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Base class for building Alignment iterators.
You should write a next() method to return Aligment objects. You may wish to redefine the __init__ method as well.
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Create an AlignmentIterator object.
handle - input file
count - optional, expected number of records per alignment
Recommend for fasta file format.
alphabet - optional, e.g. Bio.Alphabet.generic_protein
Note when subclassing:
- there should be a single non-optional argument, the handle,
and optional count and alphabet IN THAT ORDER.
- you do not have to require an alphabet (?).
- you can add additional optional arguments.
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Iterate over the entries as Alignment objects.
Example usage for (concatenated) PHYLIP files:
myFile = open("many.phy","r")
for alignment in PhylipIterator(myFile) :
print "New alignment:"
for record in alignment :
print record.id
print record.seq
myFile.close()
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Return the next alignment in the file. This method should be replaced by any derived class to do something useful. |
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