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import gfapy
import unittest
class TestAPIPositionals(unittest.TestCase):
s = {
"S1": "S\t1\t*",
"L": "L\t1\t+\t2\t+\t*",
"C": "C\t1\t+\t2\t+\t10\t*",
"P": "P\tx\t1+,2+\t*",
"S2": "S\t2\t100\t*",
"E": "E\t*\t1+\t2+\t10\t20\t30\t40\t*",
"F": "F\t1\t5+\t11\t21\t31\t41\t*",
"G": "G\t*\t1+\t2+\t1000\t1",
"U": "U\t*\t1 2 3",
"O": "O\t*\t1+ 2+ 3+",
}
f = {k:v.split("\t") for k, v in s.items()}
l = {k:gfapy.Line(v) for k, v in s.items()}
fieldnames = {
"S1":["name", "sequence"],
"L" :["from_segment", "from_orient", "to_segment", "to_orient", "overlap"],
"C" :["from_segment", "from_orient", "to_segment", "to_orient", "pos", "overlap"],
"P" :["path_name", "segment_names", "overlaps"],
"S2":["sid", "slen", "sequence"],
"E" :["eid", "sid1", "sid2", "beg1", "end1", "beg2", "end2", "alignment"],
"F" :["sid", "external", "s_beg", "s_end", "f_beg", "f_end", "alignment"],
"G" :["gid", "sid1", "sid2", "disp", "var"],
"U" :["pid", "items"],
"O" :["pid", "items"],
}
# alternative values to set tests
v1 = {
"S1":{"name":"sx", "sequence":"accg"},
"L":{"from_segment":"a1", "from_orient":"-", "to_segment":"a2", "to_orient":"-",
"overlap": gfapy.Alignment("12M")},
"C":{"from_segment":"cx", "from_orient":"-", "to_segment":"cy", "to_orient":"-",
"pos":123, "overlap": gfapy.Alignment("120M")},
"P":{"path_name":"px", "segment_names":[gfapy.OrientedLine("x","+"), gfapy.OrientedLine("y","-")],
"overlaps":[gfapy.Alignment("10M")]},
"S2":{"sid":"s2s", "slen":999, "sequence":"gggg"},
"E" :{"eid":"e2e", "sid1":gfapy.OrientedLine("s2s","-"),
"sid2":gfapy.OrientedLine("t2t","-"),
"beg1":0, "end1":gfapy.LastPos("100$"),
"beg2":10, "end2":gfapy.LastPos("110$"),
"alignment":gfapy.Alignment("10M1I10M1D80M")},
"F" :{"sid":"s2s", "external":gfapy.OrientedLine("ex2ex","-"),
"s_beg":0, "s_end":gfapy.LastPos("100$"),
"f_beg":10, "f_end":gfapy.LastPos("110$"),
"alignment":gfapy.Alignment("10M1I10M1D80M")},
"G" :{"gid":"g2g", "sid1":gfapy.OrientedLine("s2s","+"), "sid2":gfapy.OrientedLine("t2t","-"),
"disp":2000, "var":100},
"O" :{"pid":"O100", "items":[gfapy.OrientedLine("x1","+"),
gfapy.OrientedLine("x2","+"),
gfapy.OrientedLine("x3","-")]},
"U" :{"pid":"U100", "items":["x1", "x2", "x3"]},
}
v2 = {
"S1":{"name":"xs", "sequence":"aggc"},
"L":{"from_segment":"a5", "from_orient":"+", "to_segment":"a7", "to_orient":"+",
"overlap":gfapy.Alignment("9M3I3M")},
"C":{"from_segment":"cp", "from_orient":"+", "to_segment":"cl", "to_orient":"+",
"pos":213, "overlap":gfapy.Alignment("110M4D10M")},
"P":{"path_name":"pu", "segment_names":[gfapy.OrientedLine("k","-"),
gfapy.OrientedLine("l","+")], "overlaps":[gfapy.Alignment("11M")]},
"S2":{"sid":"s4s", "slen":1999, "sequence":"aaaa"},
"E" :{"eid":"e4e", "sid1":gfapy.OrientedLine("s4s","+"),
"sid2":gfapy.OrientedLine("t4t","+"),
"beg1":10, "end1":gfapy.LastPos("110$"),
"beg2":0, "end2":gfapy.LastPos("100$"),
"alignment":gfapy.Alignment("10M1I20M1D80M")},
"F" :{"sid":"s4s", "external":gfapy.OrientedLine("ex4ex", "+"),
"s_beg":10, "s_end":gfapy.LastPos("110$"),
"f_beg":0, "f_end":gfapy.LastPos("100$"),
"alignment":gfapy.Alignment("10M1I20M1D80M")},
"G" :{"gid":"g4g", "sid1":gfapy.OrientedLine("s4s","-"), "sid2":gfapy.OrientedLine("t4t","+"),
"disp":3000, "var":200},
"O" :{"pid":"O200", "items":[gfapy.OrientedLine("x7","-"),
gfapy.OrientedLine("x6","+"),
gfapy.OrientedLine("x3","+")]},
