Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-12-08

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All times shown according to UTC.

Time Nick Message
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14:36 dbolser what is the best object to model a sequence with sub-sequences?
14:36 dbolser (wan't coordinates of both)
14:40 kai what's a subsequence?
14:41 kai is that like a substring?
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14:47 dbolser its a contig in a scaffold
14:48 kai ah
14:49 kai would that be a SeqFeature then?
14:49 kai I think SeqFeatures can contain SeqFeatures
14:49 kai and I think you can set seqence information on SeqFeatures
14:52 dbolser I have bits and pieces of code to do this, I wish I'd consolidated them at some point
14:53 kai hehe
14:54 kai been there
16:59 deafferret isn't this what Bio::Assembly is for?
17:12 deafferret kai: ^
17:12 deafferret dbolser: ^
17:31 kai deafferret: dunno, I have project partners who take care of that. I get the finished genomes ;)
17:31 deafferret :)
18:12 dbolser deafferret: hi
18:12 dbolser perhaps
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19:50 dbolser how to 'flip' one of these ?http://search.cpan.org/~cjfields/BioPe​rl-1.6.1/Bio/Coordinate/Collection.pm
19:50 dbolser how to 'flip' one of these? http://search.cpan.org/~cjfields/BioPe​rl-1.6.1/Bio/Coordinate/Collection.pm
19:51 dbolser i.e. I want to reverse the whole sequence, and all mapped sub-sequences
20:02 dbolser hmm... I'm getting somewhere.... how to add a feature to a locateable?
20:18 rbuels dbolser: whatever objects you're working with, they probably implement multiple interfaces, like SeqFeatureI, AnnotatableI, etc
20:19 rbuels dbolser: so if an object implements that interface, you should be able to use the methods on it that are documented in that interface
20:23 dbolser right
20:25 dbolser just not sure how to stick one on a seq
20:25 dbolser $annseq->add_SeqFeature($feat);
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22:20 dbolser sorry, away for dinner.
22:21 dbolser what is the simplest sequence that takes a feature?
22:31 dbolser OK, what is the simplest locateable sequence that takes a feature ;-)
22:35 rbuels heh
22:35 rbuels locatableseq does not have features?
22:35 dbolser actually locatableseq is still causing problems for coordinate::Pair
22:36 dbolser MSG: Not a valid output coordinate Bio::Location [Bio::LocatableSeq=HASH(0x89411f0)]
22:36 dbolser my $agp = Bio::Coordinate::Pair->
22:36 dbolser new( -in  => $ctg_on_chr,
22:36 dbolser -out => $ctg,
22:36 dbolser );
22:37 dbolser guess which one is the locatable seq
22:37 * rbuels throws up his hands
22:37 dbolser works fine with Bio::Location::Simples
22:38 dbolser (which don't like features of course)
22:39 dbolser I guess the feature coordinates would confuse the coordinate::pair ...
22:39 rbuels dbolser: to get *all* that stuff in one object, you might need to make another one
22:39 rbuels dbolser: Bio::Seq has most of it ...
22:39 dbolser rbuels: how do you mean
22:39 dbolser yeah, bio sec triggered the same msg
22:39 dbolser yeah, bio::seq triggered the same msg
22:39 dbolser MSG: Not a valid output coordinate Bio::Location [Bio::Seq=HASH(0x89410e8)]
22:39 rbuels dbolser: Bio::Seq is not Locatable thouhg
22:40 rbuels i think ...
22:40 dbolser right, which gets us to where we began
22:40 rbuels dbolser: you maybe could make a subclass of Bio::LocatableSeq that also adds FeatureHolderI
22:41 rbuels i don't think there is an object that is both locatable and has features
22:41 rbuels right now
22:41 dbolser rbuels: it's the fact that the seq isn't playing with bio::Coordinate thats the problem
22:42 dbolser Bio::Coordinate::Pair takes two 'Bio::Location::Simple' objects and maps coordinates between them
22:42 dbolser but it won't take a Bio::LocatableSeq
22:43 dbolser MSG: Not a valid output coordinate Bio::Location [Bio::LocatableSeq=HASH(0x89411f0)]
22:43 dbolser STACK: Error::throw
22:43 dbolser STACK: Bio::Root::Root::throw /home/dmb/perl5/lib/perl5/Bio/Root/Root.pm:473
22:43 dbolser STACK: Bio::Coordinate::Pair::out /home/dmb/perl5/lib/perl5/​Bio/Coordinate/Pair.pm:166
22:43 dbolser STACK: Bio::Coordinate::Pair::new /home/dmb/perl5/lib/perl5/​Bio/Coordinate/Pair.pm:126
22:43 dbolser STACK: ./scaff.03.plx:61
22:45 dbolser all this time I've been feeding bio::coordinate::pair Bio::Location::Simples, but assumign that it would work with sequences
22:47 rbuels :-\
22:48 * dbolser masmachinates
22:48 dbolser I guess that was an unfounded assumption
22:48 dbolser I just don't wan't to keep track of my feature coordinates while I juggle sequences
22:52 dbolser OK, I think I see a path
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