Camelia, the Perl 6 bug

IRC log for #bioperl, 2011-02-02

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All times shown according to UTC.

Time Nick Message
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12:24 kai there's one really annoying thing on programming open source code for science..
12:25 kai there's code you can't release before it's published in a journal
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14:57 dbolser hello
14:57 dbolser when I load GFF into a SeqFeature::Store, what happens to the ID field?
14:58 dbolser it doesn't seem to be there when I dump it out again: http://bioperl.pastebin.com/r4fU64Ee
14:59 dbolser http://bioperl.pastebin.com/179p3LMD
15:00 dbolser I guess 37 to 44 isn't the same as the result of a more specific query...
15:07 dbolser so do they become tags in the feature?
15:09 dbolser gah, get_all_tags just returns what I already see in teh attributes
15:09 * dbolser crawls back under a boulder
15:11 dbolser my $dir1 = ($bes1->get_tag_values('parent_id'))[0] =~ $library->{forward_regexp} ? 'F' : 'R';
15:11 dbolser (parent_id is a gff attr I can see)
15:26 dbolser my $dir1 = $par1 =~ $library->{forward_regexp} ? 'F' : { $par1 =~ $library->{reverse_regexp} ? : 'R' : die };
15:48 rbuels dbolser: the ID field is usually thought of as mostly internal to the gff3.  tools tend to ignore it except for determining parent relationships
15:53 dbolser so I should make name the same as ID?
15:53 dbolser rbuels: SF::Store does return the internal load_id
15:54 rbuels dbolser: yeah, but internal_load_id is probably the PK of one of the tables
15:54 dbolser (presumably the row index of the feature in the table)
15:54 dbolser rbuels: so why return that and not ID
15:54 dbolser of the two, I'd say the former is more 'internal'
15:54 dbolser also, my 'Notes' attribute is missing
15:54 rbuels dbolser: if there is info you care about, it should not go in ID.  put it in Name.
15:55 rbuels dbolser: your notes are there.  you just might not be querying for it correctly.
15:55 dbolser rbuels: and my external id's should go in dbxref?
15:55 dbolser rbuels: indeed, I see them in gbrowse
15:55 dbolser but I don't know how else to query
15:55 dbolser looking here:
15:55 dbolser http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio​/DB/SeqFeature/Store.pm#get_feature_by_primary_id
15:55 rbuels dbolser: yeah, Dbxref is the right gff attribute for external id's
15:55 dbolser and here:
15:56 dbolser http://search.cpan.org/~birney/bi​operl-1.2.3/Bio/DB/GFF/Feature.pm
15:56 rbuels ayee, don't look in bioperl-1.2.3
15:56 rbuels the only reason that's still on cpan is because Ensembl mandates that people use 1.2.3 with their toolkit
15:56 dbolser oh sorry, wrong link
15:57 dbolser http://search.cpan.org/~cjfields/B​ioPerl-1.6.1/Bio/DB/SeqFeature.pm
15:57 dbolser don't know how that got in my browser...
15:57 dbolser get_all_tags doesn't return Notes
15:58 rbuels dbolser: have you dumped what it *does* have in it?
15:58 dbolser http://bioperl.pastebin.com/179p3LMD
15:58 rbuels dbolser: i seem to remember Notes was called something different internally, or with the new stuff, or something like that
15:59 dbolser oh wait, that doesn't answer your question directly
15:59 rbuels dbolser: if i were you, i'd look at the place in gbrowse that is getting the notes
15:59 rbuels (also, try using Data::Dump instead of Data::Dumper, it's nicer)
16:00 rbuels hmm
16:00 dbolser but when I dump "get_tag_values", I only see those two in attributes there
16:02 dbolser in essence, I'd like to round trip my GFF from file to store and back
16:02 dbolser not because that is my objective, but because I'd like to know how to get at all my gff attrs via the  store
16:03 dbolser also, where is Name?
16:04 dbolser I should prolly read the gbrowse feature summary page code
16:04 dbolser I just wish it were documented somewhere
16:04 * dbolser pines after the bioperl book that his counterfactual self wrote
16:05 dbolser I was bummed because $f->gff_string didn't recreate the attributes column, but now I don't know how it could
16:06 dbolser oh well
17:58 * deafferret waves
18:10 * dbolser waves
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22:12 driley /join #clovr
22:12 driley oops
22:44 deafferret :)
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