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, alphabet=None, mode='t', fmt=None)

Bases: abc.ABC

Base class for building SeqRecord iterators.

You should write a parse method that returns a SeqRecord generator. You may wish to redefine the __init__ method as well.

__init__(self, source, alphabet=None, mode='t', fmt=None)

Create a SequenceIterator object.

Arguments: - source - input file stream, or path to input file - alphabet - no longer used, should be None

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.

__next__(self)
__iter__(self)

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.

abstract parse(self, handle)

Start parsing the file, and return a SeqRecord iterator.

__abstractmethods__ = frozenset({'parse'})
class Bio.SeqIO.Interfaces.SequenceWriter(target, mode='w')

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.

__init__(self, target, mode='w')

Create the writer object.

clean(self, text)

Use this to avoid getting newlines in the output.

write_header(self)

Write the file header to the output file.

Write the file footer to the output file.

write_record(self, record)

Write a single record to the output file.

record - a SeqRecord object

write_records(self, records, maxcount=None)

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

records - A list or iterator returning SeqRecord objects maxcount - The maximum number of records allowed by the file format, or None if there is no maximum.

write_file(self, records, mincount=0, maxcount=None)

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

records - A list or iterator returning SeqRecord objects

class Bio.SeqIO.Interfaces.SequentialSequenceWriter(target, mode='w')

Bases: Bio.SeqIO.Interfaces.SequenceWriter

Base class for sequential sequence writers (DEPRECATED).

This class should be subclassed. It is no longer used. It was intended for sequential file formats with an (optional) header, repeated records, and an (optional) footer. It would enforce callign the methods in appropriate order. To update code using SequentialSequenceWriter, just subclass SequenceWriter and drop the ._header_written etc checks (or reimplement them).

In this case (as with interlaced file formats), the user may simply call the write_file() method and be done.

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

Users must call write_header() and write_footer() even when the file format concerned doesn’t have a header or footer. This is to try and make life as easy as possible when switching the output format.

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

__init__(self, target, mode='w')

Initialize the class.

write_header(self)

Write the file header.

If your file format defines a header, you should implement this method in order to write the header before any of the records.

The default implementation checks the private attribute ._header_written to ensure the header is only written once.

Write the file footer.

If your file format defines a footer, you should implement this method in order to write the footer after all the records.

The default implementation checks the private attribute ._footer_written to ensure the footer is only written once.

write_record(self, record)

Write a single record to the output file.

record - a SeqRecord object

Once you have called write_header() you can call write_record() and/or write_records() as many times as needed. Then call write_footer() and close().

write_records(self, records)

Write multiple record to the output file.

records - A list or iterator returning SeqRecord objects

Once you have called write_header() you can call write_record() and/or write_records() as many times as needed. Then call write_footer() and close().

Returns the number of records written.

write_file(self, records)

Use this to write an entire file containing the given records.

records - A list or iterator returning SeqRecord objects

This method can only be called once. Returns the number of records written.