Camelia, the Perl 6 bug

IRC log for #bioperl, 2011-04-01

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All times shown according to UTC.

Time Nick Message
00:15 CIA-119 bioperl-live: Scott Cain master * r848dca3 / (6 files in 5 dirs):
00:15 CIA-119 bioperl-live: A few things going on here:
00:15 CIA-119 bioperl-live:  for Bio::DB::GFF and the gff loading scripts, added a warning message if the
00:15 CIA-119 bioperl-live:  user is loading gff3.
00:15 CIA-119 bioperl-live:  for Bio::FeatureIO::gff, it's test and the knownGene.gff3 sample data, there
00:15 CIA-119 bioperl-live:  is a fix to NOT unescape URI codes in the Target values, per the GFF3 spec. - http://bit.ly/hew58N
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01:09 CIA-119 bioperl-run: kortschak master * r584dd20 / (7 files in 4 dirs): Update BEDTools module for v2.10.1 - http://bit.ly/gRNu6H
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01:30 CIA-119 bioperl6: takadonet master * rd0a6cda / lib/Bio/SeqFeature/Lite.pm : Start and stop attribute are now private. Added alias method for stop/end. Implemented start method as well - http://bit.ly/fbg7rJ
01:40 CIA-119 bioperl6: takadonet master * r8db42eb / (lib/Bio/SeqFeature/Lite.pm t/SeqFeature/Lite.t): Made name a private attribute, added a getter/setter for it and also created two aliases for name: info and seqname. - http://bit.ly/ezL6Rt
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02:30 CIA-119 bioperl6: takadonet master * r96e6e5c / (lib/Bio/LiveSeq/Mutation.pm t/LiveSeq/Mutation.t): Initial full implemention of Bio::LiveSeq::Mutation with corresponding Test file. Beat that! - http://bit.ly/h0H4QS
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03:03 CIA-119 bioperl6: takadonet master * reeba14b / (lib/Bio/PrimarySeq.pm t/PrimarySeq.t): Now passing a few more tests involving Role::Location::Split and Fuzzy for subseq - http://bit.ly/fCp74e
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05:22 CIA-119 bioperl-run: kortschak master * r32227cc / (lib/Bio/Tools/Run/Bowtie/Config.pm t/Bowtie.t): Update Bowtie module for 0.12.7 - http://bit.ly/dU2sj9
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09:55 micrypt Code critique anyone? http://perl.nopaste.dk/p3084
09:56 micrypt Tips very much appreciated.
10:00 dbolser when using a Bio::Coordinate::Collection, how do I retrieve the map (Bio::Coordinate::Pair) used to map a specific feature?
10:00 dbolser all I get back is a Bio::Coordinate::Result
10:01 dbolser micrypt: are fetchdata and remoteblast imported by Bio::Tools::Run::RemoteBlast;?
10:01 dbolser perhaps better to do that explicitly
10:01 dbolser also Getopt::Long
10:01 dbolser oh sorry ;-)
10:02 dbolser got to line 27
10:05 dbolser micrypt: looks solid
10:05 dbolser I'd pass the variables to the subs rather than having them implicitly picked up
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10:05 dbolser must have been something I said
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10:18 micrypt Code critique anyone? http://perl.nopaste.dk/p3084 Tips very much appreciated.
11:29 kai micrypt: what dbolser said, actually
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13:05 CIA-119 bioperl6: takadonet master * r1a99230 / (lib/Bio/PrimarySeq.pm t/PrimarySeq.t): Trunc is a multi method now where it now accepts a Location object. Passing a few more test - http://bit.ly/iglXMP
13:08 dbolser I found an answer (workaround) to my question, but I think I found a bug
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13:18 micrypt kai: Cool. Thanks.
13:21 dbolser if an object function says ' $self = shif; $x = $self->x ', how do I force $x to be a copy of $self->x, and not just a reference to it?
13:22 dbolser I'm trying to call http://search.cpan.org/~cjfields/BioPerl​-1.6.1/Bio/Coordinate/Collection.pm#swap on a copy of the object, but finding the object itself is swapped
13:24 dbolser $self = shif; $x = {%{$self->x}}?
13:25 dbolser Can't call method "swap" on unblessed reference...
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14:42 CIA-119 bioperl6: takadonet master * r3b0d302 / (3 files in 3 dirs):
