def test_tree_integrity_ascii(self):
with open('test_data/tree_example.p', 'rb') as file:
test_tree = pickle.load(file)
TaxTree.ranked_lineage_filepath = '../../bin/database/taxonomy/rankedlineage.dmp'
rootNode = TaxTree.TaxNode("ROOT")
TaxTree.loadRankedLineage(species_indexes,rootNode)
rootNode.countChildren()
ETETree = TaxTree.create_ETE_tree(rootNode)
ascii = TaxTree.get_ASCII_tree(ETETree)
self.assertEqual(ascii, test_tree)
def test_extract_data(self):
test_lineage = "1805293 | Candidatus Pacearchaeota archaeon CG1_02_30_18 | | | | | | | | Archaea |"
test_list = ['1805293 ', ' Candidatus Pacearchaeota archaeon CG1_02_30_18 ', ' ', ' ', ' ', ' ', ' ', ' ',
' ', ' Archaea ']
result_list = TaxTree.extract_data(test_lineage)
self.assertEqual(result_list, test_list)
def test_least(self):
with open('test_data/least_example.p', 'rb') as file:
least_test = pickle.load(file)
TaxTree.ranked_lineage_filepath = '../../bin/database/taxonomy/rankedlineage.dmp'
rootNode = TaxTree.TaxNode("ROOT")
TaxTree.loadRankedLineage(species_indexes, rootNode)
rootNode.countChildren()
ranks = ['Species', 'Genus', 'Family', 'Order',
'Class', 'Phylum', 'Kingdom', 'Superkingdom', 'All']
f = io.StringIO()
with redirect_stdout(f):
for r in ranks:
rootNode.calculateCommonnessByRank(r, 5, rootNode, False)
output = f.getvalue()
self.assertEqual(least_test, output)
def test_lineage_fix(self):
original_lineage = [['Name', ' Human immunodeficiency virus 1 '], ['Species', ' '], ['Genus', ' Lentivirus '],
['Family', ' Retroviridae '], ['Order', ' '], ['Class', ' '], ['Phylum', ' '], ['Kingdom', ' '],
['Superkingdom', ' Viruses ']]
fixed_lineage = [['Name', ' Human immunodeficiency virus 1 '], ['Species', ' Human immunodeficiency virus 1 '],
['Genus', ' Lentivirus '], ['Family', ' Retroviridae '], ['Superkingdom', ' Viruses ']]
test_lineage = TaxTree.fixLineage(original_lineage)
self.assertEqual(test_lineage,fixed_lineage)
def test_ETETree(self):
with open('test_data/ETETree_example.p', 'rb') as file:
ETETree_example = pickle.load(file)
TaxTree.ranked_lineage_filepath = '../../bin/database/taxonomy/rankedlineage.dmp'
rootNode = TaxTree.TaxNode("ROOT")
TaxTree.loadRankedLineage(species_indexes, rootNode)
rootNode.countChildren()
ETETree = TaxTree.create_ETE_tree(rootNode)
f = io.StringIO()
with redirect_stdout(f):
ETETree.describe()
ETE_describe = f.getvalue()
t = io.StringIO()
with redirect_stdout(t):
ETETree_example.describe()
ETE_test_describe = t.getvalue()
self.assertEqual(ETE_describe,ETE_test_describe)
start = time.time()
# Initial safety checks.
args = parser.parse_args()
check_tree_args(args)
args.most = check_indexing_args(args.most)
args.least = check_indexing_args(args.least)
blastXMLRecords = open_BLAST_XML_file(args) #BLAST Output + extra stats
match_names = blast_parse(blastXMLRecords)
if (args.most or args.least or args.visualise or args.ascii
or args.save_ascii): #last second fix, do refactor
species_indexes = TaxMatch.match_results_to_taxonomy(
match_names) # Matching for most/least & tree work.
TaxTree.main(species_indexes, args)
# Sample tree used in the unit tests.
#species_indexes = ["9606","63221","741158","11676","7157","842271","1350382","1289305","1427098","1042"]
# There may come a time that tree functionality will be expanded to the point of needing to generate new pickles.
# Use the above to generate them.
#
end = time.time()
print("Finished in", end - start)
#Personal reference for Tabular Output
#Query ID, Subject ID, Percentage of Identical Matches, Alignment Length, Number Of Mismatches, Number Of Gap Openings,
#Start Of Alignment Query, End Of Alignment Query, Start Of Alignment Subject, End Of Alignment Subject, Expect Value, Bit Score
# also known as:
#qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore