| Time |
Nick |
Message |
| 02:08 |
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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 |
| 12:48 |
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perl_splut left #bioperl |
| 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/bioperl-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/BioPerl-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 |
| 20:02 |
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| 22:12 |
driley |
/join #clovr |
| 22:12 |
driley |
oops |
| 22:44 |
deafferret |
:) |
| 23:54 |
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