"U" :{"pid":"U200", "items":["x6", "x7", "x4"]},
}
aliases = {
"S1":{"name":"sid"}, "P":{"path_name":"name"},
"S2":{"sid":"name"}, "E":{"eid":"name"}, "G":{"gid":"name"},
"U":{"pid":"name"}, "O":{"pid":"name"},
"L":{"from_segment": "from", "to_segment": "to"},
"C":{"from_segment":"container", "from_orient":"container_orient",
"to_segment":"contained", "to_orient":"contained_orient"}
}
def test_number_of_positionals(self):
for rt, fields in TestAPIPositionals.f.items():
gfapy.Line(fields) # nothing raised
too_less = fields.copy(); too_less.pop()
with self.assertRaises(gfapy.FormatError): gfapy.Line(too_less)
too_many = fields.copy(); too_many.append("*")
with self.assertRaises(gfapy.FormatError): gfapy.Line(too_many)
def test_positional_fieldnames(self):
for rt, line in TestAPIPositionals.l.items():
self.assertEqual(TestAPIPositionals.fieldnames[rt], line.positional_fieldnames)
def test_field_getters_and_setters(self):
for rt, fn_list in TestAPIPositionals.fieldnames.items():
for i, fn in enumerate(fn_list):
i+=1 # skip record_type
# field_to_s()
self.assertEqual(TestAPIPositionals.f[rt][i], TestAPIPositionals.l[rt].field_to_s(fn))
# validate_field/validate
TestAPIPositionals.l[rt].validate_field(fn) # nothing raised
TestAPIPositionals.l[rt].validate # nothing raised
# fieldname() == get(fieldname)
self.assertEqual(getattr(TestAPIPositionals.l[rt], fn), TestAPIPositionals.l[rt].get(fn))
# fieldname=() and fieldname()
l = TestAPIPositionals.l[rt].clone()
setattr(l,fn,TestAPIPositionals.v1[rt][fn])
self.assertEqual(TestAPIPositionals.v1[rt][fn], getattr(l, fn))
# set() and get()
l.set(fn, TestAPIPositionals.v2[rt][fn])
self.assertEqual(TestAPIPositionals.v2[rt][fn], l.get(fn))
def test_aliases(self):
for rt, aliasmap in TestAPIPositionals.aliases.items():
for orig, al in aliasmap.items():
# get(orig) == get(alias)
self.assertEqual(getattr(TestAPIPositionals.l[rt], orig), getattr(TestAPIPositionals.l[rt],al))
self.assertEqual(TestAPIPositionals.l[rt].get(orig), TestAPIPositionals.l[rt].get(al))
# validate_field/validate
TestAPIPositionals.l[rt].validate_field(al) # nothing raised
TestAPIPositionals.l[rt].validate # nothing raised
# field_to_s(orig) == field_to_s(alias)
self.assertEqual(TestAPIPositionals.l[rt].field_to_s(orig), TestAPIPositionals.l[rt].field_to_s(al))
# set(al, value) + get(orig)
l = TestAPIPositionals.l[rt].clone()
self.assertNotEqual(TestAPIPositionals.v1[rt][orig], getattr(l,orig))
l.set(al, TestAPIPositionals.v1[rt][orig])
self.assertEqual(TestAPIPositionals.v1[rt][orig], getattr(l,orig))
# alias=value + orig()
self.assertNotEqual(TestAPIPositionals.v2[rt][orig], getattr(l,orig))
setattr(l, al, TestAPIPositionals.v2[rt][orig])
self.assertEqual(TestAPIPositionals.v2[rt][orig], getattr(l,orig))
# set(orig, value) + get(alias)
self.assertNotEqual(TestAPIPositionals.v1[rt][orig], getattr(l,al))
l.set(orig, TestAPIPositionals.v1[rt][orig])
self.assertEqual(TestAPIPositionals.v1[rt][orig], getattr(l,al))
# orig=value + alias()
self.assertNotEqual(TestAPIPositionals.v2[rt][orig], getattr(l,al))
setattr(l, orig, TestAPIPositionals.v2[rt][orig])
self.assertEqual(TestAPIPositionals.v2[rt][orig], getattr(l,al))
def test_array_fields(self):
assert(isinstance(TestAPIPositionals.l["P"].segment_names, list))
assert(isinstance(TestAPIPositionals.l["P"].segment_names[0], gfapy.OrientedLine))
assert(isinstance(TestAPIPositionals.l["P"].overlaps, list))
