Bio.SeqIO.Interfaces module

Bio.SeqIO support module (not for general use).

Unless you are writing a new parser or writer for Bio.SeqIO, you should not use this module. It provides base classes to try and simplify things.

class Bio.SeqIO.Interfaces.SequenceIterator(source: IO | PathLike | str | bytes, alphabet: None = None, fmt: str | None = None)

Bases: ABC, Generic

Base class for building SeqRecord iterators.

You should write a __next__ method that returns the next SeqRecord. You may wish to redefine the __init__ method as well. You must also create a class property modes specifying the allowable file stream modes.

abstract property modes

File modes (binary or text) that the parser can handle.

This property must be “t” (for text mode only), “b” (for binary mode only), “tb” (if both text and binary mode are accepted, but text mode is preferred), or “bt” (if both text and binary mode are accepted, but binary mode is preferred).

__init__(source: IO | PathLike | str | bytes, alphabet: None = None, fmt: str | None = None) → None

Create a SequenceIterator object.

Arguments: - source - input file stream, or path to input file - alphabet - no longer used, should be None - fmt - string, mixed case format name for in error messages

This method MAY be overridden by any subclass.

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

abstract __next__()

Return the next SeqRecord.

This method must be implemented by the subclass.

__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.

__enter__()

__exit__(exc_type, exc_value, exc_traceback)

__abstractmethods__ = frozenset({'__next__', 'modes'})

__orig_bases__ = (<class 'abc.ABC'>, typing.Generic[~AnyStr])

__parameters__ = (~AnyStr,)

class Bio.SeqIO.Interfaces.SequenceWriter(target: IO | PathLike | str | bytes)

Bases: object

Base class for sequence writers. This class should be subclassed.

It is intended for sequential file formats with an (optional) header, repeated records, and an (optional) footer, as well as for interlaced file formats such as Clustal.

The user may call the write_file() method to write a complete file containing the sequences.

Alternatively, users may call the write_header(), followed by multiple calls to write_record() and/or write_records(), followed finally by write_footer().

Note that write_header() cannot require any assumptions about the number of records.

abstract property modes

File modes (binary or text) that the writer can handle.

This property must be “t” (for text mode only), “b” (for binary mode only), “tb” (if both text and binary mode are accepted, but text mode is preferred), or “bt” (if both text and binary mode are accepted, but binary mode is preferred).

__init__(target: IO | PathLike | str | bytes) → None: Create the writer object.

clean(text: str) → str: Use this to avoid getting newlines in the output.

write_header(): Write the file header to the output file.

write_footer(): Write the file footer to the output file.

write_record(record)

Write a single record to the output file.

record - a SeqRecord object

write_records(records)

Write records to the output file, and return the number of records.

records - A list or iterator returning SeqRecord objects

write_file(records)

Write a complete file with the records, and return the number of records.

records - A list or iterator returning SeqRecord objects