def test_mrna_cds(gff, expected):
"""find all cds that belong to mrna"""
genes = []
mrnas = []
cds = []
exons = []
res = {}
gf = gffhelper.GFFFile(gff)
for o in gf.get_gff_objects():
if o.type == "gene":
genes.append(o)
if o.type == "mRNA":
mrnas.append(o)
if o.type == "CDS":
cds.append(o)
if o.type == "exon":
exons.append(o)
for g in genes:
mg = [m.get_ID() for m in mrnas if g.get_ID() in m.get_Parent()]
res[g.get_ID()] = mg
for m in mg:
emg = [e.get_ID() for e in exons if m in e.get_Parent()]
res[m] = [emg]
cmg = [c.get_ID() for c in cds if m in c.get_Parent()]
res[m].append(cmg)
print(res)
assert res == expected
def test_attrib_ontology_term(gff, index, expected_Ontology_term,
expected_Dbxref):
g = gffhelper.GFFFile(gff)
o = list(g.get_gff_objects())[index]
d = [x.strip('"') for x in o.get_Dbxref()]
ot = [x.strip('"') for x in o.get_Ontology_term()]
assert d == expected_Dbxref
assert ot == expected_Ontology_term
pass
def test_attrib_id_alias_note_(gff, index, expected_id, expected_alias,
expected_note):
g = gffhelper.GFFFile(gff)
o = list(g.get_gff_objects())[index]
i = o.get_ID()
a = o.get_Alias()
print(a)
n = o.get_Note()
assert i == expected_id
try:
assert a == expected_alias
except AssertionError:
try:
assert a == []
except AssertionError:
raise AssertionError
try:
assert n == expected_note
except AssertionError:
try:
assert n == []
except AssertionError:
raise AssertionError
def test_score(gff, index, expected_score, expected_strand, expected_phase):
g = gffhelper.GFFFile(gff)
objs = list(g.get_gff_objects())
assert objs[index].score == expected_score
assert objs[index].strand == expected_strand
assert objs[index].phase == expected_phase
def test_start_end(gff, index, expected_start, expected_end):
g = gffhelper.GFFFile(gff)
objs = list(g.get_gff_objects())
assert int(objs[index].start) == expected_start
assert int(objs[index].end) == expected_end
def test_type(gff, index, expected):
g = gffhelper.GFFFile(gff)
objs = list(g.get_gff_objects())
assert objs[index].type == expected
def test_source(gff, expected):
g = gffhelper.GFFFile(gff)
for o in g.get_gff_objects():
assert o.source == expected
def test_available_types(gff, expected):
g = gffhelper.GFFFile(gff)
t = g.get_available_types()
print(t)
assert t == expected
def test_attrib_is_circular(gff, index, expected_Is_circular):
g = gffhelper.GFFFile(gff)
o = list(g.get_gff_objects())[index]
c = o.get_Is_circular()
assert c == expected_Is_circular
def test_attrib_parent(gff, index, expected_Parent):
g = gffhelper.GFFFile(gff)
objs = list(g.get_gff_objects())
p = objs[index].get_Parent()
assert p == expected_Parent
def test_metadata(gff, expected):
g = gffhelper.GFFFile(gff)
assert g.path == gff
assert g.metadata == expected
def test_attributes(gff, index, expected_attributes):
g = gffhelper.GFFFile(gff)
objs = list(g.get_gff_objects())
for e in expected_attributes:
vals = [a.value for a in objs[index].attributes if a.tag == e["tag"]]
assert vals == [list(e["value"].split(","))]