Camelia, the Perl 6 bug

IRC log for #bioperl, 2011-08-15

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All times shown according to UTC.

Time Nick Message
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20:18 ende does Bio::DB:GFF not recognize gff3 format??
20:18 ende it's not parsing ID=SOMETHING in the 9th column
20:19 ende and the documentation only mentions the format ID "SOMETHING"
20:20 deafferret hmm   http://bugzilla.open-bio.org/​buglist.cgi?quicksearch=gff3
20:21 deafferret t/SeqFeature/FeatureIO.t has 6 .gff3 files in it
20:21 deafferret are you on bioperl-live?
20:22 deafferret gff3 is in bioperl-live 156 times
20:42 ende I am
20:43 ende It's just strange that it is parsing the gff file like that
20:43 ende literally when you access $feature->attributes you're returned a hash that has "id=FOO;name=BAR" has a tag, and a blank value
20:45 CIA-72 bioperl-live: Sheena Scroggins reorganization_2.x * re1f2773 / (Bio/DasI.pm Bio/Range.pm Bio/RangeI.pm): Added missing DasI, Range and RangeI pm files - http://bit.ly/pXTlO1
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20:54 scottcain Hmm, too late to help ende with gff3; so it goes :-/
20:55 ende ?
20:55 scottcain Oh, you are here--you were asking about Bio::DB::GFF, right?
20:55 ende hey Scott
20:55 ende yes I was
20:56 ende I loaded up the gff3 file from TAIR10 with bp_load_gff, etc etc etc
20:56 ende and am having trouble accessing the feature by their id's
20:56 scottcain OK, I am reasonably sure that Bio::DB::GFF does get the ID, only it saves it as the attribute "load_id".
20:56 ende ah
20:57 scottcain I would suggest not using Bio::DB::GFF with GFF3 though, as it really isn't intended to deal with it.  You're much better off using SeqFeature::Store.
20:57 ende Ah that's right
20:58 scottcain I believe there is a config option to have GBrowse search the values of various tags in the search, so if you add "load_id" to it, it should work.
21:00 ende Is there a bp_load_gff.pl equiv for Bio::DB::SeqFeature ?
21:00 scottcain Yes: bp_seqfeature_load.pl
21:05 ende thanks Scott.  I knew my knowledge was a bit out of date

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