feat(GUNC): Added GTDB R95 dataset methods.

magna/gunc/__init__.py

@@ -0,0 +1,26 @@
+import os
+
+import pandas as pd
+
+from magna.config import MAGNA_DIR
+
+
+def gunc_max_css_scores_gtdb_r95() -> pd.DataFrame:
+    path = os.path.join(MAGNA_DIR, 'dataset', 'gunc', 'GUNC.gtdb_95.maxCSS_level.feather')
+    if not os.path.isfile(path):
+        raise IOError(f'{path} does not exist.')
+    return pd.read_feather(path)
+
+
+def gunc_contig_assignment_gtdb_r95() -> pd.DataFrame:
+    path = os.path.join(MAGNA_DIR, 'dataset', 'gunc', 'GUNC.gtdb_95.contig_assignments.feather')
+    if not os.path.isfile(path):
+        raise IOError(f'{path} does not exist.')
+    return pd.read_feather(path)
+
+
+def gunc_all_levels_gtdb_r95() -> pd.DataFrame:
+    path = os.path.join(MAGNA_DIR, 'dataset', 'gunc', 'gtdb_95.all_levels.tsv')
+    if not os.path.isfile(path):
+        raise IOError(f'{path} does not exist.')
+    return pd.read_feather(path)

setup.py

@@ -43,6 +43,6 @@ def readme():
       ],
       packages=find_packages(),
       include_package_data=True,
-      install_requires=['tqdm', 'pandas', 'pyarrow', 'numpy', 'dendropy'],
+      install_requires=['tqdm', 'pandas>=1.1.0', 'pyarrow', 'numpy', 'dendropy', 'biopython'],
       python_requires='>=3.6',
       )