Package Bio :: Package AlignIO :: Module Interfaces :: Class AlignmentIterator
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Class AlignmentIterator

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Known Subclasses:

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.

Instance Methods [hide private]
 
__init__(self, handle, seq_count=None, alphabet=SingleLetterAlphabet())
Create an AlignmentIterator object.
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__iter__(self)
Iterate over the entries as Alignment objects.
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next(self)
Return the next alignment in the file.
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Method Details [hide private]

__init__(self, handle, seq_count=None, alphabet=SingleLetterAlphabet())
(Constructor)

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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.

__iter__(self)

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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()

next(self)

source code 

Return the next alignment in the file.

This method should be replaced by any derived class to do something useful.