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.. pymzml_utils:
Utils
=====
.. General
.. ----------
.. These are the different APIS for supported file formats
.. Currently: mzML, mzML.gz, mzML.igzip
GSGW
----
.. autoclass:: pymzml.utils.GSGW.GSGW
:members:
:private-members:
:exclude-members: __del__, __enter__, __exit__, close
GSGR
----
.. autoclass:: pymzml.utils.GSGR.GSGR
:members:
:private-members:
:exclude-members: __enter__, __exit__, _read_until_zero, close
.. Creating a custom Filehandler
.. ------------------------------
.. Introduction
.. +++++++++++++
.. It is also possible to create an own API for different forms
.. of mzML files. For this, a new class needs to be written, which
.. implements a `read` and a `__getitem__` function.
.. Implementation of the API Class
.. ++++++++++++++++++++++++++++++++
Example::
.. class SQLiteDatabase(object):
.. """
.. Example implementation of a database Connector,
.. which can be used to make run accept paths to
.. sqlite db files.
.. We initialize with a path to a database and implement
.. a custom __getitem__ function to retrieve the spectra
.. """
.. def __init__(self, path):
.. """
.. """
.. connection = sqlite3.connect(path)
.. self.cursor = connection.cursor()
.. def __getitem__(self, key):
.. """
.. Execute a SQL request, process the data and return a spectrum object.
.. Args:
.. key (str or int): unique identifier for the given spectrum in the
.. database
.. """
.. self.cursor.execute('SELECT * FROM spectra WHERE id=?', key)
.. ID, element = self.cursor.fetchone()
.. element = et.XML(element)
.. if 'spectrum' in element.tag:
.. spectrum = spec.Spectrum(element)
.. elif 'chromatogram' in element.tag:
.. spectrum = spec.Chromatogram(element)
.. return spectrum
.. def get_spectrum_count(self):
.. self.cursor.execute("SELECT COUNT(*) from spectra")
.. num = self.cursor.fetchone()[0]
.. return num
.. def read(self, size=-1):
.. # implement read so it starts reading in first ID,
.. # if end reached switches to next id and so on ...
.. return '<spectrum index="0" id="controllerType=0 controllerNumber=1 scan=1" defaultArrayLength="917"></spectrum>\n'
.. Enabling the new API Class in File Interface
.. +++++++++++++++++++++++++++++++++++++++++++++
.. In order to make the run class accept the new file class, one need to edit
.. the :py:func:`_open` function in file_interface.py
Example::
.. def _open(self, path):
.. if path.endswith('.gz'):
.. if self._indexed_gzip(path):
.. self.file_handler = indexedGzip.IndexedGzip(path, self.encoding)
.. else:
.. self.file_handler = standardGzip.StandardGzip(path, self.encoding)
.. # Insert a new condition to enable your new fileclass
.. elif path.endswith('.db'):
.. self.file_handler = utils.SQLiteConnector.SQLiteDatabase(path, self.encoding)
.. else:
.. self.file_handler = standardMzml.StandardMzml(path, self.encoding)
.. return self.file_handler
.. Moby Dick as indexed Gzip
.. ---------------------------
.. Example of how to use the GSGW and GSGR class to create and access indexed Gzip files
.. .. code-block:: bash
.. python3 index_moby_dick.py
.. python3 read_moby_dick.py 10
.. Scripts
.. --------
.. pymzML ships with some usefull scripts, which are described in the following
.. Create indexed gziped conveniently
.. +++++++++++++++++++++++++++++++++++
.. blub
.. Find optimal read size
.. +++++++++++++++++++++++
.. Hard drives have different sector sizes, ....
.. utils -- A collection of useful functions
.. ++++++++++++++++++++++++++++++++++++++++++
.. blub
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