biotite 0.41.2__cp310-cp310-macosx_11_0_arm64.whl → 1.0.1__cp310-cp310-macosx_11_0_arm64.whl

biotite/application/dssp/__init__.py

@@ -9,4 +9,4 @@ A subpackage for protein secondary structure annotation using DSSP.
 __name__ = "biotite.application.dssp"
 __author__ = "Patrick Kunzmann"
 
-from .app import *
+from .app import *

biotite/application/dssp/app.py

@@ -7,11 +7,11 @@ __author__ = "Patrick Kunzmann"
 __all__ = ["DsspApp"]
 
 from tempfile import NamedTemporaryFile
-from ..localapp import LocalApp, cleanup_tempfile
-from ..application import AppState, requires_state
-from ...structure.io.pdbx.cif import CIFFile
-from ...structure.io.pdbx.convert import set_structure
 import numpy as np
+from biotite.application.application import AppState, requires_state
+from biotite.application.localapp import LocalApp, cleanup_tempfile
+from biotite.structure.io.pdbx.cif import CIFFile
+from biotite.structure.io.pdbx.convert import set_structure
 
 
 class DsspApp(LocalApp):
@@ -73,7 +73,7 @@ class DsspApp(LocalApp):
                 "occupancy", np.ones(self._array.array_length(), dtype=float)
             )
 
-        self._in_file  = NamedTemporaryFile("w", suffix=".cif",  delete=False)
+        self._in_file = NamedTemporaryFile("w", suffix=".cif", delete=False)
         self._out_file = NamedTemporaryFile("r", suffix=".dssp", delete=False)
 
     def run(self):
@@ -81,9 +81,7 @@ class DsspApp(LocalApp):
         set_structure(in_file, self._array)
         in_file.write(self._in_file)
         self._in_file.flush()
-        self.set_arguments(
-            ["-i", self._in_file.name, "-o", self._out_file.name]
-        )
+        self.set_arguments(["-i", self._in_file.name, "-o", self._out_file.name])
         super().run()
 
     def evaluate(self):
@@ -93,13 +91,12 @@ class DsspApp(LocalApp):
         sse_start = None
         for i, line in enumerate(lines):
             if line.startswith("  #  RESIDUE AA STRUCTURE"):
-                sse_start = i+1
+                sse_start = i + 1
         if sse_start is None:
             raise ValueError("DSSP file does not contain SSE records")
         # Remove "!" for missing residues
         lines = [
-            line for line in lines[sse_start:]
-            if len(line) != 0 and line[13] != "!"
+            line for line in lines[sse_start:] if len(line) != 0 and line[13] != "!"
         ]
         self._sse = np.zeros(len(lines), dtype="U1")
         # Parse file for SSE letters

biotite/application/localapp.py

@@ -9,23 +9,29 @@ __all__ = ["LocalApp"]
 import abc
 import copy
 from os import chdir, getcwd, remove
-from .application import Application, AppState, AppStateError, requires_state
-from subprocess import Popen, PIPE, SubprocessError, TimeoutExpired
+from subprocess import PIPE, Popen, SubprocessError, TimeoutExpired
+from biotite.application.application import (
+    Application,
+    AppState,
+    AppStateError,
+    requires_state,
+)
+
 
 class LocalApp(Application, metaclass=abc.ABCMeta):
     """
     The base class for all locally installed applications, that are used
     via the command line.
-    
+
     Internally this creates a :class:`Popen` instance, which handles
     the execution.
-    
+
     Parameters
     ----------
     bin_path : str
         Path of the application represented by this class.
     """
-    
+
     def __init__(self, bin_path):
         super().__init__()
         self._bin_path = bin_path
@@ -35,28 +41,28 @@ class LocalApp(Application, metaclass=abc.ABCMeta):
         self._process = None
         self._command = None
         self._stdin_file = None
-    
+
     @requires_state(AppState.CREATED)
     def set_arguments(self, arguments):
         """
         Set command line arguments for the application run.
-        
+
         PROTECTED: Do not call from outside.
-        
+
         Parameters
         ----------
         arguments : list of str
             A list of strings representing the command line options.
         """
         self._arguments = copy.copy(arguments)
-    
+
     @requires_state(AppState.CREATED)
     def set_stdin(self, file):
         """
         Set a file as standard input for the application run.
-        
+
         PROTECTED: Do not call from outside.
-        
+
         Parameters
         ----------
         file : file object
@@ -65,7 +71,7 @@ class LocalApp(Application, metaclass=abc.ABCMeta):
             such as `StringIO` are invalid.
         """
         self._stdin_file = file
-    
+
     @requires_state(AppState.CREATED)
     def add_additional_options(self, options):
         """
@@ -81,12 +87,12 @@ class LocalApp(Application, metaclass=abc.ABCMeta):
         It is recommended to use this method only, when the respective
         :class:`LocalApp` subclass does not provide a method to set the
         desired option.
-        
+
         Parameters
         ----------
         options : list of str
             A list of strings representing the command line options.
-        
+
         Notes
         -----
         In order to see which options the command line execution used,
@@ -114,27 +120,24 @@ class LocalApp(Application, metaclass=abc.ABCMeta):
         clustalo --full --in ...fa --out ...fa --force --output-order=tree-order --seqtype Protein --guidetree-out ...tree
         """
         self._options += options
-    
+
     @requires_state(
-        AppState.RUNNING | \
-        AppState.CANCELLED | \
-        AppState.FINISHED | \
-        AppState.JOINED
+        AppState.RUNNING | AppState.CANCELLED | AppState.FINISHED | AppState.JOINED
     )
     def get_command(self):
         """
         Get the executed command.
 
