Modify imports

src/pathme/cli.py

@@ -6,16 +6,11 @@
 import time
 
 import click
+import networkx as nx
 from bio2bel_chebi import Manager as ChebiManager
 from bio2bel_hgnc import Manager as HgncManager
-from pybel import from_pickle, to_pickle
-from pybel.dsl import ListAbundance
-from pybel.struct.mutation import collapse_to_genes, collapse_all_variants
-from pybel_tools.analysis.spia import bel_to_spia_matrices, spia_matrices_to_excel
-from pybel.struct.summary import count_functions
 from tqdm import tqdm
 
-import networkx as nx
 from pathme.constants import *
 from pathme.export_utils import get_all_pickles, get_files_in_folder, get_universe_graph
 from pathme.kegg.convert_to_bel import kegg_to_pickles
@@ -26,6 +21,11 @@
 from pathme.utils import CallCounted, make_downloader, statistics_to_df, summarize_helper
 from pathme.wikipathways.rdf_sparql import get_wp_statistics, wikipathways_to_pickles
 from pathme.wikipathways.utils import get_file_name_from_url, get_wikipathways_files, unzip_file
+from pybel import from_pickle, to_pickle
+from pybel.dsl import ListAbundance
+from pybel.struct.mutation import collapse_to_genes, collapse_all_variants, remove_isolated_list_abundances
+from pybel.struct.summary import count_functions
+from pybel_tools.analysis.spia import bel_to_spia_matrices, spia_matrices_to_excel
 
 logger = logging.getLogger(__name__)
 
@@ -389,6 +389,9 @@ def universe(kegg_path, reactome_path, wikipathways_path, output, no_flatten, no
     )
     click.echo(f'Number of isolates after getting universe: {nx.number_of_isolates(universe_graph)}')
 
+    # Remove isolated list abundances
+    remove_isolated_list_abundances(universe_graph)
+
     if flatten:
         universe_graph.remove_nodes_from({
             node

src/pathme/export_utils.py

@@ -6,13 +6,12 @@
 import os
 from typing import List
 
+from tqdm import tqdm
+
 from pathme.constants import KEGG, REACTOME, WIKIPATHWAYS
 from pathme.normalize_names import normalize_graph_names
 from pathme.pybel_utils import flatten_complex_nodes
-from pybel import BELGraph
-from pybel import from_pickle
-from pybel import union
-from tqdm import tqdm
+from pybel import BELGraph, from_pickle, union
 
 logger = logging.getLogger(__name__)
 
@@ -78,7 +77,7 @@ def _iterate_universe_graphs(
             continue
 
         if file in kegg_pickles:
-            graph = from_pickle(os.path.join(kegg_path, file))
+            graph = from_pickle(os.path.join(kegg_path, file), check_version=False)
 
             if flatten:
                 flatten_complex_nodes(graph)
@@ -87,7 +86,7 @@ def _iterate_universe_graphs(
                 normalize_graph_names(graph, KEGG)
 
         elif file in reactome_pickles:
-            graph = from_pickle(os.path.join(reactome_path, file))
+            graph = from_pickle(os.path.join(reactome_path, file), check_version=False)
 
             if flatten:
                 flatten_complex_nodes(graph)
@@ -96,7 +95,7 @@ def _iterate_universe_graphs(
                 normalize_graph_names(graph, REACTOME)
 
         elif file in wp_pickles:
-            graph = from_pickle(os.path.join(wikipathways_path, file))
+            graph = from_pickle(os.path.join(wikipathways_path, file), check_version=False)
 
             if flatten:
                 flatten_complex_nodes(graph)