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)

Interface to different mzML formats.

__getitem__(identifier)

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)

Initialize a object interface to mzML files.

Parameters:

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

_indexed_gzip(path)

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)

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)

Read binary data from file handler.

Keyword Arguments:  

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

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)

__getitem__(identifier)

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)

Initalize Wrapper object for standard mzML files.

Parameters:

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

_build_index(from_scratch, use_spectra_sanity_check)

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.
• use_spectra_sanity_check (bool) – Whether or not to assume all data are spectra and follow the (scan=|nativeID=”) pattern. Disable this if you have chromatograms or spectra with different ids.

Returns:

A file-like object used to access the indexed content by seeking to a particular offset for the file.

_interpol_search(target_index, chunk_size=8, fallback_cutoff=100)

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

_search_linear(seeker, index, chunk_size=8)

Fallback to linear search if interpolated search fails.

read(size=-1)

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)

__getitem__(identifier)

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)

Initalize Wrapper object for gzipped mzML files.

Parameters:

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

_build_index()

Cant build index for standard gzip files

read(size=-1)

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)

__getitem__(identifier)

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)

Initialize Wrapper object for indexed gzipped files.

Parameters:

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

_build_index()

Use the GSGR class to retrieve the index from the file and save it.

read(size=-1)

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)