def test_get_promoters(self):
upstream_tss = 1000
downstream_tss = 50
seq_record = create_fake_record()
genes, ignored_genes = cassis.ignore_overlapping(
seq_record.get_genes()) # ignore ignored_genes
# see cassis/promoterregions.png for details
# [[start_prom1, end_prom1], [start_prom2, end_prom2], ...]
expected_promoters = [
[0, 150],
[301, 550],
[1450, 1999],
[2150, 3049],
[4001, 4371],
[8950, 9603],
]
promoters = get_promoters(seq_record, genes, upstream_tss,
downstream_tss)
self.assertEqual(list(map(lambda x: [x.start, x.end], promoters)),
expected_promoters)
cassis.write_promoters_to_file(self.options.output_dir,
seq_record.name, promoters)
# read expected files and save to string variable
expected_sequences_file = ""
with open(
path.get_full_path(
__file__, "data",
"expected_promoter_sequences.fasta")) as handle:
expected_sequences_file = handle.read()
expected_sequences_file = convert_newline(
expected_sequences_file.rstrip())
expected_positions_file = ""
with open(
path.get_full_path(
__file__, "data",
"expected_promoter_positions.csv")) as handle:
expected_positions_file = handle.read()
expected_positions_file = convert_newline(
expected_positions_file.rstrip())
# read test files and save to string variable
sequences_file = ""
with open(
os.path.join(self.options.output_dir, seq_record.name +
"_promoter_sequences.fasta")) as handle:
sequences_file = handle.read()
sequences_file = convert_newline(sequences_file.rstrip())
positions_file = ""
with open(
os.path.join(self.options.output_dir, seq_record.name +
"_promoter_positions.csv")) as handle:
positions_file = handle.read()
positions_file = convert_newline(positions_file.rstrip())
self.assertEqual(sequences_file, expected_sequences_file)
self.assertEqual(positions_file, expected_positions_file)
def test_ignore_overlapping(self):
expected_not_ignored = ["gene1", "gene4", "gene5", "gene6", "gene7", "gene8", "gene9"]
expected_ignored = ["gene2", "gene3"]
seq_record = create_fake_record()
not_ignored, ignored = cassis.ignore_overlapping(seq_record.get_genes())
self.assertEqual([x.locus_tag for x in ignored], expected_ignored)
self.assertEqual([x.locus_tag for x in not_ignored], expected_not_ignored)