MAINT: format code add docstrings

phables/workflow/scripts/phables_utils/coverage_utils.py

@@ -89,6 +89,10 @@ def get_junction_pe_coverage(bam_path, output):
 
 
 def get_sub_path_coverage(sub_path_cov, bam_path, output):
+    """
+    Get coverage values of sub paths using long reads
+    """
+
     if os.path.isfile(f"{output}/sub_path_coverage.pickle"):
         sub_path_cov = defaultdict(int)
         with open(f"{output}/sub_path_coverage.pickle", "rb") as handle:

phables/workflow/scripts/phables_utils/edge_graph_utils.py

@@ -260,6 +260,10 @@ def remove_dead_ends(G_edge):
 
 
 def get_all_sub_paths(assembly_graph, unitig_names):
+    """
+    Get all sub paths of length 2 and 3
+    """
+
     sub_paths = defaultdict(int)
 
     for v in range(assembly_graph.vcount()):
@@ -273,7 +277,7 @@ def get_all_sub_paths(assembly_graph, unitig_names):
                 node3 = unitig_names[path[2]]
                 sub_paths[tuple([node1, node2, node3])] = 0
 
-            if len(path) == 2:  # Length 2 means 2 vertices (1 edge)
+            elif len(path) == 2:  # Length 2 means 2 vertices (1 edge)
                 node1 = unitig_names[path[0]]
                 node2 = unitig_names[path[1]]
                 sub_paths[tuple([node1, node2])] = 0

phables/workflow/scripts/phables_utils/long_utils.py

@@ -38,6 +38,10 @@ def resolve_long(
     output,
     nthreads,
 ):
+    """
+    Resolve genomic paths using long reads
+    """
+
     resolved_edges = set()
 
     all_resolved_paths = []

phables/workflow/scripts/phables_utils/short_utils.py

@@ -38,6 +38,10 @@ def resolve_short(
     output,
     nthreads,
 ):
+    """
+    Resolve genomic paths using short reads
+    """
+
     resolved_edges = set()
 
     all_resolved_paths = []