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¶
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class
pymzml.file_interface.
FileInterface
(path, encoding, build_index_from_scratch=False)[source]¶ Interface to different mzML formats.
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__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)
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__init__
(path, encoding, build_index_from_scratch=False)[source]¶ Initialize a object interface to mzML files.
Parameters: - path (str) – path to the mzML file
- encoding (str) – encoding of the file
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_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
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_open
(path)[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
orStandardMzml
, based on the file ending of ‘path’Return type: file_handler
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3.5.2. File Classes¶
3.5.2.1. mzML¶
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class
pymzml.file_classes.standardMzml.
StandardMzml
(path, encoding, build_index_from_scratch=False)[source]¶ -
__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)
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__init__
(path, encoding, build_index_from_scratch=False)[source]¶ Initalize Wrapper object for standard mzML files.
Parameters: - path (str) – path to the file
- encoding (str) – encoding of the file
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_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.
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_build_index_from_scratch
(seeker)[source]¶ Build an index of spectra/chromatogram data with offsets by parsing the file.
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_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
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3.5.2.2. Gzip¶
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class
pymzml.file_classes.standardGzip.
StandardGzip
(path, encoding)[source]¶ -
__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)
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3.5.2.3. iGzip¶
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class
pymzml.file_classes.indexedGzip.
IndexedGzip
(path, encoding)[source]¶ -
__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)
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