From c516810014841f13beb2c2314650be43996807d8 Mon Sep 17 00:00:00 2001
From: Ryan Wick <rrwick@gmail.com>
Date: Fri, 22 Nov 2024 13:08:34 +1100
Subject: [PATCH] Apply Black formatting

---
 src/dnaapler/utils/all.py        | 7 +++++--
 src/dnaapler/utils/bulk.py       | 7 +++++--
 src/dnaapler/utils/processing.py | 7 +++++--
 src/dnaapler/utils/util.py       | 2 +-
 4 files changed, 16 insertions(+), 7 deletions(-)

diff --git a/src/dnaapler/utils/all.py b/src/dnaapler/utils/all.py
index 46e2d19..c14543e 100644
--- a/src/dnaapler/utils/all.py
+++ b/src/dnaapler/utils/all.py
@@ -62,8 +62,11 @@ def all_process_MMseqs2_output_and_reorient(
     # read in the dataframe from MMseqs2
     try:
         MMseqs2_df = pd.read_csv(
-            MMseqs2_file, delimiter="\t", index_col=False, names=col_list,
-            dtype={"qseqid": "object"}
+            MMseqs2_file,
+            delimiter="\t",
+            index_col=False,
+            names=col_list,
+            dtype={"qseqid": "object"},
         )
 
     except Exception:
diff --git a/src/dnaapler/utils/bulk.py b/src/dnaapler/utils/bulk.py
index c26b2a7..b33b7f0 100644
--- a/src/dnaapler/utils/bulk.py
+++ b/src/dnaapler/utils/bulk.py
@@ -153,8 +153,11 @@ def bulk_process_MMseqs2_output_and_reorient(
     # read in the dataframe from MMseqs2
     try:
         MMseqs2_df = pd.read_csv(
-            MMseqs2_file, delimiter="\t", index_col=False, names=col_list,
-            dtype={"qseqid": "object"}
+            MMseqs2_file,
+            delimiter="\t",
+            index_col=False,
+            names=col_list,
+            dtype={"qseqid": "object"},
         )
 
     except Exception:
diff --git a/src/dnaapler/utils/processing.py b/src/dnaapler/utils/processing.py
index 830abd3..6c84089 100644
--- a/src/dnaapler/utils/processing.py
+++ b/src/dnaapler/utils/processing.py
@@ -50,8 +50,11 @@ def process_MMseqs2_output_and_reorient(
     # read in the dataframe from MMseqs2
     try:
         MMseqs2_df = pd.read_csv(
-            MMseqs2_file, delimiter="\t", index_col=False, names=col_list,
-            dtype={"qseqid": "object"}
+            MMseqs2_file,
+            delimiter="\t",
+            index_col=False,
+            names=col_list,
+            dtype={"qseqid": "object"},
         )
     except Exception:
         logger.error("There was an issue with parsing the MMseqs2 output file.")
diff --git a/src/dnaapler/utils/util.py b/src/dnaapler/utils/util.py
index e4fdf7e..b61e7ea 100644
--- a/src/dnaapler/utils/util.py
+++ b/src/dnaapler/utils/util.py
@@ -131,7 +131,7 @@ def check_mmseqs2_version():
 
         # The pre-built binary on GitHub reports its version using the commit hash instead of
         # a version number.
-        if mmseqs_version.startswith('45111b6'):
+        if mmseqs_version.startswith("45111b6"):
             logger.info(f"MMseqs2 version found is {mmseqs_version}")
 
         else: