Camelia, the Perl 6 bug

IRC log for #bioperl, 2012-04-13

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All times shown according to UTC.

Time Nick Message
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04:50 CIA-66 bioperl6: Chris Fields master * rbc60cb5 / (lib/Bio/Role/Range.pm t/Range.t): get Range compiling again with rakudo - http://git.io/m8Sfew
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05:35 CIA-66 bioperl-live: Florent Angly master * ra0a90b5 / (4 files in 4 dirs): New method, get_lineage_string in Bio::Tree::TreeFunctionsI (+15 more commits...) - http://git.io/TSMMeA
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19:25 CIA-66 Bio-FeatureIO: Chris Fields master * r37b298a / lib/Bio/FeatureIO/gff.pm : use for() instead of given() - http://git.io/EquLrA
19:25 CIA-66 Bio-FeatureIO: Chris Fields master * rca258c7 / lib/Bio/FeatureIO/gff.pm : flip logic - http://git.io/pPD1Xw
19:25 CIA-66 Bio-FeatureIO: Chris Fields master * rcf4f009 / t/gff3.t : deal with score oddity - http://git.io/k2ezJA
19:30 rbuels pyrimidine: i released Bio-GFF3 1.1 last night, with a parser that supports multiloc features, Derives_from, and arbitrary ordering for Parent/ID and Derives_from/ID relationships.
19:30 pyrimidine rbuels: I am planning on a branch to use this instead of the baked-in parser
19:31 pyrimidine Bio::GFF3, that  is
19:31 rbuels it was a real pain in the ass to write.
19:31 pyrimidine not surprised
19:32 rbuels i had to change its output format, and then write a compat layer for the old format.
19:32 rbuels in case other people are already using it
19:33 rbuels i finally settled on a "feature" being an arrayref of one or more feature lines that have the same ID
19:33 pyrimidine I think that's fine
19:34 rbuels and the child_features and derived_features on all of those just have pointers to the same things.
19:34 * rbuels pukes a little
19:34 pyrimidine yeah, I think all of this could be simpler
19:34 pyrimidine but that's the way it is
19:34 pyrimidine any idea what this is? https://metacpan.org/module/Bio::BioStudio::GFF3
19:35 pyrimidine It's bioperl-y
19:35 pyrimidine yet ...not
19:36 rbuels huh, i hadn't seen that
19:36 pyrimidine very new
19:36 pyrimidine (last few months)
19:37 rbuels THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE DEVELOPERS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
19:37 rbuels OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
19:37 rbuels lol
19:37 pyrimidine gotta cya
19:37 rbuels ok, have a good weekend
19:37 pyrimidine *CYA
19:37 pyrimidine no, that's for 'cover your ass'
19:38 rbuels ooooh i get it
19:38 * rbuels nods vigorously
19:38 rbuels right, right
19:38 scottcain "See you after?" alternate acronym?
19:38 pyrimidine possibly
19:39 scottcain Oh, Sarah Richardson is the person who bailed on coming to the GMOD meeting.
19:39 pyrimidine scottcain: that BioStudio stuff on CPAN also has Gbrowse stuff too: https://metacpan.org/modul​e/Bio::BioStudio::GBrowse
19:39 scottcain She's fairly brilliant
19:39 pyrimidine ah, ok
19:40 scottcain She wrote plugins for GBrowse to allow editing of not only features but DNA sequence.
19:40 rbuels O_O
19:40 scottcain She was in a synthetic yeast lab, and they used GBrowse to create versions of yeast chromosomes they wanted to make.
19:41 * rbuels looks at the code
19:41 * scottcain is looking too.
19:41 pyrimidine she's on bitbucket, but using git: https://bitbucket.org/notadoctor/biostudio
19:42 rbuels this reminds me of some of the weird stuff i did for gbrowse integration in the sgn codebase