         Cannot be called until the application has been started.
-        
+
         Returns
         -------
         command : str
             The executed command.
-        
+
         Examples
         --------
-        
+
         >>> seq1 = ProteinSequence("BIQTITE")
         >>> seq2 = ProteinSequence("TITANITE")
         >>> seq3 = ProteinSequence("BISMITE")
@@ -146,72 +149,71 @@ class LocalApp(Application, metaclass=abc.ABCMeta):
         """
         return " ".join(self._command)
 
-    
     @requires_state(AppState.CREATED)
     def set_exec_dir(self, exec_dir):
         """
         Set the directory where the application should be executed.
         If not set, it will be executed in the working directory at the
-        time the application was created. 
-        
+        time the application was created.
+
         PROTECTED: Do not call from outside.
-        
+
         Parameters
         ----------
         exec_dir : str
             The execution directory.
         """
         self._exec_dir = exec_dir
-    
+
     @requires_state(AppState.RUNNING | AppState.FINISHED)
     def get_process(self):
         """
         Get the `Popen` instance.
-        
+
         PROTECTED: Do not call from outside.
-        
+
         Returns
         -------
         process : Popen
             The `Popen` instance
         """
         return self._process
-    
+
     @requires_state(AppState.FINISHED | AppState.JOINED)
     def get_exit_code(self):
         """
         Get the exit code of the process.
-        
+
         PROTECTED: Do not call from outside.
-        
+
         Returns
         -------
         code : int
             The exit code.
         """
         return self._process.returncode
-    
+
     @requires_state(AppState.FINISHED | AppState.JOINED)
     def get_stdout(self):
         """
         Get the STDOUT pipe content of the process.
-        
+
         PROTECTED: Do not call from outside.
-        
+
         Returns
         -------
         stdout : str
             The standard output.
         """
         return self._stdout
-    
+
     @requires_state(AppState.FINISHED | AppState.JOINED)
     def get_stderr(self):
         """
         Get the STDERR pipe content of the process.
-        
+
         PROTECTED: Do not call from outside.
-        
+
         Returns
         -------
         stdout : str
@@ -221,38 +223,37 @@ class LocalApp(Application, metaclass=abc.ABCMeta):
 
     def run(self):
         cwd = getcwd()
-        chdir(self._exec_dir) 
+        chdir(self._exec_dir)
         self._command = [self._bin_path] + self._options + self._arguments
         self._process = Popen(
-            self._command, stdin=self._stdin_file, stdout=PIPE, stderr=PIPE,
-            encoding="UTF-8"
+            self._command,
+            stdin=self._stdin_file,
+            stdout=PIPE,
+            stderr=PIPE,
+            encoding="UTF-8",
         )
         chdir(cwd)
-    
+
     def is_finished(self):
         code = self._process.poll()
-        if code == None:
+        if code is None:
             return False
         else:
             self._stdout, self._stderr = self._process.communicate()
             return True
-    
+
     @requires_state(AppState.RUNNING | AppState.FINISHED)
     def join(self, timeout=None):
         # Override method as repetitive calls of 'is_finished()'
         # are not necessary as 'communicate()' already waits for the
         # finished application
         try:
-            self._stdout, self._stderr = self._process.communicate(
-                timeout=timeout
-            )
+            self._stdout, self._stderr = self._process.communicate(timeout=timeout)
         except TimeoutExpired:
             self.cancel()
-            raise TimeoutError(
-                f"The application expired its timeout ({timeout:.1f} s)"
-            )
+            raise TimeoutError(f"The application expired its timeout ({timeout:.1f} s)")
         self._state = AppState.FINISHED
-        
+
         try:
             self.evaluate()
         except AppStateError:
@@ -263,12 +264,11 @@ class LocalApp(Application, metaclass=abc.ABCMeta):
         else:
             self._state = AppState.JOINED
         self.clean_up()
-    
-    
+
     def wait_interval(self):
         # Not used in this implementation of 'join()'
         raise NotImplementedError()
-    
+
     def evaluate(self):
         super().evaluate()
         # Check if applicaion terminated correctly
@@ -276,10 +276,9 @@ class LocalApp(Application, metaclass=abc.ABCMeta):
         if exit_code != 0:
             err_msg = self.get_stderr().replace("\n", " ")
             raise SubprocessError(
-                f"'{self._bin_path}' returned with exit code {exit_code}: "
-                f"{err_msg}"
+                f"'{self._bin_path}' returned with exit code {exit_code}: " f"{err_msg}"
             )
-    
+
     def clean_up(self):
         if self.get_app_state() == AppState.CANCELLED:
             self._process.kill()
@@ -290,7 +289,7 @@ def cleanup_tempfile(temp_file):
     Close a :class:`NamedTemporaryFile` and delete it manually,
     if `delete` is set to ``False``.
     This function is a small helper function intended for usage in
-    `LocalApp` subclasses. 
+    `LocalApp` subclasses.
 
