def test_join_UnknownSeq(self):
"""Checks if UnknownSeq join correctly concatenates sequence with the spacer."""
spacer1 = UnknownSeq(5, character="-")
spacer2 = UnknownSeq(0, character="-")
spacers = [spacer1, spacer2]
self.assertEqual(
"-" * 15,
spacer1.join([UnknownSeq(5, character="-"), UnknownSeq(5, character="-")]),
)
self.assertEqual(
"N" * 5 + "-" * 10,
spacer1.join([Seq("NNNNN"), UnknownSeq(5, character="-")]),
)
example_strings = ["ATG", "ATG", "ATG", "ATG"]
example_strings_seqs = ["ATG", "ATG", Seq("ATG"), "ATG"]
# strings with empty spacer
str_concatenated = spacer2.join(example_strings)
self.assertEqual(str_concatenated, "".join(example_strings))
for spacer in spacers:
seq_concatenated = spacer.join(example_strings_seqs)
self.assertEqual(seq_concatenated, str(spacer).join(example_strings))
# Now try single sequence arguments, should join the letters
for target in example_strings + example_strings_seqs:
self.assertEqual(
str(spacer).join(str(target)), str(spacer.join(target))
)
def test_join_UnknownSeq(self):
"""Checks if UnknownSeq join correctly concatenates sequence with the spacer."""
# Only expect it to take Seq objects and/or strings in an iterable!
spacer1 = UnknownSeq(0, character="-", alphabet=generic_dna)
spacers = [
spacer1,
UnknownSeq(5, character="-", alphabet=generic_dna),
UnknownSeq(5, character="-", alphabet=generic_nucleotide)
]
example_strings = ["ATG", "ATG", "ATG", "ATG"]
example_strings_seqs = ["ATG", "ATG", Seq("ATG", generic_dna), "ATG"]
# strings with empty spacer
str_concatenated = spacer1.join(example_strings)
self.assertEqual(str(str_concatenated), "".join(example_strings))
self.assertEqual(str_concatenated.alphabet, spacer1.alphabet)
for spacer in spacers:
seq_concatenated = spacer.join(example_strings_seqs)
self.assertEqual(str(seq_concatenated),
str(spacer).join(example_strings))
self.assertEqual(seq_concatenated.alphabet, spacer.alphabet)
def test_join_UnknownSeq_mixed_alpha(self):
"""Check UnknownSeq can join incompatible alphabets."""
spacer = UnknownSeq(5, character="-", alphabet=generic_dna)
self.assertEqual(
"-" * 15,
spacer.join([
UnknownSeq(5, character="-", alphabet=generic_rna),
UnknownSeq(5, character="-", alphabet=generic_rna),
]),
)
self.assertEqual(
"N" * 5 + "-" * 10,
spacer.join([
Seq("NNNNN", generic_protein),
UnknownSeq(5, character="-", alphabet=generic_protein),
]),
)
def test_join_UnknownSeq_with_file(self):
"""Checks if UnknownSeq join correctly concatenates sequence from a file with the spacer."""
filename = 'Fasta/f003'
seqlist = [record.seq for record in SeqIO.parse(filename, 'fasta')]
seqlist_as_strings = [str(_) for _ in seqlist]
spacer = UnknownSeq(0, character="-", alphabet=generic_dna)
spacer1 = UnknownSeq(5, character="-", alphabet=generic_dna)
# seq objects with spacer
seq_concatenated = spacer.join(seqlist)
# seq objects with empty spacer
seq_concatenated1 = spacer1.join(seqlist)
ref_data = ref_data1 = ""
ref_data = str(spacer).join(seqlist_as_strings)
ref_data1 = str(spacer1).join(seqlist_as_strings)
self.assertEqual(str(seq_concatenated), ref_data)
self.assertEqual(str(seq_concatenated1), ref_data1)
with self.assertRaises(TypeError):
spacer.join(SeqIO.parse(filename, 'fasta'))
