def test_lca_none(self):
# scenario 3: top level is inconsistent
taxa = [
'k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Vibrionales;f__Vibrionaceae;g__Vibrio;s__Vibrio_tasmaniensis;t__Vibrio_tasmaniensis_LGP32',
'k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Vibrionales;f__Vibrionaceae;g__Vibrio;s__Vibrio_maritimus;t__',
'k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Vibrionales;f__Vibrionaceae;g__Aliivibrio;s__Aliivibrio_wodanis;t__',
'k__BacteriaPlasmid;p__Proteobacteria;c__Gammaproteobacteria;o__Vibrionales;f__Vibrionaceae;g__Aliivibrio;s__Aliivibrio_wodanis;t__'
]
obs = least_common_ancestor(taxa)
self.assertIsNone(obs)
def test_least_common_ancestor(self):
# normal scenario
taxa = [
'k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;s__Clostridium acetobutylicum',
'k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;s__Clostridium botulinum',
'k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;s__Clostridium aldrichii',
'k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Caminicella;s__Caminicella sporogenes'
]
obs = least_common_ancestor(taxa)
exp = 'k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae'
self.assertEqual(obs, exp)
# scenario 1: lowest level is unclassified
taxa = [
'k__Bacteria;p__Deinococcus-Thermus;c__Deinococci;o__Thermales;f__Thermaceae;g__Thermus;s__Thermus thermophilus;t__',
'k__Bacteria;p__Deinococcus-Thermus;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus;s__Deinococcus radiodurans;t__',
'k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;s__Clostridium acetobutylicum;t__',
'k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;s__Clostridium botulinum;t__'
]
obs = least_common_ancestor(taxa)
exp = 'k__Bacteria'
self.assertEqual(obs, exp)
# scenario 2: middle level is unclassified
taxa = [
'k__Viruses;p__ssDNA_viruses;c__Geminiviridae;o__;f__;g__Begomovirus;s__Sida_mosaic_Sinaloa_virus',
'k__Viruses;p__ssDNA_viruses;c__Geminiviridae;o__;f__;g__Mastrevirus;s__Panicum_streak_virus',
'k__Viruses;p__ssDNA_viruses;c__Geminiviridae;o__;f__;g__Begomovirus;s__Cotton_leaf_crumple_virus',
'k__Viruses;p__ssDNA_viruses;c__Nanoviridae;o__;f__;g__Babuvirus;s__Banana_bunchy_top_virus'
]
obs = least_common_ancestor(taxa)
exp = 'k__Viruses;p__ssDNA_viruses'
self.assertEqual(obs, exp)
# scenario 3: top level is inconsistent
taxa = [
'k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Vibrionales;f__Vibrionaceae;g__Vibrio;s__Vibrio_tasmaniensis;t__Vibrio_tasmaniensis_LGP32',
'k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Vibrionales;f__Vibrionaceae;g__Vibrio;s__Vibrio_maritimus;t__',
'k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Vibrionales;f__Vibrionaceae;g__Aliivibrio;s__Aliivibrio_wodanis;t__',
'k__BacteriaPlasmid;p__Proteobacteria;c__Gammaproteobacteria;o__Vibrionales;f__Vibrionaceae;g__Aliivibrio;s__Aliivibrio_wodanis;t__'
]
obs = least_common_ancestor(taxa)
self.assertIsNone(obs)
def test_continued_blanks(self):
# unclassified until phylum
taxa = [
'k__;p__Firmicutes;c__;o__;f__;g__Clostridium',
'k__;p__Firmicutes;c__;o__;f__;g__Clostridium',
'k__;p__Firmicutes;c__;o__;f__;g__Clostridium',
'k__;p__Firmicutes;c__;o__;f__;g__Caminicella'
]
obs = least_common_ancestor(taxa)
exp = 'k__;p__Firmicutes'
self.assertEqual(obs, exp)
def test_blanks_kingdom_class(self):
# unclassified until family
taxa = [
'k__;p__Firmicutes;c__;o__Clostridiales;f__Clostridiaceae;g__Clostridium',
'k__;p__Firmicutes;c__;o__Clostridiales;f__Clostridiaceae;g__Clostridium',
'k__;p__Firmicutes;c__;o__Clostridiales;f__Clostridiaceae;g__Clostridium',
'k__;p__Firmicutes;c__;o__Clostridiales;f__Clostridiaceae;g__Caminicella'
]
obs = least_common_ancestor(taxa)
exp = 'k__;p__Firmicutes;c__;o__Clostridiales;f__Clostridiaceae'
self.assertEqual(obs, exp)
def test_blank_class(self):
# normal scenario
taxa = [
'k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;s__Clostridium acetobutylicum',
'k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;s__Clostridium botulinum',
'k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;s__Clostridium aldrichii',
'k__Bacteria;p__Firmicutes;c__;o__Clostridiales;f__Clostridiaceae;g__Caminicella;s__Caminicella sporogenes'
]
obs = least_common_ancestor(taxa)
exp = 'k__Bacteria;p__Firmicutes'
self.assertEqual(obs, exp)
def test_lca_phylum(self):
# scenario 2: middle level is unclassified
taxa = [
'k__Viruses;p__ssDNA_viruses;c__Geminiviridae;o__;f__;g__Begomovirus;s__Sida_mosaic_Sinaloa_virus',
'k__Viruses;p__ssDNA_viruses;c__Geminiviridae;o__;f__;g__Mastrevirus;s__Panicum_streak_virus',
'k__Viruses;p__ssDNA_viruses;c__Geminiviridae;o__;f__;g__Begomovirus;s__Cotton_leaf_crumple_virus',
'k__Viruses;p__ssDNA_viruses;c__Nanoviridae;o__;f__;g__Babuvirus;s__Banana_bunchy_top_virus'
]
obs = least_common_ancestor(taxa)
exp = 'k__Viruses;p__ssDNA_viruses'
self.assertEqual(obs, exp)
def test_lca_kingdom(self):
# scenario 1: lowest level is unclassified
taxa = [
'k__Bacteria;p__Deinococcus-Thermus;c__Deinococci;o__Thermales;f__Thermaceae;g__Thermus;s__Thermus thermophilus;t__',
'k__Bacteria;p__Deinococcus-Thermus;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus;s__Deinococcus radiodurans;t__',
'k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;s__Clostridium acetobutylicum;t__',
'k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;s__Clostridium botulinum;t__'
]
obs = least_common_ancestor(taxa)
exp = 'k__Bacteria'
self.assertEqual(obs, exp)