Bio.SeqIO.XdnaIO module

Bio.SeqIO support for the “xdna” file format.

The Xdna binary format is generated by Christian Marck’s DNA Strider program and also used by Serial Cloner.

class Bio.SeqIO.XdnaIO.XdnaIterator(source)

Bases: Bio.SeqIO.Interfaces.SequenceIterator

Parser for Xdna files.

__init__(self, source)

Parse a Xdna file and return a SeqRecord object.

Argument source is a file-like object in binary mode or a path to a file.

Note that this is an “iterator” in name only since an Xdna file always contain a single sequence.

parse(self, handle)

Start parsing the file, and return a SeqRecord generator.

iterate(self, handle, header)

Parse the file and generate SeqRecord objects.

class Bio.SeqIO.XdnaIO.XdnaWriter(target)

Bases: Bio.SeqIO.Interfaces.SequenceWriter

Write files in the Xdna format.

__init__(self, target)

Initialize an Xdna writer object.

Arguments:

• target - Output stream opened in binary mode, or a path to a file.

write_file(self, records)

Write the specified record to a Xdna file.

Note that the function expects a list (or iterable) of records as per the SequenceWriter interface, but the list should contain only one record as the Xdna format is a mono-record format.