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bokulich-lab · Mar 14, 2024 · e79e9e1 · e79e9e1
1 parent 1b1fe45
commit e79e9e1
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Showing 2 changed files with 8 additions and 6 deletions.
diff --git a/q2_moshpit/eggnog/_method.py b/q2_moshpit/eggnog/_method.py
@@ -134,10 +134,12 @@ def _diamond_search_runner(input_path, diamond_db, sample_label, output_loc,
     subprocess.run(cmds, check=True)
 
 
-def _eggnog_annotate(eggnog_hits: SeedOrthologDirFmt,
-                    eggnog_db: EggnogRefDirFmt,
-                    db_in_memory: bool = False,
-                    num_cpus: int = 1) -> OrthologAnnotationDirFmt:
+def _eggnog_annotate(
+        eggnog_hits: SeedOrthologDirFmt,
+        eggnog_db: EggnogRefDirFmt,
+        db_in_memory: bool = False,
+        num_cpus: int = 1
+) -> OrthologAnnotationDirFmt:
 
     eggnog_db_fp = eggnog_db.path
 

diff --git a/q2_moshpit/partition/ortholog.py b/q2_moshpit/partition/ortholog.py
@@ -11,7 +11,6 @@
 import warnings
 
 import numpy as np
-from q2_types.feature_data_mag import OrthologAnnotationDirFmt
 from q2_types.genome_data import SeedOrthologDirFmt
 from qiime2.util import duplicate
 
@@ -38,7 +37,8 @@ def partition_orthologs(
     # TODO: this logic should move to the format itself
     orthologs = glob.glob(os.path.join(str(orthologs), "*.seed_orthologs"))
     names = [
-        os.path.basename(x).replace(".emapper.seed_orthologs", "") for x in orthologs
+        os.path.basename(x).replace(".emapper.seed_orthologs", "")
+        for x in orthologs
     ]
     orthologs = list(zip(names, orthologs))