def test_fasta_with_fungi(self):
result = fungi_from_fasta(self.fasta_with_fungi,
self.accession,
self.taxonomy_with_fungi)
self.assertEqual(list(result),
[BiologicalSequence("ATCG", id="AB21",
description="Fungi")])
def test_fasta_with_fungi(self):
result = fungi_from_fasta(self.fasta_with_fungi,
self.accession,
self.taxonomy_with_fungi)
self.assertEqual(list(result),
[Sequence("ATCG", metadata={'id': "AB21",
'description': "Fungi"})])
def test_fasta_with_many_fungi(self):
result = fungi_from_fasta(self.fasta_many_fungi, self.accession,
self.taxonomy_with_fungi)
self.assertEqual(list(result), [
BiologicalSequence("GGGG", id="AB123", description="Fungi"),
BiologicalSequence("CCCC", id="AB125", description="Fungi"),
BiologicalSequence("AAAA", id="AB126", description="Fungi"),
])
def test_fasta_with_many_fungi(self):
result = fungi_from_fasta(self.fasta_many_fungi,
self.accession,
self.taxonomy_with_fungi)
self.assertEqual(list(result), [
Sequence("GGGG", metadata={'id': "AB123", 'description': "Fungi"}),
Sequence("CCCC", metadata={'id': "AB125", 'description': "Fungi"}),
Sequence("AAAA", metadata={'id': "AB126", 'description': "Fungi"}),
])
def test_fasta_with_fungi(self):
result = fungi_from_fasta(self.fasta_with_fungi, self.accession,
self.taxonomy_with_fungi)
self.assertEqual(list(result), [
Sequence("ATCG", metadata={
'id': "AB21",
'description': "Fungi"
})
])
def test_fasta_with_many_fungi(self):
result = fungi_from_fasta(self.fasta_many_fungi,
self.accession,
self.taxonomy_with_fungi)
self.assertEqual(list(result), [
BiologicalSequence("GGGG", id="AB123", description="Fungi"),
BiologicalSequence("CCCC", id="AB125", description="Fungi"),
BiologicalSequence("AAAA", id="AB126", description="Fungi"),
])
def test_fasta_with_many_fungi(self):
result = fungi_from_fasta(self.fasta_many_fungi, self.accession,
self.taxonomy_with_fungi)
self.assertEqual(list(result), [
Sequence("GGGG", metadata={
'id': "AB123",
'description': "Fungi"
}),
Sequence("CCCC", metadata={
'id': "AB125",
'description': "Fungi"
}),
Sequence("AAAA", metadata={
'id': "AB126",
'description': "Fungi"
}),
])
def extract_fungi(
aligned_silva_file: AlignedDNAFASTAFormat,
accession_file: SilvaAccessionFormat,
taxonomy_file: SilvaTaxonomyFormat,
) -> AlignedDNAFASTAFormat:
aligned_silva_fh = aligned_silva_file.open()
accession_fh = accession_file.open()
taxonomy_fh = taxonomy_file.open()
fasta_file = AlignedDNAFASTAFormat()
skbio.write(fungi_from_fasta(aligned_silva_fh, accession_fh,
taxonomy_fh), into=str(fasta_file), format='fasta')
# TODO this code is a good example of pithy return for plugins
# TODO redo other functions in the same way by instantiating a
return fasta_file
def test_duplicate_map_numbers(self):
with self.assertRaises(ValueError):
list(
fungi_from_fasta(self.fasta_with_fungi, self.accession,
self.taxonomy_with_duplicates))
def test_fasta_with_fungi(self):
result = fungi_from_fasta(self.fasta_with_fungi, self.accession,
self.taxonomy_with_fungi)
self.assertEqual(
list(result),
[BiologicalSequence("ATCG", id="AB21", description="Fungi")])
def test_fasta_no_fungi(self):
result = fungi_from_fasta(self.fasta_no_fungi, self.accession,
self.taxonomy_no_fungi)
self.assertEqual(list(result), [])
def test_duplicate_map_numbers(self):
with self.assertRaises(ValueError):
list(fungi_from_fasta(self.fasta_with_fungi,
self.accession,
self.taxonomy_with_duplicates))
def test_fasta_no_fungi(self):
result = fungi_from_fasta(self.fasta_no_fungi,
self.accession,
self.taxonomy_no_fungi)
self.assertEqual(list(result), [])
