[Bioperl-l] Bio::DB::SeqFeature::Store issues
bix at sendu.me.uk
Tue Jan 23 10:57:04 EST 2007
I'm trying to use Bio::DB::SeqFeature::Store for the first time and have
come across some issues.
Is the documentation accurate? The synopsis has:
my $db = Bio::DB::SeqFeature::Store->new(-adaptor => 'DBI::mysql',
-dsn => 'dbi:mysql:test',
-write => 1 );
but code for new() has:
'CREATE',], at _);
Ie. naively -write doesn't do anything, and -create is undocumented. I
needed to use -create to get it to work.
Doc for store() says:
Args : list of Bio::SeqFeatureI objects
But when I tried storing Bio::SeqFeature::Annotated objects I get this
Transaction aborted because Can't locate object method "all_tags" via
package "Bio::SeqFeature::Annotated" at
/home/sendu/src/bioperl/core/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1300.
Ie. mysql.pm _update_attribute_index() method expects a
Bio::SeqFeature::Generic object (which has the all_tags method), not
just a Bio::SeqFeatureI. In fact all_tags() is just an alias to
SeqFeatureI's get_all_tags() which is deprecated. Likewise, the same
issue applies for the Generic-specific each_tag_value() alias of the
What might be the best way to resolve this? I'm thinking it would be
harmless to at least change _update_attribute_index() to call the
SeqFeatureI methods instead? Don't know if there's a desire to not use
the deprecated methods at all.
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