Author Name: Chris Fields (@cjfields)
Original Redmine Issue: 3416, https://redmine.open-bio.org/issues/3416
Original Date: 2013-02-20
Original Assignee: Bioperl Guts
A single Bio::DB::Taxonomyget_lca() test is failing when mixing remote and local databases (the wisdom of doing this could be questioned…):
[cjfields@pyrimidine-laptop bioperl-live (v1)]$ prove -lrv t/RemoteDB/Taxonomy.t
t/RemoteDB/Taxonomy.t ..
1..142
ok 1 - use Bio::DB::Taxonomy;
ok 2 - use Bio::Tree::Tree;
ok 3
ok 4 - The object isa Bio::DB::Taxonomy::entrez
ok 5 - The object isa Bio::DB::Taxonomy
...
ok 115
ok 116 - get_lca() within flatfile db
ok 117
ok 118 - get_lca() within entrez db
ok 119 # TODO Mixing databases for get_lca() not working, see bug
not ok 120 - get_lca() mixing flatfile and remote db # TODO Mixing databases for get_lca() not working, see bug
# Failed (TODO) test 'get_lca() mixing flatfile and remote db'
# at t/RemoteDB/Taxonomy.t line 228.
# got: 'Bilateria'
# expected: 'Homo'
ok 121
ok 122
...
All tests successful.
Test Summary Report
-------------------
t/RemoteDB/Taxonomy.t (Wstat: 0 Tests: 142 Failed: 0)
TODO passed: 119
Files=1, Tests=142, 24 wallclock secs ( 0.05 usr 0.01 sys + 1.73 cusr 1.23 csys = 3.02 CPU)
Result: PASS
This may be as simple as updating the data for the flatfile data, but needs to be checked. get_lca() works fine if using the same database source (flatfile or entrez).
Author Name: Chris Fields (@cjfields) Original Redmine Issue: 3416, https://redmine.open-bio.org/issues/3416 Original Date: 2013-02-20 Original Assignee: Bioperl Guts
A single
Bio::DB::Taxonomyget_lca()test is failing when mixing remote and local databases (the wisdom of doing this could be questioned…):This may be as simple as updating the data for the flatfile data, but needs to be checked.
get_lca()works fine if using the same database source (flatfile or entrez).