Bases: Mapping

Hold parsed properties of a key-value pair like a sequence’s definition line.

This object supports the Mapping interface, and keys may be accessed by attribute access notation.

__init__(mapping, original=None)[source]¶

get(k[, d]) → D[k] if k in D, else d.  d defaults to None.¶

items() → a set-like object providing a view on D's items[source]¶

keys() → a set-like object providing a view on D's keys[source]¶

values() → an object providing a view on D's values[source]¶

Bases: TwoLayerIndexedFASTA

Creates an IndexedPEFF object.

Parameters:

• source (str or file) – The file to read. If a file object, it needs to be in rb mode.

• parse (bool, optional) – Defines whether the descriptions should be parsed in the produced tuples. Default is True.

• kwargs (passed to the TwoLayerIndexedFASTA constructor.)

__init__(source, ignore_comments=False, **kwargs)[source]¶

Open source and create a two-layer index for convenient random access both by full header strings and extracted fields.

Parameters:

• source (str or file-like) – File to read. If file object, it must be opened in binary mode.

• header_pattern (str or RE or None, optional) – Pattern to match the header string. Must capture the group used for the second index. If None (default), second-level index is not created.

• header_group (int or str or None, optional) – Defines which group is used as key in the second-level index. Default is 1.

• ignore_comments (bool, optional) – If True then ignore the second and subsequent lines of description. Default is False, which concatenates multi-line descriptions into a single string.

• parser (function or None, optional) – Defines whether the FASTA descriptions should be parsed. If it is a function, that function will be given the description string, and the returned value will be yielded together with the sequence. The std_parsers dict has parsers for several formats. Hint: specify parse() as the parser to apply automatic format recognition. Default is None, which means return the header “as is”.

• arguments (Other)

build_second_index()¶

Create the mapping from extracted field to whole header string.

get_by_id(key)¶

Get the entry by value of header string or extracted field.

map(target=None, workers=None, args=None, kwargs=None, method='mp', **_kwargs)¶

Execute the target function over entries of this object in parallel. The type of parallelism is determined by the method parameter.

Results will be returned out of order.

Parameters:

• target (Callable, optional) – The function to execute over each entry. It will be given a single object yielded by the wrapped iterator as well as all of the values in args and kwargs.

• workers (int, optional) – The number of worker threads or processes to use. The default depends on the method parameter.

• args (Sequence, optional) – Additional positional arguments to be passed to the target function.

• kwargs (Mapping, optional) – Additional keyword arguments to be passed to the target function.

• method (str, optional) –

  The type of parallelism to use. Can be one of the following:

  • either one of ‘p’, ‘mp’, ‘processes’, or ‘multiprocessing’: use multiprocessing This is the default. This is also equivalent to calling pmap(), see there for details.

  • either one of ‘t’, ‘threading’, or ‘threads’: use threading This is also equivalent to calling tmap(), see there for details.

• **_kwargs – Additional keyword arguments to be passed to the target function.

Yields:

object – The work item returned by the target function.

parser(line)[source]¶

The type of the None singleton.

pmap(target=None, workers=None, args=None, kwargs=None, **_kwargs)¶

Execute the target function over entries of this object across up to workers processes.

Results will be returned out of order.

Parameters:

• target (Callable, optional) – The function to execute over each entry. It will be given a single object yielded by the wrapped iterator as well as all of the values in args and kwargs.

• workers (int or None, optional) – The number of worker processes to use. If not a positive integer, defaults to the number of available CPUs. This parameter can also be set at reader creation.

• args (Sequence, optional) – Additional positional arguments to be passed to the target function.

• kwargs (Mapping, optional) – Additional keyword arguments to be passed to the target function.

• **_kwargs – Additional keyword arguments to be passed to the target function.

Yields:

object – The work item returned by the target function.

reset()¶

Resets the iterator to its initial state.

tmap(target=None, workers=None, args=None, kwargs=None, chunk_size=None, **_kwargs)¶

Execute the target function over entries of this object across up to workers threads.

Results will be returned out of order.

Parameters:

• target (Callable, optional) –

  The function to execute over each entry. It will be given a single object yielded by the wrapped iterator as well as all of the values in args and kwargs.

  Warning

  target must be thread-safe. The target function cannot interact with the underlying file object directly.

• workers (int or None, optional) – The number of worker threads to use. If not a positive integer, defaults to the number of available CPUs.

• args (Sequence, optional) – Additional positional arguments to be passed to the target function.

• kwargs (Mapping, optional) – Additional keyword arguments to be passed to the target function.

• chunk_size (int, optional) – The number of work items to hand out to each worker thread at a time. If not specified, defaults to chunk_size attribute of this object.

• **_kwargs – Additional keyword arguments to be passed to the target function.

Yields:

object – The work item returned by the target function.