biopython v1.71.0 Bio.AlignIO.Interfaces.AlignmentIterator
Base class for building MultipleSeqAlignment iterators.
You should write a next() method to return Aligment objects. You may wish to redefine the init method as well.
Link to this section Summary
Link to this section Functions
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.
Iterate over the entries as MultipleSeqAlignment objects.
Example usage for (concatenated) PHYLIP files::
with open("many.phy","r") as myFile: for alignment in PhylipIterator(myFile): print "New alignment:" for record in alignment: print record.id print record.seq
Return the next alignment in the file.
This method should be replaced by any derived class to do something useful.
Python 2 style alias for Python 3 style next method.