Pyteomics documentation v3.4.1

xml - utilities for XML parsing

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xml - utilities for XML parsing

This module is not intended for end users. It implements the abstract classes for all XML parsers, XML and IndexedXML, and some utility functions.

Dependencies

This module requres lxml and numpy.


class pyteomics.xml.ByteCountingXMLScanner(source, indexed_tags, block_size=1000000)[source]

Bases: pyteomics.auxiliary._file_obj

Carry out the construction of a byte offset index for source XML file for each type of tag in indexed_tags.

Inheris from pyteomics.auxiliary._file_obj to support the object-oriented _keep_state() interface.

Methods

build_byte_index(*args, **kwargs) Builds a byte offset index for one or more types of tags.
scan(source, indexed_tags)
__init__(source, indexed_tags, block_size=1000000)[source]
Parameters:

indexed_tags : iterable of bytes

The XML tags (without namespaces) to build indices for.

block_size : int, optional

The size of the each chunk or “block” of the file to hold in memory as a partitioned string at any given time. Defaults to 1000000.

build_byte_index(*args, **kwargs)[source]

Builds a byte offset index for one or more types of tags.

Parameters:

lookup_id_key_mapping : Mapping, optional

A mapping from tag name to the attribute to look up the identity for each entity of that type to be extracted. Defaults to ‘id’ for each type of tag.

Returns:

defaultdict(ByteEncodingOrderedDict) :

Mapping from tag type to ByteEncodingOrderedDict from identifier to byte offset

class pyteomics.xml.FlatTagSpecificXMLByteIndex(source, indexed_tags=None, keys=None)[source]

Bases: pyteomics.xml.TagSpecificXMLByteIndex

An alternative interface on top of TagSpecificXMLByteIndex that assumes that identifiers across different tags are globally unique, as in MzIdentML.

Attributes

offsets ByteEncodingOrderedDict The mapping between ids and byte offsets.

Methods

build_index()
items()
keys()
__init__(source, indexed_tags=None, keys=None)
class pyteomics.xml.IndexedXML(*args, **kwargs)[source]

Bases: pyteomics.xml.XML

Subclass of XML which uses an index of byte offsets for some elements for quick random access.

Methods

build_id_cache(*args, **kwargs) Construct a cache for each element in the document, indexed by id
build_tree(*args, **kwargs) Build and store the ElementTree instance
clear_id_cache() Clear the element ID cache
clear_tree() Remove the saved ElementTree.
get_by_id(*args, **kwargs) Retrieve the requested entity by its id.
iterfind(*args, **kwargs) Parse the XML and yield info on elements with specified local name or by specified “XPath”.
next()
reset()
__init__(*args, **kwargs)[source]

Create an XML parser object.

Parameters:

source : str or file

File name or file-like object corresponding to an XML file.

read_schema : bool, optional

Defines whether schema file referenced in the file header should be used to extract information about value conversion. Default is True.

iterative : bool, optional

Defines whether an ElementTree object should be constructed and stored on the instance or if iterative parsing should be used instead. Iterative parsing keeps the memory usage low for large XML files. Default is True.

use_index : bool, optional

Defines whether an index of byte offsets needs to be created for elements listed in indexed_tags. This is useful for random access to spectra in mzML or elements of mzIdentML files, or for iterative parsing of mzIdentML with retrieve_refs=True. If True, build_id_cache is ignored. If False, the object acts exactly like XML. Default is True.

indexed_tags : container of bytes, optional

If use_index is True, elements listed in this parameter will be indexed. Empty set by default.

build_id_cache(*args, **kwargs)

Construct a cache for each element in the document, indexed by id attribute

build_tree(*args, **kwargs)

Build and store the ElementTree instance for the underlying file

clear_id_cache()

Clear the element ID cache

clear_tree()

Remove the saved ElementTree.

get_by_id(*args, **kwargs)[source]

Retrieve the requested entity by its id. If the entity is a spectrum described in the offset index, it will be retrieved by immediately seeking to the starting position of the entry, otherwise falling back to parsing from the start of the file.

Parameters:

elem_id : str

The id value of the entity to retrieve.

