Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-11-08

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All times shown according to UTC.

Time Nick Message
00:09 deejoe_ is now known as deejoe
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08:57 CIA-57 bioperl-live: Kai Blin master * re3c7354 / (Bio/SearchIO/hmmer.pm t/SearchIO/hmmer.t): Bio::SearchIO::hmmer: Allow caller to specify parser version using a -version parameter (+7 more commits...) - http://bit.ly/b5U1du
09:30 dbolser Lynx_: any luck?
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11:49 Lynx_ dbolser: I looked through the howtos already, did not find anything. Didn't read them all yet, though.
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15:28 dukeleto pyrimidine: remind me to talk to you about Google Code-In tasks for BioPerl :)
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18:27 deafferret huh. working with a guy named Guru is a little intimidating
18:29 dnewkirk I can imagine
18:30 deafferret ...that sounds insane. but it's Guru, so...
18:39 dnewkirk Dunno, someone on the MACS mailing list refers to himself as captainentropy, so he might have a rival :)
18:43 deafferret \o/   Cake: Rock and Roll Lifestyle
18:44 dukeleto Does bioperl support PhyloXML at all? I see a gsoc proposal about it.
18:44 dukeleto deafferret: ^^^
18:44 deafferret dunno, sorry
18:44 deafferret ack -i phylo   ?
18:46 deafferret the answer appears to be "well, there certainly is a lot of code"   ack -i phyloxml
18:46 deafferret Bio/TreeIO/phyloxml.pm might be one place to start staring?
18:47 deafferret t/Tree/TreeIO/phyloxml.t
18:49 dukeleto deafferret: yeah, i just saw that stuff. At least there are some tests
18:49 deafferret ack -l -i phyloxml     6 files
19:03 pyrimidine dukeleto: that was my student's GSoC from a few years back, now published: http://www.ncbi.nlm.nih.gov/pubmed/19860910
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19:38 deafferret haha  :)   seasick steve - I Started Out With Nothin'  (and still got most of it left)
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19:47 dukeleto pyrimidine: cool. It will be useful for SGN to export Phyloxml to send to Phylobox
19:56 pyrimidine dukeleto: let me know if you run into any problems with it.  I'll try pinging mira han about it as well.
19:57 dukeleto pyrimidine: sounds good. thanks!
20:37 CIA-57 bioperl-live: Greg Jordan topic/gjuggler_tree_fixes * r322ac7f / (17 files in 6 dirs): Rewrite the TreeIO nhx and newick parser and add a bunch of round-trip tests. - http://bit.ly/aVyKah
20:37 kblin hey pyrimidine
20:38 pyrimidine o/
20:43 kblin playing with the merged hmmer parser in my pipeline right now, seems to be working so far :)
21:07 pyrimidine rbuels, dukeleto, and I are at the GMOD Evo Hackathon, so it might get loud in here
21:10 pyrimidine or, it might not, depends on how much we get accomplished
21:12 * deafferret hates missing hackathons   :(
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22:01 CIA-57 bioperl-live: Chris Fields topic/gjuggler_tree_fixes * r651bfbe / (17 files in 6 dirs): Merge branch 'master' of https://github.com/gjuggler/bioperl-live (+25 more commits...) - http://bit.ly/cKvWA1
22:02 CIA-57 bioperl-live: Chris Fields topic/gjuggler_tree_fixes * r948af13 / (Bio/TreeIO/NewickParser.pm Bio/TreeIO/newick.pm): kill our reliance on Switch, but add a temp reliance on 5.10 - http://bit.ly/9UlTGJ
22:11 CIA-57 bioperl-live: Chris Fields topic/gjuggler_tree_fixes * re75244b / Bio/TreeIO/NewickParser.pm : remove given/when :( - http://bit.ly/9avhO6
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