Slight improvements to the generic GFLine class and to the to_gff wra…

…pper

Mikado/parsers/__init__.py

@@ -107,13 +107,16 @@ def to_gff(string, input_format=None):
     """
     Function to recognize the input file type (GFF or GTF).
     :param string:
-    :type string: str
+    :type string: (str|io.TextIOWrapper|io.BytesIO|io.BufferedReader|IO)
     :rtype: (Mikado.parsers.GTF.GTF | Mikado.parsers.GFF.GFF3)
     """
 
     # handle = open(string)
     if isinstance(string, io.TextIOWrapper):
         fname = "-"
+    elif isinstance(string, (io.BytesIO, io.BufferedReader)):
+        fname = "-"
+        string = io.TextIOWrapper(string)
     else:
         fname = string
 

Mikado/parsers/gfannotation.py

@@ -314,6 +314,24 @@ def __lt__(self, other):
             else:
                 return False
 
+    def remove_attribute(self, attribute):
+        """Method to remove attributes from the internal dictionary."""
+
+        if attribute in self.attributes:
+            del self.attributes[attribute]
+        try:
+            self.attribute_order.remove(attribute)
+        except ValueError:
+            pass
+        return
+
+    def add_attribute(self, attribute, value):
+
+        self.attributes[attribute] = value
+
+        if attribute not in self.attribute_order:
+            self.attribute_order.append(attribute)
+
     def __eq__(self, other):
 
         if self.is_exon is True: