🎨 isort

Author: enryH

src/instanexus/__main__.py

@@ -1,5 +1,6 @@
-import sys
 import argparse
+import sys
+
 from . import script_dbg, script_greedy
 
 

src/instanexus/alignment.py

@@ -26,6 +26,7 @@
 import shutil
 import subprocess
 from pathlib import Path
+
 from Bio import SeqIO
 
 logging.basicConfig(

src/instanexus/assembly.py

@@ -20,26 +20,25 @@
 __status__ = Dev
 """
 
+import argparse
+
 # import libraries
 import logging
+from collections import Counter, defaultdict
+from dataclasses import dataclass
+from itertools import combinations
+from pathlib import Path
+from typing import Any, Dict, Iterable, List, Optional, Tuple
+
+import Bio
 import networkx as nx
 import pandas as pd
-import argparse
-import Bio
+from Bio import SeqIO
+from tqdm import tqdm
 
 from . import helpers
 from . import visualization as viz
 
-from tqdm import tqdm
-from pathlib import Path
-from Bio import SeqIO
-from collections import defaultdict
-from collections import Counter
-from itertools import combinations
-from dataclasses import dataclass
-from typing import List, Tuple, Dict, Any, Iterable, Optional
-
-
 logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
 

src/instanexus/clustering.py

@@ -24,9 +24,10 @@
 import logging
 import shutil
 import subprocess
-import pandas as pd
 from pathlib import Path
 from tempfile import mkdtemp
+
+import pandas as pd
 from Bio import SeqIO
 from tqdm import tqdm
 

src/instanexus/consensus.py

@@ -21,24 +21,23 @@
 """
 
 import argparse
+import json
 import logging
 import os
-import json
 import re
 import statistics
-from tqdm import tqdm
-
-from pathlib import Path
 from collections import Counter
-from Bio import SeqIO
-from Bio.Seq import Seq
-from Bio.SeqRecord import SeqRecord
+from pathlib import Path
 
 import Bio.SeqRecord
-import pandas as pd
+import logomaker
 import matplotlib.pyplot as plt
+import pandas as pd
 import seaborn as sns
-import logomaker
+from Bio import SeqIO
+from Bio.Seq import Seq
+from Bio.SeqRecord import SeqRecord
+from tqdm import tqdm
 
 logging.basicConfig(
     level=logging.INFO, format="%(asctime)s [%(levelname)s] %(message)s"

src/instanexus/helpers.py

@@ -20,15 +20,15 @@
 __status__ = Dev
 """
 
+import json
+import os
+from pathlib import Path
+
 # import libraries
 import numpy as np
 import pandas as pd
-import os
-import json
 import plotly.express as px
 import plotly.graph_objects as go
-from pathlib import Path
-
 
 PROJECT_ROOT = Path(__file__).resolve().parents[2]
 JSON_DIR = PROJECT_ROOT / "json"

src/instanexus/main.py

@@ -23,11 +23,8 @@
 import argparse
 import logging
 from pathlib import Path
-from . import preprocessing
-from . import assembly
-from . import clustering
-from . import alignment
-from . import consensus
+
+from . import alignment, assembly, clustering, consensus, preprocessing
 
 # Setup logging
 logging.basicConfig(

src/instanexus/preprocessing.py

@@ -20,20 +20,20 @@
 __status__ = Dev
 """
 
+import json
+import logging
+
 # import libraries
 import os
 import re
-import json
-import logging
+from pathlib import Path
+
 import numpy as np
 import pandas as pd
 import plotly.express as px
 import plotly.graph_objects as go
-
-from pathlib import Path
 from Bio import SeqIO
 
-
 # PROJECT_ROOT = Path(__file__).resolve().parents[2]
 # JSON_DIR = PROJECT_ROOT / "json"
 

src/instanexus/visualization.py

@@ -21,11 +21,12 @@
 """
 
 import os
-import numpy as np
-import pandas as pd
+
 import Bio.SeqIO
 import matplotlib.patches as patches
 import matplotlib.pyplot as plt
+import numpy as np
+import pandas as pd
 import plotly.express as px
 import plotly.graph_objects as go
 import seaborn as sns

tests/test_preprocessing.py

@@ -4,18 +4,15 @@
 
 from instanexus.preprocessing import remove_modifications
 
+
 def test_remove_modifications():
     assert remove_modifications("A(ox)BC(mod)D") == "ABCD"
     assert remove_modifications("A[UNIMOD:21]BC[UNIMOD:35]D") == "ABCD"
-    assert (
-        remove_modifications("A(ox)[UNIMOD:21]BC(mod)[UNIMOD:35]D") == "ABCD"
-    )
+    assert remove_modifications("A(ox)[UNIMOD:21]BC(mod)[UNIMOD:35]D") == "ABCD"
     assert remove_modifications(None) is None
     assert remove_modifications("ACD") == "ACD"
     assert remove_modifications("A(I)BCD") == "ABCD"
     assert remove_modifications("A(ox)B(I)C(mod)D") == "ABCD"
-    assert (
-        remove_modifications("A(ox)[UNIMOD:21]B(I)C(mod)[UNIMOD:35]D") == "ABCD"
-    )
+    assert remove_modifications("A(ox)[UNIMOD:21]B(I)C(mod)[UNIMOD:35]D") == "ABCD"
     assert remove_modifications("AI BCD") == "AL BCD"
-    assert remove_modifications("A(ox)I B(mod)CD") == "AL BCD"
+    assert remove_modifications("A(ox)I B(mod)CD") == "AL BCD"