add back docs

gbouras13 · Feb 23, 2024 · b250fa1 · b250fa1
1 parent c8c63b7
commit b250fa1
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Showing 3 changed files with 12 additions and 10 deletions.
diff --git a/src/phold/io/handle_genbank.py b/src/phold/io/handle_genbank.py
@@ -140,9 +140,9 @@ def run_pool(pool, records):
                 feature.qualifiers["function"] = "unknown function"
                 feature.qualifiers["product"] = "hypothetical protein"
                 feature.qualifiers["phrog"] = "No_PHROG"
-                feature.qualifiers[
-                    "source"
-                ] = f"Pyrodigal-gv_{pyrodigal_gv.__version__}"
+                feature.qualifiers["source"] = (
+                    f"Pyrodigal-gv_{pyrodigal_gv.__version__}"
+                )
                 feature.qualifiers["transl_table"] = gene.translation_table
                 # from the API
                 # translation_table (int, optional) – An alternative translation table to use to translate the gene.

diff --git a/src/phold/results/topfunction.py b/src/phold/results/topfunction.py
@@ -346,12 +346,12 @@ def calculate_topfunctions_results(
                 if foldseek_phrog != cds_feature.qualifiers["phrog"][0]:
                     # where there was no phrog in pharokka
                     if cds_feature.qualifiers["phrog"][0] == "No_PHROG":
-                        updated_cds_dict[record_id][cds_id].qualifiers["phrog"][
-                            0
-                        ] = result_dict[record_id][cds_id]["phrog"]
-                        updated_cds_dict[record_id][cds_id].qualifiers["product"][
-                            0
-                        ] = result_dict[record_id][cds_id]["product"]
+                        updated_cds_dict[record_id][cds_id].qualifiers["phrog"][0] = (
+                            result_dict[record_id][cds_id]["phrog"]
+                        )
+                        updated_cds_dict[record_id][cds_id].qualifiers["product"][0] = (
+                            result_dict[record_id][cds_id]["product"]
+                        )
                         updated_cds_dict[record_id][cds_id].qualifiers["function"][
                             0
                         ] = result_dict[record_id][cds_id]["function"]

diff --git a/tests/test_integration.py b/tests/test_integration.py
@@ -114,7 +114,9 @@ def test_compare_pdb():
 def test_predict_fasta():
     """test phold predict with fasta input"""
     input_fasta: Path = f"{test_data}/combined_truncated_acr_defense_vfdb_card.gbk"
-    cmd = f"phold predict -i {input_fasta} -o {predict_fasta_dir} -t {threads}  --cpu -f"
+    cmd = (
+        f"phold predict -i {input_fasta} -o {predict_fasta_dir} -t {threads}  --cpu -f"
+    )
     exec_command(cmd)