Returns:

dict :

iterfind(*args, **kwargs)

Parse the XML and yield info on elements with specified local name or by specified “XPath”.

Parameters:

path : str

Element name or XPath-like expression. Only local names separated with slashes are accepted. An asterisk (*) means any element. You can specify a single condition in the end, such as: "/path/to/element[some_value>1.5]" Note: you can do much more powerful filtering using plain Python. The path can be absolute or “free”. Please don’t specify namespaces.

**kwargs : passed to self._get_info_smart().

Returns:

out : iterator

class pyteomics.xml.TagSpecificXMLByteIndex(source, indexed_tags=None, keys=None)[source]

Bases: object

Encapsulates the construction and querying of a byte offset index for a set of XML tags.

This type mimics an immutable Mapping.

Parameters:

index_tags: iterable of bytes :

The tag names to include in the index

Attributes

indexed_tags iterable of bytes The tag names to index, not including a namespace
offsets defaultdict(OrderedDict(str, int)) The hierarchy of byte offsets organized {"tag_type": {"id": byte_offset}}
indexed_tag_keys: dict(str, str)   A mapping from tag name to unique identifier attribute

Methods

build_index() Perform the byte offset index building for py:attr:source.
items()
keys()
__init__(source, indexed_tags=None, keys=None)[source]
build_index()[source]

Perform the byte offset index building for py:attr:source.

Returns:

offsets: defaultdict :

The hierarchical offset, stored in offsets

class pyteomics.xml.XML(source, read_schema=True, iterative=True, build_id_cache=False, **kwargs)[source]

Bases: pyteomics.auxiliary.FileReader

Base class for all format-specific XML parsers. The instances can be used as context managers and as iterators.

Methods

build_id_cache(*args, **kwargs) Construct a cache for each element in the document, indexed by id
build_tree(*args, **kwargs) Build and store the ElementTree instance
clear_id_cache() Clear the element ID cache
clear_tree() Remove the saved ElementTree.
get_by_id(*args, **kwargs) Parse the file and return the element with id attribute equal to elem_id.
iterfind(*args, **kwargs) Parse the XML and yield info on elements with specified local name or by specified “XPath”.
next()
reset()
__init__(source, read_schema=True, iterative=True, build_id_cache=False, **kwargs)[source]

Create an XML parser object.

Parameters:

source : str or file

File name or file-like object corresponding to an XML file.

read_schema : bool, optional

Defines whether schema file referenced in the file header should be used to extract information about value conversion. Default is True.

iterative : bool, optional

Defines whether an ElementTree object should be constructed and stored on the instance or if iterative parsing should be used instead. Iterative parsing keeps the memory usage low for large XML files. Default is True.

build_id_cache : bool, optional

Defines whether a dictionary mapping IDs to XML tree elements should be built and stored on the instance. It is used in XML.get_by_id(), e.g. when using pyteomics.mzid.MzIdentML with retrieve_refs=True.

build_id_cache(*args, **kwargs)[source]

Construct a cache for each element in the document, indexed by id attribute

build_tree(*args, **kwargs)[source]

Build and store the ElementTree instance for the underlying file

clear_id_cache()[source]

Clear the element ID cache

clear_tree()[source]

Remove the saved ElementTree.

get_by_id(*args, **kwargs)[source]

Parse the file and return the element with id attribute equal to elem_id. Returns None if no such element is found.

Parameters:

elem_id : str

The value of the id attribute to match.

Returns:

out : dict or None

iterfind(*args, **kwargs)[source]

Parse the XML and yield info on elements with specified local name or by specified “XPath”.

Parameters:

path : str

Element name or XPath-like expression. Only local names separated with slashes are accepted. An asterisk (*) means any element. You can specify a single condition in the end, such as: "/path/to/element[some_value>1.5]" Note: you can do much more powerful filtering using plain Python. The path can be absolute or “free”. Please don’t specify namespaces.

**kwargs : passed to self._get_info_smart().

Returns:

out : iterator

pyteomics.xml.xpath(tree, path, ns=None)[source]

Return the results of XPath query with added namespaces. Assumes the ns declaration is on the root element or absent.

Parameters:

tree : ElementTree

path : str

ns : str or None, optional

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