Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-04-16

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All times shown according to UTC.

Time Nick Message
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01:47 Topic for #opentreeoflife is now Open Tree Of Life | opentreeoflife.org | github.com/opentreeoflife | http://irclog.perlgeek.de/opentreeoflife/today
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13:52 josephwb @towodo did you get my email?
13:53 towodo yes, my dumbness, didn't notice it was .tgz rather than .gz
13:59 josephwb phew. glad it worked.
14:12 towodo I've asked the  Quest for Orthologs folks to try again.  They could really use that spanning tree for given tip set feature… I've told them we'll be working on it but it isn't ready yet.  Thanks for your help.
14:27 josephwb @towodo: was that directed at me? Not sure what "spanning tree for given tip set feature" regards.
14:29 towodo yes that was for you, giving background on why I wanted the tree now.  They have a set of 147 tips and want to know their relationships, so need the subtree of the synthetic tree that spans that particular tip set. I'm told we have code for that but it's not available as a service.
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15:34 josephwb i believe we do have such code buried in there.
15:35 josephwb yes, i see it. the arguments are a list of comma-delimited (no spaces) ottIDs
15:36 josephwb i don't think it is available as a service. i'll ask cody.
15:39 josephwb ok, just tested it, and it is broke.
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15:56 josephwb will track this down after my meeting. in the meantime, there are ways to remove all tips except for a list of taxa. I could do that pretty easily if they could provide the list (with ottIds for disambiguation)
15:59 towodo josephwb, I have the list
16:00 josephwb please send it along. and if it is not the root of the tree, please provide the clade of interest.
16:00 josephwb e.g. birds, or metazoa, or whatever
16:00 towodo the list has NCBI ids, not OTT ids… not hard to map though
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16:29 towodo list of ott ids sent in email
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17:38 josephwb @towodo I was hoping to carry this out in R, but the "knuckle" (https://github.com/OpenTreeOfLife/treemachine/issues/49) issue prevents this.
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18:12 towodo ouch.
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