14:42 CIA-119 bioperl6: Subseq can now accept Bio::Role::Location type object/role for subseq method.
14:42 CIA-119 bioperl6: Fixed a bug where $min and $max would be initialized as match object and not
14:42 CIA-119 bioperl6: integer. This causes issue where type constraints in method signature in Subseq.
14:42 CIA-119 bioperl6: Passing the last test for PrimarySeq.t - http://bit.ly/f1owyh
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16:20 CIA-119 bioperl6: takadonet master * rbb9d78a / (lib/Bio/PrimarySeq.pm t/PrimarySeq.t): Passing two more tests. Implemented initial version of guess_alphabet and created getter/setter for seq attribute - http://bit.ly/h6AB4i
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16:49 CIA-119 bioperl-live: Lincoln Stein master * r417ea7a / (3 files in 3 dirs): fixed regression in Bio::DB::GFF and removed deprecated TYPE=MYISAM directives - http://bit.ly/gxKMu2
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17:17 CIA-119 bioperl6: takadonet master * r46b5405 / (lib/Bio/PrimarySeq.pm lib/Bio/Role/Identify.pm):
17:17 CIA-119 bioperl6: Made $!id a private attribute and created getter/setter with method name: id and
17:17 CIA-119 bioperl6: display_id. Allowed in constructor both 'id' and 'display_id' to both initalize
17:17 CIA-119 bioperl6: $!id. Same with 'desc' and 'description' - http://bit.ly/hBk7F9
17:17 CIA-119 bioperl6: takadonet master * r9ffac69 / (lib/Bio/Role/Describe.pm t/PrimarySeq.t): Now can use either 'desc' or 'description' methods to set private attribute 'description'. Added a test. - http://bit.ly/dWGXbQ
17:46 CIA-119 bioperl6: takadonet master * r05041b1 / (lib/Bio/Annotation/SimpleValue.pm t/Annotation/Annotation.t): Initial implementation of Annotation::SimpleValue.pm with corresponding test file. - http://bit.ly/i48azS
18:01 CIA-119 bioperl6: takadonet master * r461e64e / (3 files in 2 dirs): initial version of Annotation::DBLink done with tests to go along - http://bit.ly/i1x2jE
18:04 perl_splut http://www.nature.com/nature/jour​nal/v471/n7340/full/471569a.html
18:04 perl_splut I wonder what the reaction at the NIH will be to that
18:19 deafferret probably all sciency and stuff
18:19 deafferret oh - ha!   my reaction to that is "$32? blow me"  :)
18:20 rbuels yeah these paywalls on all the journals are so crappy
18:23 rbuels deafferret: http://solgenomics.net/data/u​ser_requests/rob/471569a.pdf
18:23 rbuels deafferret: tell me when you've got it
18:28 deafferret rbuels: got it, as did all my social network friends (~2000) and wikileaks. thanks
18:29 rbuels hehehe
18:29 perl_splut guess that is one advantage of being on a Uni computer.
18:29 perl_splut I doubt wikileaks will care, heheh
18:29 * rbuels had to use cornell's library proxy
18:29 deafferret ya, i think i can still backdoor through UN med center if I needed to
18:30 rbuels it's pretty nice one: once you have the university's auth cookie, you just add .proxy.library.cornell.edu to the hostname in the url  you're trying to get
18:30 * deafferret really likes the cartoon  :)
18:31 perl_splut I much prefer the second cartoon
18:33 CIA-119 bioperl6: takadonet master * r11097c8 / (3 files in 2 dirs): Added basic implementation for Collection.pm and TypeManage.pm. Added basic tests as well. - http://bit.ly/gILdNp
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19:00 dbolser rbuels: host again plz?
19:00 rbuels gah
19:01 rbuels dbolser: ok hit it
19:01 CIA-119 bioperl6: takadonet master * rd0015ce / (4 files in 2 dirs):
19:01 CIA-119 bioperl6: Made method database a multi because Reference is a sub class and need to
19:01 CIA-119 bioperl6: override it. Initial implementation of Comment and Reference Annotation classes.
19:01 CIA-119 bioperl6: Just enough to get test passing. Added more tests - http://bit.ly/fWcujR
19:01 dbolser rbuels: ty
19:01 rbuels np :-)
19:02 * dbolser uploads to scribd
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19:16 dbolser I can't believe that graph!
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