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.. obo:
.. default-domain:: py
################
OBO parser Class
################
.. automodule:: obo
******************************
Accessing specific OBO MS tags
******************************
This section describes how to access some common MS tags by their names as they
are defined in the OBO file.
First pymzML is imported and the run is defined.
>>> example_file = get_example_file.open_example('dta_example.mzML')
>>> import pymzml
>>> msrun = pymzml.run.Reader(example_file)
Now, we can fetch specific imformations from the spectrum object.
MS level:
>>> for spectrum in msrun:
... print(spectrum['ms level'])
Total Ion current:
>>> for spectrum in msrun:
... print(spectrum['total ion current'])
Furthermore we can also check for presence of parameters, therefore the
proprties of the spectrum.
Differentiation of e.g. HCD and CID fractionation:
>>> for spectrum in msrun:
... if spctrum['ms level'] == 2:
... if 'collision-induced dissociation' in spectrum.keys():
... print('Spectrum {0} is a CID spectrum'.format(spectrum['id']))
... elif 'high-energy collision-induced dissociation' in spectrum.keys():
... print('Spectrum {0} is a HCD spectrum'.format(spectrum['id']))
*********************
Minimal accession set
*********************
The following dictionary shows the minimal accession necessary to run pymzML.
::
MIN_REQ = [
#
#!NOTE! exact names will be extracted of current OBO File, comments are just an orientation
# pymzml comes with a little script (queryOBO.py) to query the obo file
#
# $ ./example_scripts/queryOBO.py "scan time"
# MS:1000016
# scan time
# "The time taken for an acquisition by scanning analyzers." [PSI:MS]
# Is a: MS:1000503 ! scan attribute
#
('MS:1000016',['value'] ), #"scan time"
# -> Could also be ['value','unitName'] to retrieve a
# tuple of time and unit by calling spectrum['scan time']
('MS:1000040',['value'] ), #"m/z"
('MS:1000041',['value'] ), #"charge state"
('MS:1000127',['name'] ), #"centroid spectrum"
('MS:1000128',['name'] ), #"profile spectrum"
('MS:1000133',['name'] ), #"collision-induced dissociation"
('MS:1000285',['value'] ), #"total ion current"
('MS:1000422',['name'] ), #"high-energy collision-induced dissociation"
('MS:1000511',['value'] ), #"ms level"
('MS:1000512',['value'] ), #"filter string"
('MS:1000514',['name'] ), #"m/z array"
('MS:1000515',['name'] ), #"intensity array"
('MS:1000521',['name'] ), #"32-bit float"
('MS:1000523',['name'] ), #"64-bit float"
('MS:1000744',['value'] ), # legacy precursor mz value ...
]
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