def test_get_list_of_edges_no_repeat_blocks(self):
# depending on the fragment type adjacencies to be considered in BreakpointGraph are differ
# in case of circular genome, additional adjacency is added between to outermost vertices
# in case of linear genome, two extremity (infinity) vertices are appended to the start and end of the vertices list
parsed_data = ("@", [("+", "a"), ("-", "b"), ("-", "a")])
result = GRIMMReader.get_edges_from_parsed_data(parsed_data)
reference = [(TaggedBlockVertex("at"), TaggedBlockVertex("at")),
(TaggedBlockVertex("ah"), TaggedBlockVertex("bh")),
(TaggedBlockVertex("bt"), TaggedBlockVertex("ah"))]
self.assertDictEqual(Counter(result), Counter(reference))
parsed_data = ("$", [("+", "a"), ("-", "b"), ("-", "a")])
result = GRIMMReader.get_edges_from_parsed_data(parsed_data)
reference = [(TaggedInfinityVertex("at"), TaggedBlockVertex("at")),
(TaggedBlockVertex("ah"), TaggedBlockVertex("bh")),
(TaggedBlockVertex("bt"), TaggedBlockVertex("ah")),
(TaggedBlockVertex("at"), TaggedInfinityVertex("at"))]
self.assertDictEqual(Counter(result), Counter(reference))
parsed_data = ("@", [("+", "a")])
result = GRIMMReader.get_edges_from_parsed_data(parsed_data)
reference = [(TaggedBlockVertex("ah"), TaggedBlockVertex("at"))]
self.assertDictEqual(Counter(result), Counter(reference))
parsed_data = ("$", [("-", "a"), ("-", "a")])
result = GRIMMReader.get_edges_from_parsed_data(parsed_data)
reference = [(TaggedInfinityVertex("ah"), TaggedBlockVertex("ah")),
(TaggedBlockVertex("at"), TaggedBlockVertex("ah")),
(TaggedBlockVertex("at"), TaggedInfinityVertex("at"))]
self.assertDictEqual(Counter(result), Counter(reference))
def test_get_list_of_edges_repeat_blocks_at_extremities(self):
# if a fragment starts and / or ends with repeat block, that is denoted in a form of
# repeat_block_name__repeat
# IF this block is preserved as a block (i.e. located inside the fragment),
# it will be transformed into a block "repeat_block_name" with
# an empty tag -- value "repeat" -- None
# IF the block is not preserved (flanking repeat), it will be dismissed and its outermost extremity
# will be used to make its name (i.e. "repeat_block_name"h and it will be added as a tag to the infinity vertex
# created for a linear fragment
# such information shall be recorded in respective infinity vertex, if a fragment is linear,
# and in a normal tagged vertex, if fragment is circular
# single repeat on the left extremity of linear fragment
parsed_data = ("$", [("+", "a__repeat"), ("-", "b"),
("+", "c__tag:1")])
result = GRIMMReader.get_edges_from_parsed_data(parsed_data)
left_iv = TaggedInfinityVertex("bh")
left_iv.add_tag("repeat", "ah")
ch_vertex, ct_vertex = TaggedBlockVertex("ch"), TaggedBlockVertex("ct")
ch_vertex.add_tag("tag", "1")
ct_vertex.add_tag("tag", "1")
reference = [(left_iv, TaggedBlockVertex("bh")),
(TaggedBlockVertex("bt"), ct_vertex),
(ch_vertex, TaggedInfinityVertex("ch"))]
self.assertDictEqual(Counter(result), Counter(reference))
# both extremities are "flanked" by repeats
parsed_data = ("$", [("+", "a__repeat"), ("-", "b"),
("+", "c__tag:1:2"), ("-", "a__repeat")])
result = GRIMMReader.get_edges_from_parsed_data(parsed_data)
left_iv = TaggedInfinityVertex("bh")
left_iv.add_tag("repeat", "ah")
right_iv = TaggedInfinityVertex("ch")
right_iv.add_tag("repeat", "ah")
ch_vertex, ct_vertex = TaggedBlockVertex("ch"), TaggedBlockVertex("ct")
ch_vertex.add_tag("tag", "1:2")
ct_vertex.add_tag("tag", "1:2")
reference = [(left_iv, TaggedBlockVertex("bh")),
(TaggedBlockVertex("bt"), ct_vertex),
(ch_vertex, right_iv)]
self.assertDictEqual(Counter(result), Counter(reference))
# fragment is specified as circular, all repeats shall be treated as normal blocks with half empty tags
parsed_data = ("@", [("+", "a__repeat"), ("-", "b"), ("+", "c__tag:1"),
("-", "a__repeat")])
result = GRIMMReader.get_edges_from_parsed_data(parsed_data)
ch_vertex, ct_vertex = TaggedBlockVertex("ch"), TaggedBlockVertex("ct")
ct_vertex.add_tag("tag", "1")
ch_vertex.add_tag("tag", "1")
ah_vertex, at_vertex = TaggedBlockVertex("ah"), TaggedBlockVertex("at")
ah_vertex.add_tag("repeat", None)
at_vertex.add_tag("repeat", None)
reference = [(ah_vertex, TaggedBlockVertex("bh")),
(TaggedBlockVertex("bt"), ct_vertex),
(ch_vertex, ah_vertex), (at_vertex, at_vertex)]
self.assertDictEqual(Counter(result), Counter(reference))