set 0 in profile for partially covered exons, affects exon counting and

fixes #229
ablab · Sep 3, 2024 · ab95731 · ab95731
1 parent fd6407d
commit ab95731
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Showing 2 changed files with 5 additions and 2 deletions.
diff --git a/src/long_read_profiles.py b/src/long_read_profiles.py
@@ -139,7 +139,8 @@ def construct_profile_for_features(self, read_features, mapped_region=(0, 0), po
  matched_features[read_pos].append(gene_pos)
  gene_pos += 1
  elif overlaps(read_feature, isoform_feature):
- intron_profile[gene_pos] = -1
+ if self.absence_condition(mapped_region, isoform_feature):
+ intron_profile[gene_pos] = -1
  gene_pos += 1
 
  # eliminating non unique features

diff --git a/tests/test_long_read_profile.py b/tests/test_long_read_profile.py
@@ -72,7 +72,9 @@ def test_intron_profile(self, known_features, gene_region, read_exons, polya_pos
  ([(20, 60), (90, 110), (180, 200)], (20, 200), [(20, 60), (90, 110)],
  -1, -1, 3, [1, 1, 0], [1, 1]),
  ([(20, 60), (90, 110), (180, 200)], (20, 200), [(90, 110), (180, 200)],
- -1, -1, 3, [0, 1, 1], [1, 1])
+ -1, -1, 3, [0, 1, 1], [1, 1]),
+ ([(20, 60), (90, 110), (180, 200)], (20, 200), [(20, 60), (90, 100)],
+ -1, -1, 3, [1, 0, 0], [1, -1]),
  ])
  def test_exon_profile(self, known_features, gene_region, read_exons, polya_pos, polyt_pos, delta, expected_gene, expected_read):
  exon_profile_constructor = \