def test_tree_annotation(self):
t = PhyloTree( "((9598, 9606), 10090);" )
t.annotate_ncbi_taxa()
self.assertEqual(t.sci_name, 'Euarchontoglires')
homi = (t&'9606').up
self.assertEqual(homi.sci_name, 'Homininae')
self.assertEqual(homi.taxid, 207598)
self.assertEqual(homi.rank, 'subfamily')
self.assertEqual(homi.named_lineage, [u'root', u'cellular organisms', u'Eukaryota', u'Opisthokonta', u'Metazoa', u'Eumetazoa', u'Bilateria', u'Deuterostomia', u'Chordata', u'Craniata', u'Vertebrata', u'Gnathostomata', u'Teleostomi', u'Euteleostomi', u'Sarcopterygii', u'Dipnotetrapodomorpha', u'Tetrapoda', u'Amniota', u'Mammalia', u'Theria', u'Eutheria', u'Boreoeutheria', u'Euarchontoglires', u'Primates', u'Haplorrhini', u'Simiiformes', u'Catarrhini', u'Hominoidea', u'Hominidae', u'Homininae'])
self.assertEqual(homi.lineage, [1, 131567, 2759, 33154, 33208, 6072, 33213, 33511, 7711, 89593, 7742, 7776, 117570, 117571, 8287, 1338369, 32523, 32524, 40674, 32525, 9347, 1437010, 314146, 9443, 376913, 314293, 9526, 314295, 9604, 207598] )
human = t&'9606'
self.assertEqual(human.sci_name, 'H**o sapiens')
self.assertEqual(human.taxid, 9606)
self.assertEqual(human.rank, 'species')
self.assertEqual(human.named_lineage, [u'root', u'cellular organisms', u'Eukaryota', u'Opisthokonta', u'Metazoa', u'Eumetazoa', u'Bilateria', u'Deuterostomia', u'Chordata', u'Craniata', u'Vertebrata', u'Gnathostomata', u'Teleostomi', u'Euteleostomi', u'Sarcopterygii', u'Dipnotetrapodomorpha', u'Tetrapoda', u'Amniota', u'Mammalia', u'Theria', u'Eutheria', u'Boreoeutheria', u'Euarchontoglires', u'Primates', u'Haplorrhini', u'Simiiformes', u'Catarrhini', u'Hominoidea', u'Hominidae', u'Homininae', u'H**o', u'H**o sapiens'])
self.assertEqual(human.lineage, [1, 131567, 2759, 33154, 33208, 6072, 33213, 33511, 7711, 89593, 7742, 7776, 117570, 117571, 8287, 1338369, 32523, 32524, 40674, 32525, 9347, 1437010, 314146, 9443, 376913, 314293, 9526, 314295, 9604, 207598, 9605, 9606])
def test_tree_annotation(self):
t = PhyloTree("((9598, 9606), 10090);")
t.annotate_ncbi_taxa()
self.assertEqual(t.sci_name, 'Euarchontoglires')
homi = (t & '9606').up
self.assertEqual(homi.sci_name, 'Homininae')
self.assertEqual(homi.taxid, 207598)
self.assertEqual(homi.rank, 'subfamily')
self.assertEqual(homi.named_lineage, [
u'root', u'cellular organisms', u'Eukaryota', u'Opisthokonta',
u'Metazoa', u'Eumetazoa', u'Bilateria', u'Deuterostomia',
u'Chordata', u'Craniata', u'Vertebrata', u'Gnathostomata',
u'Teleostomi', u'Euteleostomi', u'Sarcopterygii',
u'Dipnotetrapodomorpha', u'Tetrapoda', u'Amniota', u'Mammalia',
u'Theria', u'Eutheria', u'Boreoeutheria', u'Euarchontoglires',
u'Primates', u'Haplorrhini', u'Simiiformes', u'Catarrhini',
u'Hominoidea', u'Hominidae', u'Homininae'
])
self.assertEqual(homi.lineage, [
1, 131567, 2759, 33154, 33208, 6072, 33213, 33511, 7711, 89593,
7742, 7776, 117570, 117571, 8287, 1338369, 32523, 32524, 40674,
32525, 9347, 1437010, 314146, 9443, 376913, 314293, 9526, 314295,
9604, 207598
])
human = t & '9606'
self.assertEqual(human.sci_name, 'H**o sapiens')
self.assertEqual(human.taxid, 9606)
self.assertEqual(human.rank, 'species')
self.assertEqual(human.named_lineage, [
u'root', u'cellular organisms', u'Eukaryota', u'Opisthokonta',
u'Metazoa', u'Eumetazoa', u'Bilateria', u'Deuterostomia',
u'Chordata', u'Craniata', u'Vertebrata', u'Gnathostomata',
u'Teleostomi', u'Euteleostomi', u'Sarcopterygii',
u'Dipnotetrapodomorpha', u'Tetrapoda', u'Amniota', u'Mammalia',
u'Theria', u'Eutheria', u'Boreoeutheria', u'Euarchontoglires',
u'Primates', u'Haplorrhini', u'Simiiformes', u'Catarrhini',
u'Hominoidea', u'Hominidae', u'Homininae', u'H**o', u'H**o sapiens'
])
self.assertEqual(human.lineage, [
1, 131567, 2759, 33154, 33208, 6072, 33213, 33511, 7711, 89593,
7742, 7776, 117570, 117571, 8287, 1338369, 32523, 32524, 40674,
32525, 9347, 1437010, 314146, 9443, 376913, 314293, 9526, 314295,
9604, 207598, 9605, 9606
])
def test_ncbi_compare(self): t = PhyloTree( "((9606, (9598, 9606)), 10090);", sp_naming_function=lambda x: x.name ) t.annotate_ncbi_taxa()
def test_ncbi_compare(self):
t = PhyloTree("((9606, (9598, 9606)), 10090);",
sp_naming_function=lambda x: x.name)
t.annotate_ncbi_taxa()
