Ensure universe folder exists

PathwayMerger · Mar 6, 2019 · 39ad163 · 39ad163
1 parent 135c706
commit 39ad163
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Showing 2 changed files with 3 additions and 1 deletion.
diff --git a/src/pathme/cli.py b/src/pathme/cli.py
@@ -347,7 +347,7 @@ def export_to_spia(kegg_path, reactome_path, wikipathways_path, output):
 @click.option('-k', '--kegg-path', help='KEGG BEL folder', default=KEGG_BEL, show_default=True)
 @click.option('-r', '--reactome-path', help='Reactome BEL folder.', default=REACTOME_BEL, show_default=True)
 @click.option('-w', '--wikipathways-path', help='WikiPathways BEL folder', default=WIKIPATHWAYS_BEL, show_default=True)
-@click.option('-o', '--output', help='Output directory', default=SPIA_DIR, show_default=True)
+@click.option('-o', '--output', help='Output directory', default=UNIVERSE_DIR, show_default=True)
 @click.option('--no-explode', is_flag=True, help='Do not explode complex/reactions nodes')
 @click.option('--no-harmonize-names', is_flag=True, help='Do not harmonize names')
 def export_harmonized_universe(kegg_path, reactome_path, wikipathways_path, output, no_explode, no_harmonize_names):

diff --git a/src/pathme/constants.py b/src/pathme/constants.py
@@ -24,6 +24,7 @@ def ensure_pathme_folders():
     os.makedirs(WIKIPATHWAYS_DIR, exist_ok=True)
     os.makedirs(KEGG_CACHE, exist_ok=True)
     os.makedirs(SPIA_DIR, exist_ok=True)
+    os.makedirs(UNIVERSE_DIR, exist_ok=True)
 
     os.makedirs(KEGG_BEL, exist_ok=True)
     os.makedirs(REACTOME_BEL, exist_ok=True)
@@ -50,6 +51,7 @@ def ensure_pathme_folders():
 REACTOME_DIR = os.path.join(DATA_DIR, REACTOME)
 WIKIPATHWAYS_DIR = os.path.join(DATA_DIR, WIKIPATHWAYS)
 SPIA_DIR = os.path.join(DATA_DIR, 'spia')
+UNIVERSE_DIR = os.path.join(DATA_DIR, 'universe')
 
 KEGG_BEL = os.path.join(KEGG_DIR, 'bel')
 REACTOME_BEL = os.path.join(REACTOME_DIR, 'bel')