def test_get_issues_no_such_gff_file():
"""
Test :py:func:`riboviz.check_fasta_gff.get_issues`
with FASTA file (:py:const:`TEST_FASTA_CHECK_FILE`) and
a non-existent GFF file raises an exception.
"""
with pytest.raises(FileNotFoundError):
check_fasta_gff.get_issues(TEST_FASTA_CHECK_FILE, "nosuch.gff")
def test_get_issues_no_such_fasta_file():
"""
Test :py:func:`riboviz.check_fasta_gff.get_issues`
with an empty FASTA file and GFF file
(:py:const:`TEST_GFF_CHECK_FILE`) raises an exception.
"""
with pytest.raises(FileNotFoundError):
check_fasta_gff.get_issues("nosuch.fasta", TEST_GFF_CHECK_FILE)
def test_get_issues_empty_gff_file(tmpdir):
"""
Test :py:func:`riboviz.check_fasta_gff.get_issues`
with FASTA file (:py:const:`TEST_FASTA_CHECK_FILE`) and
an empty GFF file raises an exception.
:param tmpdir: Temporary directory (pytest built-in fixture)
:type tmpdir: py._path.local.LocalPath
"""
# Cast to str to avoid "'LocalPath' object is not subscriptable"
# error from gff library.
gff_file = str(tmpdir.join("gff.gff"))
open(gff_file, 'a').close()
with pytest.raises(ValueError):
check_fasta_gff.get_issues(TEST_FASTA_CHECK_FILE, gff_file)
def test_get_issues_empty_fasta_file(tmpdir):
"""
Test :py:func:`riboviz.check_fasta_gff.get_issues`
with an empty FASTA file and GFF file
(:py:const:`TEST_GFF_CHECK_FILE`) raises an exception.
:param tmpdir: Temporary directory (pytest built-in fixture)
:type tmpdir: py._path.local.LocalPath
"""
# Cast to str to avoid "'LocalPath' object is not subscriptable"
# error from gff library.
fasta_file = str(tmpdir.join("fasta.fasta"))
open(fasta_file, 'a').close()
with pytest.raises(FastaIndexingError):
check_fasta_gff.get_issues(fasta_file, TEST_GFF_CHECK_FILE)
def test_get_issues_feature_format():
"""
Test :py:func:`riboviz.check_fasta_gff.get_issues`
with FASTA file (:py:const:`TEST_FASTA_CHECK_FILE`) and GFF file
(:py:const:`TEST_GFF_CHECK_FILE`) and custom
``cds_feature_format``.
"""
cds_feature_format = "{}-Custom"
num_sequences, num_features, num_cds_features, issues = \
check_fasta_gff.get_issues(TEST_FASTA_CHECK_FILE,
TEST_GFF_CHECK_FILE,
feature_format=cds_feature_format)
assert num_sequences == TEST_NUM_SEQUENCES, \
"Unexpected number of sequences"
assert num_features == TEST_NUM_FEATURES, \
"Unexpected number of features"
assert num_cds_features == TEST_NUM_CDS_FEATURES, \
"Unexpected number of CDS features"
# Create expected results for custom cds_feature_format.
test_check_issues = TEST_CHECK_ISSUES.copy()
test_check_issues.remove(TEST_NO_ID_NAME_ATTR_ISSUE)
test_check_issues.append(
(TEST_NO_ID_NAME_ATTR_ISSUE[0],
cds_feature_format.format(TEST_NO_ID_NAME_ATTR_PREFIX),
TEST_NO_ID_NAME_ATTR_ISSUE[2], TEST_NO_ID_NAME_ATTR_ISSUE[3]))
for issue in issues:
assert issue in test_check_issues
def test_get_issues_use_feature_name_true():
"""
Test :py:func:`riboviz.check_fasta_gff.get_issues`
with FASTA file (:py:const:`TEST_FASTA_CHECK_FILE`) and GFF file
(:py:const:`TEST_GFF_CHECK_FILE`) and ``use_feature_name=True``.
"""
num_sequences, num_features, num_cds_features, issues = \
check_fasta_gff.get_issues(TEST_FASTA_CHECK_FILE,
TEST_GFF_CHECK_FILE,
use_feature_name=True)
assert num_sequences == TEST_NUM_SEQUENCES, \
"Unexpected number of sequences"
assert num_features == TEST_NUM_FEATURES, \
"Unexpected number of features"
assert num_cds_features == TEST_NUM_CDS_FEATURES, \
"Unexpected number of CDS features"
# Create expected results when use_feature_name=True.
test_check_issues = TEST_CHECK_ISSUES.copy()
test_check_issues.remove(TEST_NO_ATG_START_ID_NAME_ATTR_ISSUE)
test_check_issues.append((TEST_NO_ATG_START_ID_NAME_ATTR_ISSUE[0],
TEST_NO_ATG_START_ID_NAME_ATTR_NAME,
TEST_NO_ATG_START_ID_NAME_ATTR_ISSUE[2],
TEST_NO_ATG_START_ID_NAME_ATTR_ISSUE[3]))
for issue in issues:
assert issue in test_check_issues
def test_get_issues():
"""
Test :py:func:`riboviz.check_fasta_gff.get_issues`
with FASTA file (:py:const:`TEST_FASTA_CHECK_FILE`) and GFF file
(:py:const:`TEST_GFF_CHECK_FILE`) and check all issues match
expected issues in :py:const:`TEST_CHECK_ISSUES`).
"""
num_sequences, num_features, num_cds_features, issues = \
check_fasta_gff.get_issues(TEST_FASTA_CHECK_FILE,
TEST_GFF_CHECK_FILE)
assert num_sequences == TEST_NUM_SEQUENCES, \
"Unexpected number of sequences"
assert num_features == TEST_NUM_FEATURES, \
"Unexpected number of features"
assert num_cds_features == TEST_NUM_CDS_FEATURES, \
"Unexpected number of CDS features"
for issue in issues:
assert issue in TEST_CHECK_ISSUES
def test_get_issues_start_codons():
"""
Test :py:func:`riboviz.check_fasta_gff.get_issues`
with FASTA file (:py:const:`TEST_FASTA_CHECK_FILE`) and GFF file
(:py:const:`TEST_GFF_CHECK_FILE`) and custom ``start_codons``.
"""
num_sequences, num_features, num_cds_features, issues = \
check_fasta_gff.get_issues(TEST_FASTA_CHECK_FILE,
TEST_GFF_CHECK_FILE,
start_codons=TEST_START_CODONS)
assert num_sequences == TEST_NUM_SEQUENCES, \
"Unexpected number of sequences"
assert num_features == TEST_NUM_FEATURES, \
"Unexpected number of features"
assert num_cds_features == TEST_NUM_CDS_FEATURES, \
"Unexpected number of CDS features"
# TEST_START_CODONS includes all start codons in test data so
# expect no NO_START_CODON issues in results.
test_check_issues = [(s, f, i, d) for (s, f, i, d) in TEST_CHECK_ISSUES
if i != check_fasta_gff.NO_START_CODON]
for issue in issues:
assert issue in test_check_issues