make mode consistent (biopython#4858)

Bio/Align/bigbed.py

@@ -217,7 +217,7 @@ class AlignmentWriter(interfaces.AlignmentWriter):
     """Alignment file writer for the bigBed file format."""
 
     fmt = "bigBed"
-    mode = "wb"
+    mode = "b"
 
     def __init__(
         self,

Bio/Align/interfaces.py

@@ -208,11 +208,11 @@ class AlignmentWriter(ABC):  # noqa: B024
     followed finally by write_footer().
 
     Subclasses may define the following class attributes:
-    - mode   - 'w' or 'wb' for text or binary files, respectively
+    - mode   - 't' or 'b' for text or binary files, respectively
     - fmt    - a human-readable name for the file format.
     """
 
-    mode = "w"  # assume text files by default
+    mode = "t"  # assume text files by default
     fmt: Optional[str] = None  # to be defined in the subclass
 
     def __init__(self, target):
@@ -229,18 +229,18 @@ def __init__(self, target):
         """
         if target is not None:
             # target is None if we only use the writer to format strings.
-            if self.mode == "w":
+            if self.mode == "t":
                 try:
                     target.write("")
                 except TypeError:
                     # target was opened in binary mode
                     raise StreamModeError("File must be opened in text mode.") from None
                 except AttributeError:
                     # target is a path
-                    stream = open(target, self.mode)
+                    stream = open(target, "w" + self.mode)
                 else:
                     stream = target
-            elif self.mode == "wb":
+            elif self.mode == "b":
                 try:
                     target.write(b"")
                 except TypeError:
@@ -250,13 +250,12 @@ def __init__(self, target):
                     ) from None
                 except AttributeError:
                     # target is a path
-                    stream = open(target, self.mode)
+                    stream = open(target, "w" + self.mode)
                 else:
                     stream = target
             else:
                 raise RuntimeError("Unknown mode '%s'" % self.mode)
             self._stream = stream
-
         self._target = target
 
     def write_header(self, stream, alignments):
@@ -280,9 +279,11 @@ def format_alignment(self, alignment):
 
         alignment - an Alignment object
         """
-        raise NotImplementedError("This method should be implemented")
+        if self.mode == "t":
+            raise NotImplementedError("This method should be implemented")
         ###################################################
         # You MUST implement this method in the subclass. #
+        # if the file mode is text.                       #
         ###################################################
 
     def write_single_alignment(self, stream, alignments):
@@ -318,7 +319,7 @@ def write_multiple_alignments(self, stream, alignments):
     write_alignments = write_multiple_alignments
 
     def write_file(self, stream, alignments):
-        """Write the alignments to the file strenm, and return the number of alignments.
+        """Write the alignments to the file stream, and return the number of alignments.
 
         alignments - A list or iterator returning Alignment objects
         stream     - Output file stream.