ref

strainy/clustering/cluster.py

@@ -12,7 +12,7 @@
 from strainy.clustering import build_data as build_data
 from strainy.clustering import build_adj_matrix as matrix
 from strainy.params import *
-import strainy.gfa_operations.gfa_ops as gfa_ops
+import strainy.graph_operations.gfa_ops as gfa_ops
 
 
 logger = logging.getLogger()

strainy/clustering/cluster_postprocess.py

@@ -4,7 +4,7 @@
 from strainy.clustering.community_detection import find_communities
 from strainy.clustering import build_adj_matrix as matrix
 from strainy.clustering import build_data
-from strainy.gfa_operations import gfa_ops
+from strainy.graph_operations import gfa_ops
 from strainy.params import *
 
 logger = logging.getLogger()

strainy/gfa_operations/asm_graph_ops.py → strainy/graph_operations/asm_graph_ops.py

@@ -1,5 +1,5 @@
 import logging
-from strainy.gfa_operations import gfa_ops
+from strainy.graph_operations import gfa_ops
 from strainy.unitig_statistics import utg_stats
 from strainy.clustering import build_data
 from strainy.params import *

strainy/gfa_operations/overlap_graph_ops.py → strainy/graph_operations/overlap_graph_ops.py

@@ -2,8 +2,8 @@
 import pygraphviz as gv
 from collections import Counter, deque, defaultdict
 import logging
-from strainy.gfa_operations import gfa_ops
-from strainy.gfa_operations import asm_graph_ops
+from strainy.graph_operations import gfa_ops
+from strainy.graph_operations import asm_graph_ops
 from strainy.params import *
 
 
@@ -18,26 +18,26 @@
 
 """
 
-
 def build_paths_graph(cons, full_paths_roots, full_paths_leafs, cluster_distances):
     """
     Create an "overlap" graph for clusters within a unitig, based on flye distance
     """
     M = cluster_distances
     G = gfa_ops.from_pandas_adjacency_notinplace(M, create_using = nx.DiGraph)
     G.remove_edges_from(list(nx.selfloop_edges(G)))
+    G = remove_nested(G, cons)
     try:
         G.remove_node(0)
     except:
         pass
-    #todo move it to parental function
     G, full_paths_roots, full_paths_leafs = \
         remove_leaf_root_subnodes(G,full_paths_roots,full_paths_leafs)
-    G = remove_nested(G, cons)
     G = remove_transitive(G)
     return G
 
 
+
+
 def remove_transitive(G):
     path_remove = []
     for node in G.nodes():
@@ -47,35 +47,43 @@ def remove_transitive(G):
                 if len(n_path) == 3:
                     path_remove.append(n_path)
     for n_path in path_remove:
-        try:
-            G.remove_edge(n_path[0], n_path[1])
-        except:
-            continue
+         try:
+             G.remove_edge(n_path[0], n_path[1])
+         except:
+             continue
     return G
 
 
+
+
 def remove_leaf_root_subnodes(G,full_paths_roots,full_paths_leafs):
     node_remove = []
-    for node in full_paths_leafs+full_paths_roots:
-        if node in full_paths_leafs:
-            neighbors = list(full_paths_leafs)
-        else:
-            neighbors = list(full_paths_roots)
+    for node in full_paths_leafs:
+        neighbors = list(full_paths_leafs)
         for neighbor in list(neighbors):
-            for n_path in nx.algorithms.all_simple_paths(G, node, neighbor, cutoff = 2):
+            for n_path in nx.algorithms.all_simple_paths(G, node, neighbor, cutoff=2):
+                print(n_path)
                 if len(n_path) == 2:
                     node_remove.append(neighbor)
+    for node in full_paths_roots:
+         neighbors = list(full_paths_roots)
+         for neighbor in list(neighbors):
+             for n_path in nx.algorithms.all_simple_paths(G,  neighbor,node, cutoff = 2):
+                 print(n_path)
+                 if len(n_path) == 2:
+                     node_remove.append(neighbor)
     for node in node_remove:
-        try:
+         try:
             G.remove_node(node)
             logger.debug("REMOVE " + str(node))
             full_paths_roots.remove(node)
             full_paths_leafs.remove(node)
-        except:
-            continue
+         except:
+             continue
     return (G,full_paths_roots,full_paths_leafs)
 
 
+
 def remove_bubbles(graph, source_nodes):
     for node in source_nodes:
         neighbors = list(source_nodes)
@@ -99,7 +107,6 @@ def find_full_paths(G, paths_roots, paths_leafs):
             pass
         for path in list(paths_nx):
             paths.append(path)
-
     return paths
 
 

strainy/transform.py

@@ -15,9 +15,9 @@
 from strainy.clustering import build_adj_matrix as matrix
 from strainy.clustering import cluster_postprocess as postprocess
 from strainy.simplification import simplify_links as smpl
-from strainy.gfa_operations import gfa_ops
-from strainy.gfa_operations import asm_graph_ops
-from strainy.gfa_operations import overlap_graph_ops
+from strainy.graph_operations import gfa_ops
+from strainy.graph_operations import asm_graph_ops
+from strainy.graph_operations import overlap_graph_ops
 from strainy.unitig_statistics import utg_stats
 from strainy.flye_consensus import FlyeConsensus
 from strainy.clustering import build_data
@@ -27,11 +27,11 @@
 from strainy.reports.call_variants import produce_strainy_vcf
 from strainy.preprocessing import gfa_to_fasta
 from strainy.phase import color_bam
-
+from dataclasses import dataclass
 logger = logging.getLogger()
 
 
-from dataclasses import dataclass
+