biopython v1.71.0 Bio.SeqIO.Interfaces.SequenceIterator

Base class for building SeqRecord iterators.

You should write a next method to return SeqRecord objects. You may wish to redefine the init method as well.

Link to this section Summary

Functions

__init__()

Create a SequenceIterator object

__iter__()

Iterate over the entries as a SeqRecord objects

__next__()

Return the next record in the file

next()

Python 2 style alias for Python 3 style next method

Link to this section Functions

__init__()

Create a SequenceIterator object.

Arguments:

handle - input file
alphabet - optional, e.g. Bio.Alphabet.generic_protein

This method MAY be overridden by any subclass, for example if you need to process a header or accept additional arguments.

Note when subclassing:

there should be a single non-optional argument, the handle.
you do not have to require an alphabet.
you can add additional optional arguments.

__iter__()

Iterate over the entries as a SeqRecord objects.

Example usage for Fasta files::

with open("example.fasta","r") as myFile:
    myFastaReader = FastaIterator(myFile)
    for record in myFastaReader:
        print(record.id)
        print(record.seq)

This method SHOULD NOT be overridden by any subclass. It should be left as is, which will call the subclass implementation of next to actually parse the file.

__next__()

Return the next record in the file.

This method’s stub-implementation MUST be overridden by any subclass to actually parse the file and return the next entry as a SeqRecord object.

next()

Python 2 style alias for Python 3 style next method.