19:44 rbuels except mine was all full of moose and didn't hardcode anything
19:44 scottcain http://biostudio.bme.jhu.edu/sc2/ synthetic yeast home page
19:45 * rbuels recommends as supplemental material for "full of moose" the picture of the norwegian moose in the apple tree
19:45 pyrimidine we have a group doing the same thing locally (the yeast engineering, not the Biostudio stuff)
19:46 pyrimidine very interesting, though
19:47 pyrimidine scottcain: any idea if/when the GFF3 suggestions on SO would be adopted?  I'm planning on focusing on Bio::FeatureIO over the next few months, we need it for some work internally
19:47 pyrimidine guess that's up to Barry?
19:47 pyrimidine (and Lincoln?)
19:48 scottcain I don't think Barry would do anything without Lincoln's blessing, and he's on paternity leave.
19:49 scottcain I suppose it's possible that if we went to him with a diff to a new spec, he'd say OK but I still expect a delay.
19:49 pyrimidine ok
19:49 scottcain Of course, that assumes that we had such a diff.
19:49 pyrimidine ah, yes, Canada's paternity leave
19:49 pyrimidine can be quite long :)
19:49 scottcain 3 months I think, and he just started a week or two ago.
19:50 pyrimidine it's a full year, split between the parents
19:50 rbuels oh wow
19:50 scottcain Really?  Wow.
19:50 pyrimidine yep
19:52 pyrimidine have a sister-in-law that has worked 3 yrs in the last 7, 4 yrs off with child(ren)
19:52 pyrimidine that's not the norm.  she's just lazy :)
19:53 pyrimidine (her other kids went to day care during that time)
19:53 rbuels lazy, eh?
19:53 * rbuels guffaws
19:53 scottcain I imagine a year unpaid might be difficult for many.
19:53 pyrimidine it's NOT unpaid, that's the kicker
19:54 pyrimidine they have to pay a minimal percentage of the salary for that time
19:54 scottcain crazy.
19:54 scottcain communists.
19:54 * leont didn't know that. That sounds almost Scandinavian :-p
19:55 pyrimidine http://en.wikipedia.org/wi​ki/Parental_leave#Americas
19:55 pyrimidine 55% up to $485/week for 50 weeks (15 weeks maternity + 35 weeks parental leave shared with father)
19:55 pyrimidine so, there you go
19:55 rbuels "up to $485/week"
19:55 rbuels so there's a cap
19:56 pyrimidine yes, but that's better than nothing
19:56 rbuels so it's not *that* lush.
19:56 rbuels well, but it's long
19:56 pyrimidine no, that's what is covered as a minimum by the gov, IIRC
19:56 leont Here it's 16 weeks 100% for the mother, and a whopping two days for the father :-|
19:56 pyrimidine most actually pay more (% of salary)
19:56 leont (at least, the paid leave)
19:57 pyrimidine oh, yeah, forgot, Quebec has to do its own thing:
19:57 pyrimidine cap is higher
19:58 pyrimidine but, again, that's gov-mandated, and I think most companies pay higher than 55%
19:58 pyrimidine quebec is 70%
19:58 rbuels ooo
19:58 scottcain Still don't really want to move to Montreal.
19:59 pyrimidine too cold?
19:59 scottcain Definitely.
19:59 pyrimidine try Regina in December
19:59 pyrimidine -40deg C
19:59 scottcain or -40 deg F
19:59 pyrimidine I don't think it makes much difference when it's that cold
20:00 leont It's the point where they're equal
20:00 scottcain :-)  I don't think it ever makes a difference if it's -40 we're talking about
20:00 pyrimidine yep
20:00 pyrimidine might as well be kelvin
20:01 leont Fortunately, that isn't possible :-p
20:04 * pyrimidine heading for a brewski and a bit of hackery
20:04 pyrimidine o/
20:04 rbuels ooo brewski
20:04 * rbuels will have one soon as well
20:04 rbuels soon.
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