ott to include tips only
19:52 kcranstn that would work
19:52 jorrit sweet!  thanks for your help
19:52 kcranstn np
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