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

Functions

__init__()

Create an AlignmentIterator object

__iter__()

Iterate over the entries as MultipleSeqAlignment objects

__next__()

Return the next alignment in the file

next()

Python 2 style alias for Python 3 style next method

Link to this section Functions

__init__()

Create an AlignmentIterator object.

Arguments:

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__()

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

__next__()

Return the next alignment in the file.

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

next()

Python 2 style alias for Python 3 style next method.