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warnings.warn(warntext)
else:
for identifier in self.container[specfile]:
si = msrunContainer.sic[specfile][identifier]
for sii in self.container[specfile][identifier]:
for attribute in attributes:
setattr(sii, attribute,
getattr(si, attribute, None)
)"
1957,"def calcMz(self, specfiles=None, guessCharge=True, obsMzKey='obsMz'):
""""""Calculate the exact mass for ``Sii`` elements from the
``Sii.peptide`` sequence.
:param specfiles: the name of an ms-run file or a list of names. If None
all specfiles are selected.
:param guessCharge: bool, True if the charge should be guessed if the
attribute ``charge`` is missing from ``Sii``. Uses the calculated
peptide mass and the observed m/z value to calculate the charge.
:param obsMzKey: attribute name of the observed m/z value in ``Sii``.
""""""
#TODO: important to test function, since changes were made
_calcMass = maspy.peptidemethods.calcPeptideMass
_calcMzFromMass = maspy.peptidemethods.calcMzFromMass
_massProton = maspy.constants.atomicMassProton
_guessCharge = lambda mass, mz: round(mass / (mz - _massProton), 0)
if specfiles is None:
specfiles = [_ for _ in viewkeys(self.info)]
else:
specfiles = aux.toList(specfiles)
tempMasses = dict()
for specfile in specfiles:
if specfile not in self.info:
warntext = 'Error while calling ""SiiContainer.calcMz()"": '\
'""%s"" is not present in ""SiiContainer.info""!'\
% (specfile, )
warnings.warn(warntext)
else:
for sii in self.getItems(specfiles=specfile):
peptide = sii.peptide
if peptide not in tempMasses:
if hasattr(sii, 'diPeptide'):
tempMasses[peptide] = (_calcMass(sii.peptide1) +
_calcMass(sii.peptide2)
)
else:
tempMasses[peptide] = _calcMass(peptide)
peptideMass = tempMasses[peptide]
if sii.charge is not None:
sii.excMz = _calcMzFromMass(peptideMass, sii.charge)
elif guessCharge:
guessedCharge = _guessCharge(peptideMass,
getattr(sii, obsMzKey)
)
sii.excMz = _calcMzFromMass(peptideMass, guessedCharge)
sii.charge = guessedCharge
else:
sii.excMz = None
del(tempMasses)"
1958,"def getArrays(self, attr=None, specfiles=None, sort=False, reverse=False,
selector=None, defaultValue=None):
""""""Return a condensed array of data selected from :class:`Fi` instances
from ``self.container`` for fast and convenient data processing.
:param attr: list of :class:`Fi` item attributes that should be added
to the returned array. The attributes ""id"" and ""specfile"" are always
included, in combination they serve as a unique id.
:param defaultValue: if an item is missing an attribute, the
""defaultValue"" is added to the array instead.
:param specfiles: filenames of ms-run files - if specified return only
items from those files
:type specfiles: str or [str, str, ...]
:param sort: if ""sort"" is specified the returned list of items is sorted
according to the :class:`Fi` attribute specified by ""sort"", if the
attribute is not present the item is skipped.
:param reverse: bool, set True to reverse sort order
:param selector: a function which is called with each `Fi` item and has
to return True (include item) or False (discard item).
Default function is: ``lambda si: True``. By default only items with
``Fi.isValid == True`` are returned.
:returns: {'attribute1': numpy.array(),
'attribute2': numpy.array(),
...
}
""""""
selector = (lambda fi: fi.isValid) if selector is None else selector
attr = attr if attr is not None else []
attr = set(['id', 'specfile'] + aux.toList(attr))
items = self.getItems(specfiles, sort, reverse, selector)
return _getArrays(items, attr, defaultValue)"
1959,"def getItems(self, specfiles=None, sort=False, reverse=False,
selector=None):
""""""Generator that yields filtered and/or sorted :class:`Fi` instances
from ``self.container``.
:param specfiles: filenames of ms-run files - if specified return only
items from those files
:type specfiles: str or [str, str, ...]