3.5. File Access

pymzML offers support for different kinds of mzML files. The following classes are wrappers for access of different types of mzML files, which allows the implementation of file type specific search and data retrieving algorithms. An explanation of how to implement your own file class can be found in the advanced usage section.

3.5.1. File Interface

class pymzml.file_interface.FileInterface(path, encoding, build_index_from_scratch=False, index_regex=None)[source]

Interface to different mzML formats.

Methods

read([size])

Read binary data from file handler.

__getitem__(identifier)[source]

Access the item with id ‘identifier’ in the file.

Parameters:: identifier (str) – native id of the item to access
Returns:: text associated with the given identifier
Return type:: data (str)

__init__(path, encoding, build_index_from_scratch=False, index_regex=None)[source]

Initialize a object interface to mzML files.

Parameters:

path (str) – path to the mzML file
encoding (str) – encoding of the file

_indexed_gzip(path)[source]

Check if the given file is an indexed gzip file or not.

Parameters:: path (str) – path to the file
Returns:: True if path is a gzip file with index, else False
Return type:: bool

_open(path_or_file)[source]

Open a file like object resp. a wrapper for a file like object.

Parameters:: path (str) – path to the mzml file
Returns:: instance of StandardGzip, IndexedGzip or StandardMzml, based on the file ending of ‘path’
Return type:: file_handler

read(size=-1)[source]

Read binary data from file handler.

Keyword Arguments:

size (int) – Number of bytes to read from file, -1 to
file (read to end of)

Returns:

byte string with defined size of the input data

Return type:

data (str)

3.5.2. File Classes

3.5.2.1. mzML

class pymzml.file_classes.standardMzml.StandardMzml(path, encoding, build_index_from_scratch=False, index_regex=None)[source]

Methods

read([size])

Read binary data from file handler.

get_binary_file_handler
get_file_handler

__getitem__(identifier)[source]

Access the item with id ‘identifier’.

Either use linear, binary or interpolated search.

Parameters:: identifier (str) – native id of the item to access
Returns:: text associated with the given identifier
Return type:: data (str)

__init__(path, encoding, build_index_from_scratch=False, index_regex=None)[source]

Initalize Wrapper object for standard mzML files.

Parameters:

path (str) – path to the file
encoding (str) – encoding of the file

_binary_search(target_index)[source]

Retrieve spectrum for a given spectrum ID using binary jumps

Parameters:: target_index (int) – native id of the spectrum to access
Returns:: pymzML spectrum
Return type:: Spectrum (pymzml.spec.Spectrum)

_build_index(from_scratch=False)[source]

Build an index.

A list of offsets to which a file pointer can seek directly to access a particular spectrum or chromatogram without parsing the entire file.

Parameters:: from_scratch (bool) – Whether or not to force building the index from scratch, by parsing the file, if no existing index can be found.
Returns:: A file-like object used to access the indexed content by seeking to a particular offset for the file.

_build_index_from_scratch(seeker)[source]: Build an index of spectra/chromatogram data with offsets by parsing the file.

_interpol_search(target_index, chunk_size=8, fallback_cutoff=100)[source]

Use linear interpolation search to find spectra faster.

Parameters:: target_index (str or int) – native id of the item to access
Keyword Arguments:: chunk_size (int) – size of the chunk to read in one go in kb

_read_extremes()[source]

Read min and max spectrum ids. Required for binary jumps.

Returns:: list of tuples containing spec_id and file_offset
Return type:: seek_list (list)

_search_linear(seeker, index, chunk_size=8)[source]: Fallback to linear search if interpolated search fails.

read(size=-1)[source]

Read binary data from file handler.

Keyword Arguments:: size (int) – Number of bytes to read from file, -1 to read to end of file
Returns:: byte string of len size of input data
Return type:: data (str)

3.5.2.2. Gzip

class pymzml.file_classes.standardGzip.StandardGzip(path, encoding)[source]

Methods

read([size])

Read binary data from file handler.

close

__getitem__(identifier)[source]

Access the item with id ‘identifier’ in the file by iterating the xml-tree.

Parameters:: identifier (str) – native id of the item to access
Returns:: text associated with the given identifier
Return type:: data (str)

__init__(path, encoding)[source]

Initalize Wrapper object for gzipped mzML files.

Parameters:

path (str) – path to the file
encoding (str) – encoding of the file

_build_index()[source]: Cant build index for standard gzip files

read(size=-1)[source]

Read binary data from file handler.

Keyword Arguments:: size (int) – Number of bytes to read from file, -1 to read to end of file
Returns:: byte string of len size of input data
Return type:: data (str)

3.5.2.3. iGzip

class pymzml.file_classes.indexedGzip.IndexedGzip(path, encoding)[source]

Methods

read([size])

Read binary data from file handler.

__getitem__(identifier)[source]

Access the item with id ‘identifier’ in the file.

Parameters:: identifier (str) – native id of the item to access
Returns:: text associated with the given identifier
Return type:: data (str)

__init__(path, encoding)[source]

Initialize Wrapper object for indexed gzipped files.

Parameters:

path (str) – path to the file
encoding (str) – encoding of the file

_build_index()[source]: Use the GSGR class to retrieve the index from the file and save it.

read(size=-1)[source]

Read binary data from file handler.

Keyword Arguments:: size (int) – Number of bytes to read from file, -1 to read to end of file
Returns:: byte string of len size of input data
Return type:: data (str)