assert(isinstance(TestAPIPositionals.l["P"].overlaps[0], gfapy.AlignmentPlaceholder))
assert(isinstance(TestAPIPositionals.l["O"].items, list))
assert(isinstance(TestAPIPositionals.l["O"].items[0], gfapy.OrientedLine))
assert(isinstance(TestAPIPositionals.l["U"].items, list))
assert(isinstance(TestAPIPositionals.l["U"].items[0], str))
def test_orientation(self):
# orientation is symbol
self.assertEqual("+", TestAPIPositionals.l["L"].from_orient)
self.assertEqual("+", TestAPIPositionals.l["L"].to_orient)
# invert
self.assertEqual("-", gfapy.invert(TestAPIPositionals.l["L"].to_orient))
self.assertEqual("+", gfapy.invert("-"))
self.assertEqual("-", gfapy.invert("+"))
# string representation
self.assertEqual("+", TestAPIPositionals.l["L"].field_to_s("from_orient"))
# assigning the string representation
l = TestAPIPositionals.l["L"].clone()
l.from_orient = "+"
self.assertEqual("+", l.from_orient)
self.assertEqual("-", gfapy.invert(l.from_orient))
# non "+"/"-" symbols is an error
with self.assertRaises(gfapy.FormatError):
l.from_orient = "x"
l.validate()
# only "+"/"-" and their string representations are accepted
with self.assertRaises(gfapy.FormatError):
l.from_orient = "x"
l.validate()
with self.assertRaises(gfapy.FormatError):
l.from_orient = 1
l.validate()
def test_oriented_segment(self):
os = TestAPIPositionals.l["P"].segment_names[0]
# getter methods
self.assertEqual("1", os.line)
self.assertEqual("+", os.orient)
# invert
self.assertEqual("1", os.inverted().line)
self.assertEqual("-", os.inverted().orient)
self.assertEqual("-", gfapy.invert(os.orient))
# setter methods
os.line = "one"
os.orient = "-"
self.assertEqual("one", os.line)
self.assertEqual("-", os.orient)
# name
self.assertEqual("one", os.name)
os.line = TestAPIPositionals.l["S1"]
self.assertEqual(TestAPIPositionals.l["S1"], os.line)
self.assertEqual(TestAPIPositionals.l["S1"].name, os.name)
def test_sequence(self):
# placeholder
assert(gfapy.is_placeholder(TestAPIPositionals.l["S1"].sequence))
assert(gfapy.is_placeholder(TestAPIPositionals.l["S2"].sequence))
s = TestAPIPositionals.l["S1"].clone()
s.sequence = "ACCT"
assert(not gfapy.is_placeholder(s.sequence))
# sequence is string
self.assertEqual("ACCT", s.sequence)
# rc
self.assertEqual("AGGT", gfapy.sequence.rc(s.sequence))
# GFA2 allowed alphabet is larger than GFA1
s.validate # nothing raised
s.sequence = ";;;{}"
with self.assertRaises(gfapy.FormatError): s.validate()
s = TestAPIPositionals.l["S2"].clone()
s.sequence = ";;;{}"
s.validate() # nothing raised
# Sequence
assert(isinstance(gfapy.sequence.Sequence("*"),gfapy.Placeholder))
assert(isinstance(gfapy.sequence.Sequence("ACG"),str))
def test_sequence_rc(self):
self.assertEqual("gcatcgatcgt",gfapy.sequence.rc("acgatcgatgc"))
# case
self.assertEqual("gCaTCgatcgt",gfapy.sequence.rc("acgatcGAtGc"))
# wildcards
self.assertEqual("gcatcnatcgt",gfapy.sequence.rc("acgatngatgc"))
self.assertEqual("gcatcYatcgt",gfapy.sequence.rc("acgatRgatgc"))
# RNA
self.assertEqual("gcaucgaucgu",gfapy.sequence.rc("acgaucgaugc",rna=True))
self.assertEqual("===.",gfapy.sequence.rc(".==="))
# valid
with self.assertRaises(gfapy.ValueError): gfapy.sequence.rc("acgatXgatgc")
gfapy.sequence.rc("acgatXgatgc",valid=True) # nothing raised
# placeholder
self.assertEqual("*",gfapy.sequence.rc("*"))
with self.assertRaises(gfapy.ValueError): gfapy.sequence.rc("**")
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