Author Name: Ni Zhang (Ni Zhang)
Original Redmine Issue: 3420, https://redmine.open-bio.org/issues/3420
Original Date: 2013-03-01
Original Assignee: Bioperl Guts
With get_taxon(name) it is possible to receive multiple results,
ie. There were multiple ids (55087 1386) matching ‘Bacillus’, using ‘55087’
would get us a genus of stick insect instead of the bacterial genus that comes to mind.
A possible fix would be to provide the option to search under a specific node of the taxonomy tree: I was told that there were no nodes with identical names under kingdoms.
This might require the addition of some sort of Ancestor checking in Bio::Taxon
Along with modifications to the get_taxon code itself in Bio::DB::Taxonomy
I did come up with a preliminary attempt at doing this myself in Bio::DB::Taxonomy::flatfile, but with less than 4 months of Perl experience, much less BioPerl, I think this would be better placed as a feature request rather than some form of pull request.
Author Name: Ni Zhang (Ni Zhang) Original Redmine Issue: 3420, https://redmine.open-bio.org/issues/3420 Original Date: 2013-03-01 Original Assignee: Bioperl Guts
With get_taxon(name) it is possible to receive multiple results, ie. There were multiple ids (55087 1386) matching ‘Bacillus’, using ‘55087’ would get us a genus of stick insect instead of the bacterial genus that comes to mind.
A possible fix would be to provide the option to search under a specific node of the taxonomy tree: I was told that there were no nodes with identical names under kingdoms. This might require the addition of some sort of Ancestor checking in Bio::Taxon Along with modifications to the get_taxon code itself in Bio::DB::Taxonomy
I did come up with a preliminary attempt at doing this myself in Bio::DB::Taxonomy::flatfile, but with less than 4 months of Perl experience, much less BioPerl, I think this would be better placed as a feature request rather than some form of pull request.