Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-04-15

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All times shown according to UTC.

Time Nick Message
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16:08 josephwb @towodo and @kcranstn: got a specific format you want for the tip labels?
16:09 josephwb 1) Stellula_calliope_536234
16:09 josephwb 2) Stellula_calliope_ott536234
16:09 josephwb 3) other?
16:09 towodo I don't have enough experience with Newick in the wild to know what is customary.
16:09 towodo What do the labels look like currently?  Stellula_calliope ?
16:09 josephwb yes
16:09 josephwb underscores are common; colons are a no-no
16:10 josephwb no parentheses either
16:10 towodo Yes I know about :, it's special. And spaces are no-no?
16:10 josephwb correct
16:10 towodo command and semicolon are out too.
16:10 towodo and probably ' and "
16:10 josephwb yep
16:10 josephwb periods are acceptable, but underscores are nicer
16:11 josephwb i guess 'ott' should be there, especially for taxa labels that already contain numbers
16:11 towodo Who am I to say, but I think I would have put the id at the beginning, 536234_Stellula_calliope - it's less ambiguous since many names already have numbers at the end
16:12 towodo Hmm… I don't think 'ott' helps. anyone making serious use of this is going to massage it
16:12 towodo The customer I have in mind really wants a tree of NCBI ids. They can take an OTT Newick and join it against the OTT taxonomy file
16:13 josephwb so, just the ott ids?
16:13 josephwb putting the ott id first would not be useful for someone sorting taxon labels
16:13 towodo hmm.
16:14 towodo ok, at end. in that case maybe with the ott, your #2 above
16:14 josephwb okay, will do
16:14 towodo We may have to live with this for a while. Put the plan out for review on the software list?
16:15 towodo There will be scripts that knows the format, etc.
16:15 towodo s/knows/know/
16:16 josephwb yes
16:16 josephwb wondering how common this will be requested
16:17 towodo I think a lot since the ott id can be mapped so easily to/from ncbi, gbif, etc.
16:17 josephwb ok, so this should be the default output then.
16:18 towodo Newicks are not supposed to have repeated tip names, right? So *some* kind of disambiguation is required
16:18 josephwb yes!
16:19 towodo will you send the email or should I?
16:19 josephwb i believe that treemachine does not account for this; part of the reason it will not open in FigTree
16:19 towodo right
16:19 josephwb we use Dendroscope, as it deals with this
16:19 josephwb a good reason to treat it as the default
16:20 josephwb can you send the email?
16:20 towodo sure.
16:20 josephwb i'll hold off until hearing how everyone votes
16:30 towodo email sent
16:34 towodo josephwb, whether to include the ott id can be an option, yes? two services, or a flag?
16:34 towodo just saw stephen's email
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17:03 pmidford @towodo : I've uploaded new IF files - if the cycle problem is only in those two places, it should be fixed.
17:05 towodo ok… I had been pushing to get as much taxonomy stuff done before stephen froze the tree, but given that he's done it, suddenly taxonomy is low priority for me. gotta catch up on my dryad work
17:05 towodo but thanks, will get to it soon
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18:31 josephwb @towodo question: do you want internal nodes (that map to taxonomy) to be so-labelled as well? or just leaves?
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19:15 josephwb @towodo: i have the tree labelled as requested. how should i get it to you?
19:16 towodo I think we should put it on files.opentreeoflife.org . Do you have an account there? (same as the previous dev.opentreeoflife.org)
19:17 towodo or it could go here: https://bitbucket.org/blackrim/avatol-taxonomies/downloads
19:19 towodo josephwb, internal nodes labeled, if possible
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19:21 josephwb done
19:22 towodo which?
19:22 josephwb the name change, i mena
19:22 towodo ok
19:24 josephwb i do not have access to http://dev.opentreeoflife.org/
19:24 josephwb Permission denied (publickey).
19:25 towodo oh.  well do you have any suggestions? I can pick it up from anywhere. if you like you can email me your publickey and I can make you an account
19:27 josephwb Gotta run right now. Will send key later. For now, tree is here: https://www.dropbox.com/s/8is030yjdavn8gn/Life_v2.6_mapcompat_14April.tre.tgz
19:27 towodo you have an account. the public key begins ssh-rsa AAAAB3NzaC1yc2EA...
19:27 towodo ok thanks
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