[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/cbioportal.py

@@ -173,4 +173,3 @@ def try_except_middle_int(str_in):
         return int(str_in[1:-1])
     except ValueError:
         return None
-

missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/kinase_schema.py

@@ -525,7 +525,8 @@ def create_kinase_models_from_df(
 
     return dict_kinase_models
 
-def get_sequence_max_with_exception(list_in: list[int| None]) -> int:
+
+def get_sequence_max_with_exception(list_in: list[int | None]) -> int:
     """Get maximum sequence length from dictionary of dictionaries.
 
     Parameters
@@ -543,9 +544,12 @@ def get_sequence_max_with_exception(list_in: list[int| None]) -> int:
     except ValueError:
         return 0
 
+
 def replace_none_with_max_len(dict_in):
     dict_max_len = {
-        key1: get_sequence_max_with_exception([len(val2) for val2 in val1.values() if val2 is not None])
+        key1: get_sequence_max_with_exception(
+            [len(val2) for val2 in val1.values() if val2 is not None]
+        )
         for key1, val1 in dict_in.items()
     }
 

missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/plot.py

@@ -1,13 +1,15 @@
 import numpy as np
-from pydantic.dataclasses import dataclass
-from bokeh.plotting import figure
+from bokeh.layouts import gridplot
+
 # from bokeh.models import ColumnDataSource, Plot, Grid, Range1d
 from bokeh.models import ColumnDataSource, Range1d
-from bokeh.models.glyphs import Text, Rect
-from bokeh.layouts import gridplot
+from bokeh.models.glyphs import Rect, Text
+from bokeh.plotting import figure
+from pydantic.dataclasses import dataclass
+
 
 @dataclass
-class SequenceAlignment():
+class SequenceAlignment:
     list_sequences: list[str]
     """List of sequences to show in aligner."""
     list_ids: list[str]
@@ -28,22 +30,22 @@ def get_colors(
         dict_colors: dict[str, str],
     ) -> list[str]:
         """Get colors for residue in a given sequence.
-        
+
         Parameters
         ----------
         list_str : str
             List of residues in a sequence.
         dict_colors : dict[str, str]
             Dictionary of colors for each residue.
-        
+
         Returns
         -------
         list[str]
             List of colors for each residue.
         """
         list_colors = [dict_colors[i] for i in list_str]
         return list_colors
-    
+
     def generate_alignment(self) -> None:
         """Generate sequence alignment plot adapted from https://dmnfarrell.github.io/bioinformatics/bokeh-sequence-aligner."""
 
@@ -52,9 +54,9 @@ def generate_alignment(self) -> None:
         colors = self.get_colors(list_text, self.dict_colors)
 
         N = len(self.list_sequences[0])
-        S = len(self.list_sequences)    
+        S = len(self.list_sequences)
 
-        x = np.arange(1, N+1)
+        x = np.arange(1, N + 1)
         y = np.arange(0, S, 1)
         # creates a 2D grid of coords from the 1D arrays
         xx, yy = np.meshgrid(x, y)
@@ -66,74 +68,74 @@ def generate_alignment(self) -> None:
         # now we can create the ColumnDataSource with all the arrays
         source = ColumnDataSource(
             dict(
-                x               = gx, 
-                y               = gy, 
-                recty           = recty, 
-                text            = list_text,
-                colors          = colors,
+                x=gx,
+                y=gy,
+                recty=recty,
+                text=list_text,
+                colors=colors,
             )
         )
-        x_range = Range1d(0, N+1, bounds="auto")
+        x_range = Range1d(0, N + 1, bounds="auto")
         if N > 100:
             viewlen = 100
         else:
             viewlen = N
 
         # entire sequence view (no text, with zoom)
         p = figure(
-            title               = None, 
-            frame_width         = self.plot_width, 
-            frame_height        = 50,
-            x_range             = x_range, 
-            y_range             = (0, S), 
-            tools               = "xpan, xwheel_zoom, reset, save",
-            min_border          = 0, 
-            toolbar_location    = "below",
+            title=None,
+            frame_width=self.plot_width,
+            frame_height=50,
+            x_range=x_range,
+            y_range=(0, S),
+            tools="xpan, xwheel_zoom, reset, save",
+            min_border=0,
+            toolbar_location="below",
         )
         rects = Rect(
-            x                   = "x", 
-            y                   = "recty",
-            width               = 1, 
-            height              = 1, 
-            fill_color          = "colors",
-            line_color          = None, 
-            fill_alpha          = 0.6,
+            x="x",
+            y="recty",
+            width=1,
+            height=1,
+            fill_color="colors",
+            line_color=None,
+            fill_alpha=0.6,
         )
         p.add_glyph(source, rects)
         p.yaxis.visible = False
-        p.grid.visible = False  
+        p.grid.visible = False
 
