refactor imports

bakta/config.py

@@ -2,7 +2,6 @@
 import multiprocessing as mp
 import os
 import re
-import shutil
 import sys
 import tempfile
 

bakta/expert/protein_sequences.py

@@ -5,13 +5,13 @@
 from pathlib import Path
 from typing import Sequence
 
+from Bio import SeqIO
+from xopen import xopen
+
 import bakta.config as cfg
 import bakta.constants as bc
 import bakta.features.orf as orf
 
-from Bio import SeqIO
-from xopen import xopen
-
 
 log = logging.getLogger('EXPERT_AA_SEQ')
 

bakta/features/cds.py

@@ -13,8 +13,8 @@
 import pyhmmer
 
 from Bio import SeqIO
-from Bio.Seq import Seq
 from Bio import SeqFeature
+from Bio.Seq import Seq
 from Bio.SeqUtils.ProtParam import ProteinAnalysis
 from xopen import xopen
 

bakta/features/orf.py

@@ -1,5 +1,4 @@
 import logging
-import subprocess as sp
 
 from collections import OrderedDict
 from pathlib import Path

bakta/plot.py

@@ -8,9 +8,9 @@
 from pathlib import Path
 
 import yaml
+import Bio as bp
 
 from Bio import SeqUtils
-import Bio as bp
 
 import bakta
 import bakta.utils as bu

bakta/utils.py

@@ -4,11 +4,11 @@
 import hashlib
 import logging
 import os
-import shutil
 import platform as pf
+import re
+import shutil
 import sys
 import subprocess as sp
-import re
 
 from argparse import Namespace
 from datetime import datetime