def test_conversion_highlevel(path):
"""
Test whether the high-level GFF3 interface can properly read
the features from a GFF3 file and write these properties to a file
without data changing.
The 'phase' is tested additionally, since it is not part of a
`Feature` object.
"""
file = gff.GFFFile()
file.read(join(data_dir, path))
ref_annot = gff.get_annotation(file)
ref_phases = []
for _, _, type, _, _, _, _, phase, _ in file:
if type == "CDS":
ref_phases.append(phase)
file = gff.GFFFile()
gff.set_annotation(file, ref_annot)
temp_file_name = biotite.temp_file("gff3")
file.write(temp_file_name)
file = gff.GFFFile()
file.read(temp_file_name)
test_annot = gff.get_annotation(file)
test_phases = []
for _, _, type, _, _, _, _, phase, _ in file:
if type == "CDS":
test_phases.append(phase)
assert ref_annot == test_annot
assert test_phases == ref_phases
def test_conversion_highlevel(path):
"""
Test whether the high-level GFF3 interface can properly read
the features from a GFF3 file and write these properties to a file
without data changing.
The 'phase' is tested additionally, since it is not part of a
`Feature` object.
"""
gff_file = gff.GFFFile.read(join(data_dir("sequence"), path))
ref_annot = gff.get_annotation(gff_file)
ref_phases = []
for _, _, type, _, _, _, _, phase, _ in gff_file:
if type == "CDS":
ref_phases.append(phase)
gff_file = gff.GFFFile()
gff.set_annotation(gff_file, ref_annot)
temp = TemporaryFile("w+")
gff_file.write(temp)
temp.seek(0)
gff_file = gff.GFFFile.read(temp)
temp.close()
test_annot = gff.get_annotation(gff_file)
test_phases = []
for _, _, type, _, _, _, _, phase, _ in gff_file:
if type == "CDS":
test_phases.append(phase)
assert ref_annot == test_annot
assert test_phases == ref_phases
def test_genbank_consistency(path):
"""
Test whether the same annotation (if reasonable) can be read from a
GFF3 file and a GenBank file.
"""
file = gb.GenBankFile()
file.read(join(data_dir, path))
ref_annot = gb.get_annotation(file)
file = gff.GFFFile()
file.read(join(data_dir, path[:-3] + ".gff3"))
test_annot = gff.get_annotation(file)
# Remove qualifiers, since they will be different
# in GFF3 and GenBank
ref_annot = seq.Annotation(
[seq.Feature(feature.key, feature.locs) for feature in ref_annot]
)
test_annot = seq.Annotation(
[seq.Feature(feature.key, feature.locs) for feature in test_annot]
)
for feature in test_annot:
# Only CDS, gene, intron and exon should be equal
# in GenBank and GFF3
if feature.key in ["CDS", "gene", "intron", "exon"]:
try:
assert feature in test_annot
except AssertionError:
print(feature.key)
for loc in feature.locs:
print(loc)
raise
def test_conversion_lowlevel(path):
"""
Test whether the low-level GFF3 interface can properly read
a GenBank file and write a file, without data changing.
"""
file = gff.GFFFile()
file.read(join(data_dir, path))
ref_entries = [entry for entry in file]
file = gff.GFFFile()
for entry in ref_entries:
file.append(*entry)
temp_file_name = biotite.temp_file("gff3")
file.write(temp_file_name)
file = gff.GFFFile()
file.read(temp_file_name)
test_entries = [field for field in file]
assert test_entries == ref_entries
def test_percent_encoding():
"""
Test whether percent encoding is working correctly based on an
artificial test file.
"""
file = gff.GFFFile()
file.read(join(data_dir, "percent_test.gff3"))
seqid, source, type, start, end, score, strand, phase, attrib \
= file[0]
assert seqid == "123,456"
assert source == "ääh"
assert type == "regi&n"
assert attrib == {
"ID" : "AnID;AnotherID",
"Name" : "Ångström",
"c$l$r": "red\tgreen\tblue"
}
file2 = gff.GFFFile()
file.append(seqid, source, type, start, end, score, strand, phase, attrib)
assert (seqid, source, type, start, end, score, strand, phase, attrib) \
== file[0]
def test_feature_without_id():
"""
A feature without 'ID' should raise an error if it has multiple
locations and consequently multiple entries in the GFF3 file.
"""
annot = seq.Annotation(
[seq.Feature(
key = "CDS",
locs = [seq.Location(1,2), seq.Location(4,5)],
qual = {"some" : "qualifiers"}
)]
)
file = gff.GFFFile()
with pytest.raises(ValueError):
gff.set_annotation(file, annot)
def test_entry_indexing():
"""
Test whether a GFF3 file is indexed correctly based on an artificial
test file with multiple directives, including '##FASTA'.
"""
file = gff.GFFFile()
with pytest.warns(UserWarning):
file.read(join(data_dir, "indexing_test.gff3"))
assert file._directives == [
("directive 1", 1),
("directive 2", 2),
("directive 3", 7),
("FASTA", 8),
]
assert file._entries == [3,4,6]
def test_file_access():
"""
Test getting, setting, deleting and inserting entries in a GFF3
file.
"""
file = gff.GFFFile()
entry_scaffold = ("ab", "cd", 1, 2, None, None, None, {"Id":"foo"})
entry = ("a",) + entry_scaffold
file.append(*entry)
assert file[0] == entry
file.append(*(("b",) + entry_scaffold))
file.insert(1, *(("c",) + entry_scaffold))
file[1] = ("d",) + entry_scaffold
file.insert(3, *(("e",) + entry_scaffold))
del file[2]
assert [seqid for seqid, _, _, _, _, _, _, _, _ in file] \
== ["a", "d", "e", ]
def test_conversion_lowlevel(path):
"""
Test whether the low-level GFF3 interface can properly read
a GenBank file and write a file, without data changing.
"""
gff_file = gff.GFFFile.read(join(data_dir("sequence"), path))
ref_entries = [entry for entry in gff_file]
gff_file = gff.GFFFile()
for entry in ref_entries:
gff_file.append(*entry)
temp = TemporaryFile("w+")
gff_file.write(temp)
temp.seek(0)
gff_file = gff.GFFFile.read(temp)
temp.close()
test_entries = [field for field in gff_file]
assert test_entries == ref_entries
def test_error():
"""
Assert that certain exceptions are raised
"""
file = gff.GFFFile()
with pytest.raises(ValueError):
# 'seqid' beginning with '>' is not legal
file.append(">xyz", "ab", "cd", 1, 2, None, None, None, {"Id":"foo"})
with pytest.raises(ValueError):
# String fields must not be empty
file.append("", "ab", "cd", 1, 2, None, None, None, {"Id":"foo"})
with pytest.raises(ValueError):
# String fields must not be empty
file.append("xyz", "", "cd", 1, 2, None, None, None, {"Id":"foo"})
with pytest.raises(ValueError):
# String fields must not be empty
file.append("xyz", "ab", "", 1, 2, None, None, None, {"Id":"foo"})
with pytest.raises(ValueError):
# Attributes not be empty
file.append("xyz", "ab", "cd", 1, 2, None, None, None, {})
