guide.py

guide.py

@@ -169,7 +169,7 @@ class Alignment():
         return len(self.seqs)
     def __getitem__(self, ndx):
         return self.seqs[ndx]
-    def calcDistances(self, measure, a=1.0):
+    def calcDistances(self, measure = 'fractional', a=1.0):
         """ Calculate the evolutionary distance between all pairs of sequences
         in this alignment, using the given measure. Measure can be one of
         'fractional', 'poisson', 'gamma', 'jc' or 'k2p'. If 'gamma' or 'k2p' is
@@ -201,7 +201,7 @@ class Alignment():
                         L += 1
                         if seqA[k] != seqB[k]:
                             D += 1
-                p = float(D)/L
+                p = D / L
                 # Now calculate the specified measure based on p
                 if measure == 'fractional':
                     dist = p
@@ -214,7 +214,7 @@ class Alignment():
         symbolsPerLine = 60
         maxNameLength =  self.namelen + 1
         mystring = u''
-        wholeRows = self.alignlen / symbolsPerLine
+        wholeRows = self.alignlen // symbolsPerLine
         for i in range(wholeRows):
             for j in range(len(self.seqs)):
                 mystring += self.seqs[j].name.ljust(maxNameLength) + u' '
@@ -235,7 +235,7 @@ class Alignment():
         html = u''.ljust(self.namelen) + u' '
         for i in range(self.alignlen - 1):
             if (i+1) % 10 == 0:
-                html += str(i/10+1)[-1]
+                html += str(i//10+1)[-1]
             else:
                 html += ' '
         html += u'%s\n' % (self.alignlen)
@@ -504,7 +504,7 @@ def readClustalString(string, alphabet):
             continue
         sections = line.split()
         name, seq = sections[0:2]
-        if seqs.has_key(name):
+        if name in seqs:
             seqs[name] += seq
         else:
             seqs[name] = seq