Add hipathia export option

src/pathme/cli.py

@@ -12,10 +12,11 @@
 import pathme.kegg.cli
 import pathme.reactome.cli
 import pathme.wikipathways.cli
+import pybel
 from pybel import to_pickle
 from pybel.struct.mutation import collapse_all_variants, collapse_to_genes, remove_isolated_list_abundances
 from pybel.struct.summary import count_functions
-from .constants import CX_DIR, KEGG_BEL, PPI_DIR, REACTOME_BEL, SPIA_DIR, UNIVERSE_DIR, WIKIPATHWAYS_BEL
+from .constants import CX_DIR, HIPATHIA_DIR, KEGG_BEL, PPI_DIR, REACTOME_BEL, SPIA_DIR, UNIVERSE_DIR, WIKIPATHWAYS_BEL
 from .export_utils import export_helper, get_universe_graph, iterate_universe_graphs
 
 logger = logging.getLogger(__name__)
@@ -121,6 +122,26 @@ def cx(kegg_path, reactome_path, wikipathways_path, output, no_flatten, no_norma
             to_cx_file(graph, file)
 
 
+@export.command()
+@kegg_path_option
+@reactome_path_option
+@wikipathways_path_option
+@click.option('-o', '--output', help='Output directory', default=HIPATHIA_DIR, show_default=True)
+@no_flatten_option
+@no_normalize_names_option
+def hipathia(kegg_path, reactome_path, wikipathways_path, output, no_flatten, no_normalize_names):
+    """Export to hipathia directories."""
+    click.echo(f'Results will be exported to {output}')
+    for source, path, graph in iterate_universe_graphs(
+        kegg_path=kegg_path,
+        reactome_path=reactome_path,
+        wikipathways_path=wikipathways_path,
+        flatten=(not no_flatten),
+        normalize_names=(not no_normalize_names),
+    ):
+        pybel.to_hipathia(graph, os.path.join(output, os.path.basename(path)))
+
+
 @export.command()
 @kegg_path_option
 @reactome_path_option

src/pathme/constants.py

@@ -46,6 +46,7 @@ def get_data_dir() -> str:
 
 SPIA_DIR = os.path.join(DATA_DIR, 'spia')
 CX_DIR = os.path.join(DATA_DIR, 'cx')
+HIPATHIA_DIR = os.path.join(DATA_DIR, 'hipathia')
 PPI_DIR = os.path.join(DATA_DIR, 'ppi')
 UNIVERSE_DIR = os.path.join(DATA_DIR, 'universe')