Adding missing __repr__ docstrings in Wise and UniGene

Removed a redundant __str__ definition, if not defined then
Python defaults to using __repr__ anyway (thanks Markus!).

See flake8 D105.

Bio/UniGene/__init__.py

@@ -130,6 +130,7 @@ def _init_from_text(self, text):
             setattr(self, key.lower(), val)
 
     def __repr__(self):
+        """Return UniGene SequenceLine object as a string."""
         return self.text
 
 
@@ -165,6 +166,7 @@ def _init_from_text(self, text):
             setattr(self, key.lower(), val)
 
     def __repr__(self):
+        """Return UniGene ProtsimLine object as a string."""
         return self.text
 
 
@@ -195,6 +197,7 @@ def _init_from_text(self, text):
             setattr(self, key.lower(), val)
 
     def __repr__(self):
+        """Return UniGene STSLine object as a string."""
         return self.text
 
 
@@ -246,6 +249,7 @@ def __init__(self):
         self.txmap = []  # TXMAP entries, array of TXMap entries
 
     def __repr__(self):
+        """Represent the UniGene Record object as a string for debugging."""
         return "<%s> %s %s\n%s" % (self.__class__.__name__,
                                    self.ID, self.symbol, self.title)
 

Bio/Wise/dnal.py

@@ -111,6 +111,7 @@ def identity_fraction(self):
     header = "identity_fraction\tmatches\tmismatches\tgaps\textensions"
 
     def __str__(self):
+        """Statistics as a tab separated string."""
         return "\t".join(str(x) for x in (self.identity_fraction(),
                                           self.matches, self.mismatches,
                                           self.gaps, self.extensions))

Bio/Wise/psw.py

@@ -63,7 +63,8 @@ def __init__(self, column_unit):
         list.__init__(self, [column_unit.column, None])
 
     def __repr__(self):
-        return "%s(%s, %s)" % (self.kind, self[0], self[1])
+        """Represent the AlignmentColumn object as a string for debugging."""
+        return "%s(%r, %r)" % (self.kind, self[0], self[1])
 
     def append(self, column_unit):
         """Add a unit to the Column."""
@@ -85,10 +86,9 @@ def __init__(self, unit, column, kind):
         self.column = column
         self.kind = kind
 
-    def __str__(self):
-        return "ColumnUnit(unit=%s, column=%s, %s)" % (self.unit, self.column, self.kind)
-
-    __repr__ = __str__
+    def __repr__(self):
+        """Represent the ColumnUnit object as a string for debugging."""
+        return "ColumnUnit(unit=%r, column=%r, kind=%r)" % (self.unit, self.column, self.kind)
 
 
 _re_unit = re.compile(r"^Unit +([01])- \[ *(-?\d+)- *(-?\d+)\] \[(\w+)\]$")
@@ -100,9 +100,9 @@ def parse_line(line):
     >>> print(parse_line("Column 0:"))
     None
     >>> parse_line("Unit  0- [  -1-   0] [SEQUENCE]")
-    ColumnUnit(unit=0, column=0, SEQUENCE)
+    ColumnUnit(unit=0, column=0, kind='SEQUENCE')
     >>> parse_line("Unit  1- [  85-  86] [SEQUENCE]")
-    ColumnUnit(unit=1, column=86, SEQUENCE)
+    ColumnUnit(unit=1, column=86, kind='SEQUENCE')
     """
     match = _re_unit.match(line.rstrip())
 

Tests/test_psw.py

@@ -74,13 +74,13 @@ def test_AlignmentColumn_assertions(self):
 
     def test_ColumnUnit(self):
         self.assertEqual(repr(psw.ColumnUnit(0, 33, "SEQUENCE")),
-                         "ColumnUnit(unit=0, column=33, SEQUENCE)")
+                         "ColumnUnit(unit=0, column=33, kind='SEQUENCE')")
 
         self.assertEqual(repr(psw.ColumnUnit(1, 33, "INSERT")),
-                         "ColumnUnit(unit=1, column=33, INSERT)")
+                         "ColumnUnit(unit=1, column=33, kind='INSERT')")
 
         self.assertEqual(repr(psw.ColumnUnit(1, 33, "END")),
-                         "ColumnUnit(unit=1, column=33, END)")
+                         "ColumnUnit(unit=1, column=33, kind='END')")
 
     PARSED = "[SEQUENCE(39, 22), SEQUENCE(40, 23), SEQUENCE(41, 24), SEQUENCE(42, 25), SEQUENCE(43, 26), SEQUENCE(44, 27), END(0, 27)]"