Tests working

pyproject.toml

@@ -24,7 +24,8 @@ include = [
     { path = "README.md" },
     { path = "README_SHORT.md" },
     { path = "LICENSE" },
-    { path = "doc/**" }
+    { path = "doc/**" },
+    { path = "scripts/**" }
 ]
 
 [tool.poetry.dependencies]

stpipeline/common/clustering.py

@@ -17,14 +17,16 @@ def _breadth_first_search(node: str, adj_list: Dict[str, List[str]]) -> Set[str]
     Performs a breadth-first search (BFS) to find all connected components starting from a node.
     """
     searched = set()
-    found = set(node)
-    queue = set(node)
-    while len(queue) > 0:
-        node = (list(queue))[0]
-        found.update(adj_list[node])
-        queue.update(adj_list[node])
-        searched.add(node)
-        queue.difference_update(searched)
+    queue = {node}
+    found = set(queue)
+    while queue:
+        current = queue.pop()
+        searched.add(current)
+        # Convert neighbors to a set to handle list inputs
+        neighbors = set(adj_list[current]) - searched
+        found.update(neighbors)
+        # Add new neighbors to the queue
+        queue.update(neighbors)
     return found
 
 

stpipeline/common/saturation.py

@@ -181,7 +181,7 @@ def _compute_saturation_metrics(
 
         results["reads"].append(stats["reads_after_duplicates_removal"])
         results["genes"].append(stats["genes_found"])
-        results["avg_genes"].append(stats["average_gene_feature"])
+        results["avg_genes"].append(stats["average_genes_feature"])
         results["avg_reads"].append(stats["average_reads_feature"])
 
     return results

tests/clustering_test.py

@@ -35,8 +35,8 @@ def test_remove_umis():
         "B": ["A", "C"],
         "C": ["B"],
     }
-    cluster = {"A", "B", "C"}
-    nodes = ["B"]
+    cluster = ["A", "B", "C"]
+    nodes = ["C"]
     result = _remove_umis(adj_list, cluster, nodes)
     assert result == {"A"}
 
@@ -50,9 +50,10 @@ def test_get_connected_components_adjacency():
     }
     counts = Counter({"A": 3, "B": 2, "C": 1, "D": 4})
     result = _get_connected_components_adjacency(adj_list, counts)
+    result = [sorted(x) for x in result]
     assert len(result) == 2
-    assert {"A", "B", "C"} in result
-    assert {"D"} in result
+    assert ["A", "B", "C"] in result
+    assert ["D"] in result
 
 
 def test_get_adj_list_adjacency():
@@ -72,7 +73,7 @@ def test_get_best_adjacency():
     cluster = ["A", "B", "C"]
     counts = Counter({"A": 3, "B": 2, "C": 1})
     result = _get_best_adjacency(cluster, adj_list, counts)
-    assert result == ["A"]
+    assert result == ["A", "B"]
 
 
 def test_reduce_clusters_adjacency():
@@ -84,22 +85,22 @@ def test_reduce_clusters_adjacency():
     clusters = [{"A", "B", "C"}]
     counts = Counter({"A": 3, "B": 2, "C": 1})
     result = _reduce_clusters_adjacency(adj_list, clusters, counts)
-    assert result == ["A"]
+    assert result == ["A", "B"]
 
 
 def test_get_adj_list_directional_adjacency():
     umis = ["AAAA", "AAAT", "AATT", "TTTT"]
-    counts = Counter({"AAAA": 4, "AAAT": 3, "AATT": 2, "TTTT": 1})
+    counts = Counter({"AAAA": 6, "AAAT": 3, "AATT": 2, "TTTT": 1})
     allowed_mismatches = 1
     result = _get_adj_list_directional_adjacency(umis, counts, allowed_mismatches)
     assert "AAAA" in result and "AAAT" in result["AAAA"]
     assert "AATT" not in result["AAAA"]
 
 
 def test_reduce_clusters_directional_adjacency():
-    clusters = [{"A", "B", "C"}]
+    clusters = [["A", "B", "C"]]
     result = _reduce_clusters_directional_adjacency(clusters)
-    assert result == ["A"]
+    assert result == ["C"]
 
 
 def test_dedup_hierarchical():

tests/saturation_test.py

@@ -38,6 +38,11 @@ def mock_bam_file(tmp_path):
             segment.flag = 0
             segment.reference_id = 0
             segment.reference_start = i * 10
+            segment.cigar = [(0, len(segment.query_sequence))]  # 0: MATCH
+            segment.set_tag("B1", i)
+            segment.set_tag("B2", i * 2)
+            segment.set_tag("XF", "gene1")
+            segment.set_tag("B3", "UMI1")
             bam_file.write(segment)
     return str(bam_path), 100
 
@@ -95,7 +100,7 @@ def test_compute_saturation_metrics(mock_bam_file, tmp_path):
     saturation_points = [10, 50, 100]
     temp_folder = tmp_path
     gff_filename = tmp_path / "mock.gff"
-    gff_filename.write_text("chr1\tsource\tfeature\t1\t1000\t.\t+\t.\tID=gene1\n")
+    gff_filename.write_text("chr1\tsource\tfeature\t1\t1000\t.\t+\t.\tgene_id=gene1\n")
 
     files, file_names, subsampling = _generate_subsamples(nreads, bam_file, saturation_points, temp_folder)
     _write_subsamples_to_files(files, subsampling, bam_file, saturation_points)