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"""Tests for FASTA sequence format writer.
"""
from unittest import TestCase
from cogent3.core.alignment import Alignment
from cogent3.core.info import Info
from cogent3.core.sequence import Sequence
from cogent3.format.fasta import alignment_to_fasta
class FastaTests(TestCase):
"""Tests for Fasta writer."""
def setUp(self):
"""Setup for Fasta tests."""
self.strings = ["AAAA", "CCCC", "gggg", "uuuu"]
self.labels = ["1st", "2nd", "3rd", "4th"]
self.infos = ["Dog", "Cat", "Mouse", "Rat"]
self.sequences_with_labels = list(map(Sequence, self.strings))
self.sequences_with_names = list(map(Sequence, self.strings))
for l, sl, sn in zip(
self.labels, self.sequences_with_labels, self.sequences_with_names
):
sl.label = l
sn.name = l
self.fasta_no_label = ">0\nAAAA\n>1\nCCCC\n>2\ngggg\n>3\nuuuu\n"
self.fasta_with_label = ">1st\nAAAA\n>2nd\nCCCC\n>3rd\nGGGG\n>4th\nUUUU\n"
self.fasta_with_label_lw2 = (
">1st\nAA\nAA\n>2nd\nCC\nCC\n>3rd\nGG\nGG\n>4th\nUU\nUU\n"
)
self.alignment_dict = {
"1st": "AAAA",
"2nd": "CCCC",
"3rd": "GGGG",
"4th": "UUUU",
}
self.alignment_object = Alignment(self.alignment_dict)
for label, info in zip(self.labels, self.infos):
self.alignment_object.named_seqs[label].info = Info(species=info)
self.fasta_with_label_species = (
">1st:Dog\nAAAA\n>2nd:Cat\nCCCC\n>3rd:Mouse\nGGGG\n>4th:Rat\nUUUU\n"
)
self.alignment_object.RowOrder = ["1st", "2nd", "3rd", "4th"]
def test_alignment_to_fasta(self):
"""should return correct fasta string."""
self.assertEqual(alignment_to_fasta({}), "")
self.assertEqual(alignment_to_fasta(self.alignment_dict), self.fasta_with_label)
self.assertEqual(
alignment_to_fasta(self.alignment_dict, block_size=2),
self.fasta_with_label_lw2,
)
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