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| 00:09 |
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deejoe_ is now known as deejoe |
| 03:14 |
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| 08:57 |
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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 |
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dbolser |
Lynx_: any luck? |
| 10:59 |
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| 11:49 |
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Lynx_ |
dbolser: I looked through the howtos already, did not find anything. Didn't read them all yet, though. |
| 12:48 |
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| 15:00 |
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| 15:28 |
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dukeleto |
pyrimidine: remind me to talk to you about Google Code-In tasks for BioPerl :) |
| 15:36 |
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| 16:09 |
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| 18:18 |
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| 18:27 |
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deafferret |
huh. working with a guy named Guru is a little intimidating |
| 18:29 |
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dnewkirk |
I can imagine |
| 18:30 |
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deafferret |
...that sounds insane. but it's Guru, so... |
| 18:39 |
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dnewkirk |
Dunno, someone on the MACS mailing list refers to himself as captainentropy, so he might have a rival :) |
| 18:43 |
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deafferret |
\o/ Cake: Rock and Roll Lifestyle |
| 18:44 |
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dukeleto |
Does bioperl support PhyloXML at all? I see a gsoc proposal about it. |
| 18:44 |
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dukeleto |
deafferret: ^^^ |
| 18:44 |
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deafferret |
dunno, sorry |
| 18:44 |
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deafferret |
ack -i phylo ? |
| 18:46 |
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deafferret |
the answer appears to be "well, there certainly is a lot of code" ack -i phyloxml |
| 18:46 |
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deafferret |
Bio/TreeIO/phyloxml.pm might be one place to start staring? |
| 18:47 |
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deafferret |
t/Tree/TreeIO/phyloxml.t |
| 18:49 |
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dukeleto |
deafferret: yeah, i just saw that stuff. At least there are some tests |
| 18:49 |
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deafferret |
ack -l -i phyloxml 6 files |
| 19:03 |
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pyrimidine |
dukeleto: that was my student's GSoC from a few years back, now published: http://www.ncbi.nlm.nih.gov/pubmed/19860910 |
| 19:20 |
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| 19:38 |
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deafferret |
haha :) seasick steve - I Started Out With Nothin' (and still got most of it left) |
| 19:44 |
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| 19:47 |
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dukeleto |
pyrimidine: cool. It will be useful for SGN to export Phyloxml to send to Phylobox |
| 19:56 |
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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 |
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dukeleto |
pyrimidine: sounds good. thanks! |
| 20:37 |
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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 |
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kblin |
hey pyrimidine |
| 20:38 |
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pyrimidine |
o/ |
| 20:43 |
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kblin |
playing with the merged hmmer parser in my pipeline right now, seems to be working so far :) |
| 21:07 |
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pyrimidine |
rbuels, dukeleto, and I are at the GMOD Evo Hackathon, so it might get loud in here |
| 21:10 |
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pyrimidine |
or, it might not, depends on how much we get accomplished |
| 21:12 |
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* deafferret |
hates missing hackathons :( |
| 21:56 |
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| 22:01 |
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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 |
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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 |
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CIA-57 |
bioperl-live: Chris Fields topic/gjuggler_tree_fixes * re75244b / Bio/TreeIO/NewickParser.pm : remove given/when :( - http://bit.ly/9avhO6 |
| 22:27 |
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