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|
The dnaio API
=============
.. module:: dnaio
The open function
-----------------
.. autofunction:: open
The ``SequenceRecord`` class
------------------------------
.. autoclass:: dnaio.SequenceRecord
:members:
:special-members: __len__, __getitem__
.. automethod:: __init__(name: str, sequence: str, qualities: Optional[str] = None)
Reader and writer interfaces
----------------------------
.. autoclass:: SingleEndReader
:members: __iter__
.. autoclass:: PairedEndReader
:members: __iter__
.. autoclass:: SingleEndWriter
:members: write
.. autoclass:: PairedEndWriter
:members: write
.. autoclass:: MultipleFileWriter
:members: write, write_iterable
Reader and writer classes
-------------------------
The `dnaio.open` function returns an instance of one of the following classes.
They can also be used directly if needed.
.. autoclass:: FastaReader
:show-inheritance:
.. autoclass:: FastaWriter
:show-inheritance:
.. autoclass:: FastqReader
:show-inheritance:
.. autoclass:: FastqWriter
:show-inheritance:
.. autoclass:: BamReader
:show-inheritance:
.. autoclass:: TwoFilePairedEndReader
:show-inheritance:
.. autoclass:: TwoFilePairedEndWriter
:show-inheritance:
.. autoclass:: InterleavedPairedEndReader
:show-inheritance:
.. autoclass:: InterleavedPairedEndWriter
:show-inheritance:
.. autoclass:: MultipleFileReader
:members: __iter__
.. autoclass:: MultipleFastaWriter
:show-inheritance:
.. autoclass:: MultipleFastqWriter
:show-inheritance:
Chunked reading of sequence records
-----------------------------------
The following functions can be used to very quickly split up the input file(s)
into similarly-sized chunks without actually parsing the records. The chunks
can then be distributed to worker threads or subprocesses and be parsed and
processed there.
.. autofunction:: read_chunks
.. autofunction:: read_paired_chunks
Functions
---------
.. autofunction:: records_are_mates
Exceptions
----------
.. autoexception:: UnknownFileFormat
.. autoexception:: FileFormatError
.. autoexception:: FastaFormatError
:show-inheritance:
.. autoexception:: FastqFormatError
:show-inheritance:
|