         # sequence text view with ability to scroll along x axis
         # view_range is for the close up view
         view_range = (0, viewlen)
         plot_height = S * 15 + 50
         p1 = figure(
-            title               = None, 
-            frame_width         = self.plot_width, 
-            frame_height        = plot_height,
-            x_range             = view_range, 
-            y_range             = self.list_ids[::-1], 
-            tools               = "xpan,reset",
-            min_border          = 0, 
-            toolbar_location    = "below",
-        )        
+            title=None,
+            frame_width=self.plot_width,
+            frame_height=plot_height,
+            x_range=view_range,
+            y_range=self.list_ids[::-1],
+            tools="xpan,reset",
+            min_border=0,
+            toolbar_location="below",
+        )
         glyph = Text(
-            x                   = "x", 
-            y                   = "y", 
-            text                = "text", 
-            text_align          = "center",
-            text_color          = "black",
+            x="x",
+            y="y",
+            text="text",
+            text_align="center",
+            text_color="black",
             # text_font           = "monospace",
-            text_font_size      = f"{str(self.font_size)}pt",
+            text_font_size=f"{str(self.font_size)}pt",
         )
         rects = Rect(
-            x                   = "x", 
-            y                   = "recty",  
-            width               = 1, 
-            height              = 1, 
-            fill_color          = "colors",
-            line_color          = None,
-            fill_alpha          = 0.4,
+            x="x",
+            y="recty",
+            width=1,
+            height=1,
+            fill_color="colors",
+            line_color=None,
+            fill_alpha=0.4,
         )
         p1.add_glyph(source, glyph)
         p1.add_glyph(source, rects)
@@ -142,7 +144,7 @@ def generate_alignment(self) -> None:
         p1.yaxis.minor_tick_line_width = 0
         p1.yaxis.major_tick_line_width = 0
 
-        self.plot = gridplot([[p],[p1]], toolbar_location="below")
+        self.plot = gridplot([[p], [p1]], toolbar_location="below")
 
     def show_plot(self) -> None:
         """Show sequence alignment plot via Bokeh."""

missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/protvar.py

@@ -1,6 +1,7 @@
-import logging
 import json
+import logging
 from enum import Enum
+
 from pydantic.dataclasses import dataclass
 
 from missense_kinase_toolkit.databases import requests_wrapper
@@ -11,6 +12,7 @@
 
 class ScoreDatabase(str, Enum):
     """Enum class to define the score database."""
+
     Conservation = "CONSERV"
     EVE = "EVE"
     ESM1b = "ESM"
@@ -20,7 +22,7 @@ class ScoreDatabase(str, Enum):
 @dataclass
 class ProtvarScore(RESTAPIClient):
     """Class to interact with Protvar API."""
-    
+
     database: ScoreDatabase
     """Database to query for score: Conservation (CONSERV), EVE (EVE), ESM1b (ESM) and AlphaMissense (AM) scores."""
     uniprot_id: str
@@ -47,12 +49,11 @@ def create_query_url(self):
             mut_new = self.mut
 
         self.url_query = (
-            self.url
-                .replace("<UNIPROT>", self.uniprot_id)
-                .replace("<POS>", str(self.pos))
-                .replace(mut_old, mut_new)
-                .replace("<DATABASE>", self.database)
-            )
+            self.url.replace("<UNIPROT>", self.uniprot_id)
+            .replace("<POS>", str(self.pos))
+            .replace(mut_old, mut_new)
+            .replace("<DATABASE>", self.database)
+        )
 
     def query_api(self) -> dict:
         header = {"Accept": "application/json"}
@@ -62,4 +63,4 @@ def query_api(self) -> dict:
             self._protvar_score = json.loads(res.text)
         else:
             print(f"Error: {res.status_code}")
-            self._protvar_scores = None
+            self._protvar_scores = None