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import gfapy
import unittest
class TestAPILinesCollections(unittest.TestCase):
def test_gfa1_collections(self):
gfa = gfapy.Gfa.from_file("tests/testdata/all_line_types.gfa1.gfa")
# comments
self.assertEqual(1, len(gfa.comments))
self.assertRegex(gfa.comments[0].content, r'collections')
# containments
self.assertEqual(2, len(gfa.containments))
self.assertEqual({"2_to_6", "1_to_5"}, {x.name for x in gfa.containments})
# dovetails
self.assertEqual(4, len(gfa.dovetails))
self.assertEqual(set(["1_to_2", "1_to_3", "11_to_12", "11_to_13"]),
set([x.name for x in gfa.dovetails]))
# edges
self.assertEqual(6, len(gfa.edges))
self.assertEqual(set(["1_to_2", "1_to_3", "11_to_12",
"11_to_13", "2_to_6", "1_to_5"]),
set([x.name for x in gfa.edges]))
# segments
self.assertSetEqual(set(["1", "3", "5", "13", "11", "12", "4", "6", "2"]),
set([x.name for x in gfa.segments]))
# segment_names
self.assertSetEqual(set(["1", "3", "5", "13", "11", "12", "4", "6", "2"]),
set(gfa.segment_names))
# paths
self.assertSetEqual(set(["14", "15"]), set([x.name for x in gfa.paths]))
# path_names
self.assertSetEqual(set(["14", "15"]), set(gfa.path_names))
# names
self.assertSetEqual(set(gfa.segment_names + gfa.path_names +
gfa.edge_names), set(gfa.names))
# lines
self.assertEqual(set([str(x) for x in gfa.comments + gfa.headers + gfa.segments + gfa.edges +
gfa.paths]), set([str(x) for x in gfa.lines]))
def test_gfa2_collections(self):
gfa = gfapy.Gfa.from_file("tests/testdata/all_line_types.gfa2.gfa")
# comments
self.assertEqual(3, len(gfa.comments))
self.assertRegex(gfa.comments[0].content, r'collections')
# edges
self.assertSetEqual(set(["1_to_2", "2_to_6", "1_to_3",
"11_to_12", "11_to_13", "1_to_5"]),
set([x.name for x in gfa.edges]))
# edge_names
self.assertSetEqual(set(["1_to_2", "2_to_6", "1_to_3",
"11_to_12", "11_to_13", "1_to_5"]),
set(gfa.edge_names))
# dovetails
self.assertSetEqual(set(["1_to_2", "1_to_3", "11_to_12", "11_to_13"]),
set([x.name for x in gfa.dovetails]))
# containments
self.assertSetEqual(set(["2_to_6", "1_to_5"]),
set([x.name for x in gfa.containments]))
# gaps
self.assertSetEqual(set(["1_to_11", "2_to_12"]), set([x.name for x in gfa.gaps]))
# gap_names
self.assertSetEqual(set(["1_to_11", "2_to_12"]), set(gfa.gap_names))
# sets
self.assertSetEqual(set(["16", "16sub"]), set([x.name for x in gfa.sets]))
# set_names
self.assertSetEqual(set(["16", "16sub"]), set(gfa.set_names))
# paths
self.assertSetEqual(set(["14", "15"]), set([x.name for x in gfa.paths]))
# path_names
self.assertSetEqual(set(["14", "15"]), set(gfa.path_names))
# segments
self.assertSetEqual(set(["1", "3", "5", "13", "11", "12", "4", "6", "2"]),
set([x.name for x in gfa.segments]))
# segment_names
self.assertSetEqual(set(["1", "3", "5", "13", "11", "12", "4", "6", "2"]),
set(gfa.segment_names))
# fragments
self.assertSetEqual(set(["read1_in_2", "read2_in_2"]),
set([x.get("id") for x in gfa.fragments]))
# external_names
self.assertSetEqual(set(["read1", "read2"]), set(gfa.external_names))
# custom_record_keys
self.assertSetEqual(set(["X", "Y"]), set(gfa.custom_record_keys))
# custom_records
self.assertEqual(3, len(gfa.custom_records))
self.assertSetEqual(set(["X", "X", "Y"]), set([x.record_type for x in gfa.custom_records]))
# custom_records("X")
self.assertSetEqual(set(["X", "X"]), set([x.record_type for x in gfa.custom_records_of_type("X")]))
# names
self.assertSetEqual(set(gfa.segment_names + gfa.edge_names + gfa.gap_names +
gfa.path_names + gfa.set_names), set(gfa.names))
# lines
self.assertSetEqual(set([str(x) for x in gfa.comments + gfa.headers + gfa.segments + gfa.edges +
gfa.paths + gfa.sets + gfa.gaps + gfa.fragments +
gfa.custom_records]), set([str(x) for x in gfa.lines]))
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