     The manual deletion is necessary, as Windows does not allow to open
     a :class:`NamedTemporaryFile` as second time
@@ -302,5 +301,8 @@ def cleanup_tempfile(temp_file):
         The temporary file to be closed and deleted.
     """
     temp_file.close()
-    if not temp_file.delete:
-        remove(temp_file.name)
+    try:
+        remove(temp_file.name)
+    except FileNotFoundError:
+        # File was already deleted, e.g. due to `TemporaryFile(delete=True)`
+        pass

biotite/application/mafft/__init__.py

@@ -9,4 +9,4 @@ A subpackage for multiple sequence alignments using MAFFT.
 __name__ = "biotite.application.mafft"
 __author__ = "Patrick Kunzmann"
 
-from .app import *
+from .app import *

biotite/application/mafft/app.py

@@ -6,25 +6,19 @@ __name__ = "biotite.application.mafft"
 __author__ = "Patrick Kunzmann"
 __all__ = ["MafftApp"]
 
-import re
 import os
-from ..msaapp import MSAApp
-from ..application import AppState, requires_state
-from ...sequence.sequence import Sequence
-from ...sequence.seqtypes import NucleotideSequence, ProteinSequence
-from ...sequence.io.fasta.file import FastaFile
-from ...sequence.align.alignment import Alignment
-from ...sequence.phylo.tree import Tree
-
+import re
+from biotite.application.application import AppState, requires_state
+from biotite.application.msaapp import MSAApp
+from biotite.sequence.phylo.tree import Tree
 
 _prefix_pattern = re.compile(r"\d*_")
 
 
-
 class MafftApp(MSAApp):
     """
     Perform a multiple sequence alignment using MAFFT.
-    
+
     Parameters
     ----------
     sequences : list of Sequence
@@ -33,7 +27,7 @@ class MafftApp(MSAApp):
         Path of the MUSCLE binary.
     matrix : SubstitutionMatrix, optional
         A custom substitution matrix.
-    
+
     Examples
     --------
 
@@ -51,19 +45,19 @@ class MafftApp(MSAApp):
     -BISMITE
     --IQLITE
     """
-    
+
     def __init__(self, sequences, bin_path="mafft", matrix=None):
         super().__init__(sequences, bin_path, matrix)
         self._tree = None
         self._out_tree_file_name = self.get_input_file_path() + ".tree"
-    
+
     def run(self):
         args = [
             "--quiet",
             "--auto",
             "--treeout",
             # Get the reordered alignment in order for
-            # get_alignment_order() to work properly 
+            # get_alignment_order() to work properly
             "--reorder",
         ]
         if self.get_seqtype() == "protein":
@@ -75,7 +69,7 @@ class MafftApp(MSAApp):
         args += [self.get_input_file_path()]
         self.set_arguments(args)
         super().run()
-    
+
     def evaluate(self):
         with open(self.get_output_file_path(), "w") as f:
             # MAFFT outputs alignment to stdout
@@ -89,7 +83,7 @@ class MafftApp(MSAApp):
             # -> remove the '<n>_' prefix
             newick = re.sub(_prefix_pattern, "", raw_newick)
             self._tree = Tree.from_newick(newick)
-    
+
     def clean_up(self):
         os.remove(self._out_tree_file_name)
 
@@ -97,26 +91,26 @@ class MafftApp(MSAApp):
     def get_guide_tree(self):
         """
         Get the guide tree created for the progressive alignment.
-        
+
         Returns
         -------
         tree : Tree
             The guide tree.
         """
         return self._tree
-    
+
     @staticmethod
     def supports_nucleotide():
         return True
-    
+
     @staticmethod
     def supports_protein():
         return True
-    
+
     @staticmethod
     def supports_custom_nucleotide_matrix():
         return True
-    
+
     @staticmethod
     def supports_custom_protein_matrix():
         return True