def test_join_Seq(self):
"""Checks if Seq join correctly concatenates sequence with the spacer."""
spacer = Seq("NNNNN")
self.assertEqual(
"N" * 15, spacer.join([Seq("NNNNN"), Seq("NNNNN")]),
)
spacer1 = Seq("")
spacers = [spacer1, Seq("NNNNN"), Seq("GGG")]
example_strings = ["ATG", "ATG", "ATG", "ATG"]
example_strings_seqs = ["ATG", "ATG", Seq("ATG"), "ATG"]
# strings with empty spacer
str_concatenated = spacer1.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_Seq_mixed_alpha(self):
"""Check Seq can join incompatible alphabets."""
spacer = Seq("NNNNN", generic_dna)
self.assertEqual(
"N" * 15,
spacer.join([Seq("NNNNN", generic_rna),
Seq("NNNNN", generic_rna)]),
)
self.assertEqual(
"N" * 15,
spacer.join(
[Seq("NNNNN", generic_protein),
Seq("NNNNN", generic_protein)]),
)
def test_join_Seq(self):
"""Checks if Seq join correctly concatenates sequence with the spacer."""
# Only expect it to take Seq objects and/or strings in an iterable!
spacer1 = Seq("", generic_dna)
spacers = [
spacer1,
Seq("NNNNN", generic_dna),
Seq("GGG", 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)
# 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_Seq_with_file(self):
"""Checks if Seq 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 = Seq('NNNNN')
spacer1 = Seq('')
# 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'))
def test_join_Seq(self):
"""Checks if Seq join correctly concatenates sequence with the spacer."""
# Only expect it to take Seq objects and/or strings in an iterable!
spacer1 = Seq('', generic_dna)
spacers = [spacer1, Seq('NNNNN', generic_dna), Seq('GGG', 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)
