Commit 85897a23 by Mikael Boden

### guide.py

parent 8625943a
 ... ... @@ -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 ... ...
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