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.. _example_scripts:
Example Scripts
================
Parsing a mzML file (new syntax)
--------------------------------
.. autofunction:: simple_parser.main
.. include:: code_inc/simple_parser.inc
Parsing a mzML file (old syntax)
--------------------------------
.. autofunction:: simple_parser_v2.main
.. include:: code_inc/simple_parser_v2.inc
Query the obo files
-------------------
.. autofunction:: queryOBO.main
.. include:: code_inc/queryOBO.inc
Plotting a chromatogram
-----------------------
.. autofunction:: plot_chromatogram.main
.. include:: code_inc/plot_chromatogram.inc
Plotting a spectrum
-------------------
.. autofunction:: plot_spectrum.main
.. include:: code_inc/plot_spectrum.inc
Plotting a spectrum with annotation
-----------------------------------
.. autofunction:: plot_spectrum_with_annotation.main
.. include:: code_inc/plot_spectrum_with_annotation.inc
Extracting highest peaks
------------------------
.. autofunction:: highest_peaks.main
.. include:: code_inc/highest_peaks.inc
Compare spectra
---------------
.. autofunction:: compare_spectra.main
.. include:: code_inc/compare_spectra.inc
Find m/z values
---------------
.. autofunction:: has_peak.main
.. include:: code_inc/has_peak.inc
Extract ion chromatogram
------------------------
.. autofunction:: extract_ion_chromatogram.main
.. include:: code_inc/extract_ion_chromatogram.inc
Find abundant precursors
------------------------
.. autofunction:: get_precursors.main
.. include:: code_inc/get_precursors.inc
Access polarity of spectra
--------------------------
.. autofunction:: polarity.main
.. include:: code_inc/polarity.inc
Check old to new function name mapping
--------------------------------------
.. autofunction:: deprecation_check.main
.. include:: code_inc/deprecation_check.inc
Convert mzML(.gz) to mzML.gz (igzip)
------------------------------------
.. autofunction:: gzip_mzml.main
.. include:: code_inc/gzip_mzml.inc
Multi threading conversion of mzML(.gz) to mzML.gz (igzip)
----------------------------------------------------------
.. autofunction:: multi_threading_file_compression.main
.. include:: code_inc/multi_threading_file_compression.inc
Acces run infos
---------------
.. autofunction:: access_run_info.main
.. include:: code_inc/access_run_info.inc
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 Conncetor,
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
|
