update unit tests from previous change

iva/tests/qc_test.py

@@ -99,7 +99,7 @@ def test_map_cds_to_assembly(self):
  expected = [line.rstrip() for line in open(expected_out)][1:]
  got = [line.rstrip() for line in open(self.qc.cds_nucmer_coords_in_assembly)][1:]
  self.assertEqual(expected, got)
- 
+
 
  def test_mummer_coords_file_to_dict(self):
  '''test _mummer_coords_file_to_dict'''
@@ -218,7 +218,7 @@ def test_calculate_cds_assembly_stats(self):
  'assembled_ok': False,
  }
  }
- 
+
  self.maxDiff = None
  self.assertEqual(expected, self.qc.cds_assembly_stats)
 
@@ -292,31 +292,35 @@ def test_calculate_refseq_assembly_stats(self):
  'bases_assembled': 1000,
  'assembled': True,
  'assembled_ok': True,
+ 'longest_matching_contig': 1000,
  },
  'ref2': {
  'hits': 1,
  'bases_assembled': 800,
  'assembled': False,
  'assembled_ok': False,
+ 'longest_matching_contig': 800,
  },
  'ref3': {
  'hits': 2,
  'bases_assembled': 1000,
  'assembled': True,
  'assembled_ok': False,
+ 'longest_matching_contig': 500,
  },
  'ref4': {
  'hits': 0,
  'bases_assembled': 0,
  'assembled': False,
  'assembled_ok': False,
+ 'longest_matching_contig': 0,
  }
  }
 
  self.qc._calculate_refseq_assembly_stats()
  self.maxDiff = None
  self.assertEqual(expected, self.qc.refseq_assembly_stats)
- 
+
 
  def test_invert_list(self):
  '''test _invert_list'''
@@ -340,7 +344,7 @@ def test_invert_list(self):
  assert len(coords) == len(expected)
  for i in range(len(coords)):
  self.assertEqual(self.qc._invert_list(coords[i], 42), expected[i])
- 
+
 
  def test_calculate_ref_positions_covered_by_contigs(self):
  '''test _calculate_ref_positions_covered_by_contigs'''
@@ -370,20 +374,20 @@ def test_get_overlapping_qry_hits(self):
  h4 = mummer.NucmerHit('\t'.join(['1', '10', '29', '40', '100', '100', '100.00', '100', '100', '1', '+', 'ref1', 'qry1']))
  h5 = mummer.NucmerHit('\t'.join(['1', '10', '70', '90', '100', '100', '100.00', '100', '100', '1', '+', 'ref1', 'qry1']))
  hits = [h1, h2, h3, h4, h5]
- 
+
  expected = [
  [],
  [h3, h4],
  [h2, h4],
  [h2, h3],
  []
  ]
- 
+
  self.assertEqual(len(hits), len(expected))
 
  for i in range(len(hits)):
  self.assertEqual(self.qc._get_overlapping_qry_hits(hits, hits[i]), expected[i])
- 
+
 
  def test_get_unique_and_repetitive_from_contig_hits(self):
  '''test _get_unique_and_repetitive_from_contig_hits'''
@@ -400,17 +404,6 @@ def test_get_unique_and_repetitive_from_contig_hits(self):
  self.assertEqual(expect_repetitive, got_repetitive)
 
 
- def test_get_longest_hit_index(self):
- '''test _get_longest_hit_index'''
- h1 = mummer.NucmerHit('\t'.join(['1', '10', '1', '10', '100', '100', '100.00', '100', '100', '1', '+', 'ref1', 'qry1']))
- h2 = mummer.NucmerHit('\t'.join(['1', '10', '11', '1', '100', '100', '100.00', '100', '100', '1', '+', 'ref1', 'qry1']))
- h3 = mummer.NucmerHit('\t'.join(['1', '10', '9', '1', '100', '100', '100.00', '100', '100', '1', '+', 'ref1', 'qry1']))
- self.assertEqual(None, self.qc._get_longest_hit_index([]))
- self.assertEqual(0, self.qc._get_longest_hit_index([h1]))
- self.assertEqual(1, self.qc._get_longest_hit_index([h1, h2]))
- self.assertEqual(1, self.qc._get_longest_hit_index([h1, h2, h3]))
-
-
  def test_contig_placement_in_reference(self):
  '''test _contig_placement_in_reference'''
  h1 = mummer.NucmerHit('\t'.join(['1', '90', '100', '10', '100', '100', '100.00', '100', '100', '1', '+', 'ref1', 'qry1']))
@@ -445,7 +438,7 @@ def test_calculate_contig_placement(self):
  'F:1-2341:-': [(fastaq.intervals.Interval(0, 2340), 'F', fastaq.intervals.Interval(0, 2340), False, False)],
  }
  self.assertEqual(expected_placement, self.qc.contig_placement)
- 
+
 
  def test_get_R_plot_contig_order_from_contig_placement(self):
  '''test _get_R_plot_contig_order_from_contig_placement'''