def test_join():
loc = {
"type": "join",
"segments": [
{"type": "span", "from": 2, "to": 3},
{"type": "span", "from": 5, "to": 7}
]
}
t.eq(t.extract("ACGTACGT", loc), ("CGACG", (False, False)))
def test_fuzzy_internal_join():
mod1 = {"from": "fuzzy"}
mod2 = {"to": "fuzzy"}
loc = {
"type": "join",
"segments": [
{"type": "span", "from": 2, "to": 3},
{"type": "span", "from": 4, "to": 5, "modifiers": mod1},
{"type": "span", "from": 6, "to": 7}
]
}
t.raises(ValueError, t.extract, "ACGTATACACT", loc)
loc["segments"][1]["modifiers"] = mod2
t.raises(ValueError, t.extract, "ACGTATACACT", loc)
del loc["segments"][1]["modifiers"]
t.eq(t.extract("ACGTATACACT", loc), ("CGTATA", (False, False)))
def test_fuzzy_join():
mod1 = {"from": "fuzzy"}
mod2 = {"to": "fuzzy"}
loc = {
"type": "join",
"segments": [
{"type": "span", "from": 2, "to": 3, "modifiers": mod1},
{"type": "span", "from": 5, "to": 7, "modifiers": mod2}
]
}
t.eq(t.extract("TGGCACGTAA", loc), ("GGACG", (True, True)))
loc["segments"][0]["modifiers"] = mod2
t.raises(ValueError, t.extract, "ACGTATACACT", loc)
del loc["segments"][0]["modifiers"]
loc["segments"][1]["modifiers"] = mod1
t.raises(ValueError, t.extract, "ACGTATACACT", loc)
def test_basic():
loc = {"type": "span", "from": 2, "to": 3}
t.eq(t.extract("ACGT", loc), ("CG", (False, False)))
def test_fuzzy_span():
mods = {"from": "fuzzy", "to": "fuzzy"}
loc = {"type": "span", "from": 2, "to": 3, "modifiers": mods}
t.eq(t.extract("TCGGGA", loc), ("CG", (True, True)))
def test_index():
loc = {"type": "index", "position": 3}
t.eq(t.extract("ACGTAG", loc), ("G", (False, False)))
def test_complement():
loc = {
"type": "complement",
"segment": {"type": "span", "from": 2, "to": 6}
}
t.eq(t.extract("ACCGTT", loc), ("AACGG", (False, False)))
