some fixes

Author: carlosp420

Bio/Blast/Applications.py

@@ -1545,8 +1545,8 @@ def __init__(self, cmd="makeblastdb", **kwargs):
         ]
         AbstractCommandline.__init__(self, cmd, **kwargs)
 
-    def _input_type_checker(command, x):
-        return x in ("asn1_bin", "asn1_txt", "blastdb", "fasta")
+    def _input_type_checker(self, command):
+        return command in ("asn1_bin", "asn1_txt", "blastdb", "fasta")
 
     def _validate(self):
         incompatibles = {
@@ -1556,7 +1556,7 @@ def _validate(self):
         }
 
         # Copied from _NcbibaseblastCommandline class above.
-        # Code repeated here for python2 and 3 comptaibility,
+        # Code repeated here for python2 and 3 compatibility,
         # because this is not a _NcbibaseblastCommandline subclass.
         for a in incompatibles:
             if self._get_parameter(a):

Bio/Seq.py

@@ -803,7 +803,7 @@ def complement(self):
         >>> my_protein.complement()
         Seq('KTIBKCY')
 
-        Here "M" was interpretted as the IUPAC ambiguity code for
+        Here "M" was interpreted as the IUPAC ambiguity code for
         "A" or "C", with complement "K" for "T" or "G". Likewise
         "A" has complement "T". The letter "I" has no defined
         meaning under the IUPAC convention, and is unchanged.
@@ -2263,7 +2263,7 @@ def extend(self, other):
     def toseq(self):
         """Return the full sequence as a new immutable Seq object.
 
-        >>> from Bio.Seq import Seq
+        >>> from Bio.Seq import MutableSeq
         >>> my_mseq = MutableSeq("MKQHKAMIVALIVICITAVVAAL")
         >>> my_mseq
         MutableSeq('MKQHKAMIVALIVICITAVVAAL')

Bio/SeqFeature.py

@@ -1271,7 +1271,7 @@ def _set_strand(self, value):
     def __add__(self, other):
         """Combine locations, or shift the location by an integer offset.
 
-        >>> from Bio.SeqFeature import FeatureLocation, CompoundLocation
+        >>> from Bio.SeqFeature import FeatureLocation
         >>> f1 = FeatureLocation(15, 17) + FeatureLocation(20, 30)
         >>> print(f1)
         join{[15:17], [20:30]}