def subjects(hits):
return [
classes.Subject(hits=[hits[0]],
ipg="1",
start=14044,
end=14641,
strand="-"),
classes.Subject(hits=[hits[1]],
ipg="2",
start=11815,
end=13459,
strand="+"),
classes.Subject(hits=[hits[2]],
ipg="3",
start=9656,
end=11184,
strand="+"),
classes.Subject(hits=[hits[3], hits[4], hits[5]],
ipg="4",
start=1234,
end=5678,
strand="+"),
classes.Subject(hits=[hits[3], hits[4], hits[5]],
ipg="4",
start=9656,
end=11184,
strand="+"),
]
def subjects_clustering():
return [
classes.Subject(start=0, end=1000, strand="+"),
classes.Subject(start=2000, end=3000, strand="+"),
classes.Subject(start=5000, end=6000, strand="+"),
classes.Subject(start=9000, end=10000, strand="+"),
classes.Subject(start=14000, end=15000, strand="+"),
]
def subjects(hits):
return [
classes.Subject(name="s1", hits=[hits[0]], ipg="1", start=0, end=1000, strand="-"),
classes.Subject(name="s2", hits=[hits[1]], ipg="2", start=2000, end=3000, strand="+"),
classes.Subject(name="s3", hits=[hits[2]], ipg="3", start=5000, end=6000, strand="+"),
classes.Subject(name="s4", hits=[hits[3], hits[4], hits[5]], ipg="4", start=9000, end=10000, strand="+"),
classes.Subject(name="s5", hits=[hits[3], hits[4], hits[5]], ipg="4", start=14000, end=15000, strand="+"),
]
def subjects(hits):
return [
classes.Subject("id1", hits[:2], "subject1", "ipg1", "0", "100", -1),
classes.Subject("id1", [hits[1], hits[0]], "subject1", "ipg1", 0, 100,
-1),
classes.Subject("id2", hits[2:3], "subject2", "ipg2", 1200, 6000, 1),
classes.Subject("id3", hits[3:4], "subject3", "ipg3", 500, "1000", 1),
classes.Subject("id4", hits[4:5], "subject4", "ipg4", 6453, 8000, 1),
classes.Subject("id5",
name="intermediate subject",
start=8100,
end=9000),
]
def test_subject_empty_instantiation():
assert [[], None, None, None, None, None] == [
getattr(classes.Subject(), val)
for val in ["hits", "ipg", "name", "start", "end", "strand"]
]