def __init__(self, resultFilenames, database, sortFilenames=True):
if isinstance(resultFilenames, str):
resultFilenames = [resultFilenames]
if sortFilenames:
self.resultFilenames = numericallySortFilenames(resultFilenames)
else:
self.resultFilenames = resultFilenames
self._database = database
# Add a dictionary that will allow us to look up database subjects
# by title.
self._subjects = dict((subject.read.id, subject.read.sequence)
for subject in database.getSubjects())
# Prepare application parameters in order to initialize self.
self._reader = self._getReader(self.resultFilenames[0])
params = copy.deepcopy(self._reader.params)
applicationParams = ReadsAlignmentsParams('light',
applicationParams=params,
subjectIsNucleotides=False)
# We will add to self._reads as we go through the results (which
# contain the read ids and sequences). Note that this means the
# reads will not be available to the ReadsAlignments instance until
# after all results have been read.
self._reads = Reads()
ReadsAlignments.__init__(self, self._reads, applicationParams)
def __init__(self,
reads,
blastFilenames,
scoreClass=HigherIsBetterScore,
sortBlastFilenames=True,
randomizeZeroEValues=True):
if type(blastFilenames) == str:
blastFilenames = [blastFilenames]
if sortBlastFilenames:
self.blastFilenames = numericallySortFilenames(blastFilenames)
else:
self.blastFilenames = blastFilenames
self.randomizeZeroEValues = randomizeZeroEValues
# Prepare application parameters in order to initialize self.
self._reader = self._getReader(self.blastFilenames[0], scoreClass)
application = self._reader.application
blastParams = copy.deepcopy(self._reader.params)
subjectIsNucleotides = application != 'blastx'
scoreTitle = ('Bit score' if scoreClass is HigherIsBetterScore else
'$- log_{10}(e)$')
applicationParams = ReadsAlignmentsParams(
application,
blastParams,
subjectIsNucleotides=subjectIsNucleotides,
scoreTitle=scoreTitle)
ReadsAlignments.__init__(self,
reads,
applicationParams,
scoreClass=scoreClass)
def __init__(self, reads, filenames, databaseFilename=None,
databaseDirectory=None, sqliteDatabaseFilename=None,
scoreClass=HigherIsBetterScore, sortFilenames=False,
randomizeZeroEValues=True):
if type(filenames) == str:
filenames = [filenames]
if sortFilenames:
self.filenames = numericallySortFilenames(filenames)
else:
self.filenames = filenames
self._databaseFilename = databaseFilename
self._sqliteDatabaseFilename = sqliteDatabaseFilename
self._databaseDirectory = databaseDirectory
self._subjectTitleToSubject = None
self.randomizeZeroEValues = randomizeZeroEValues
# Prepare diamondTask parameters in order to initialize self.
self._reader = self._getReader(self.filenames[0], scoreClass)
diamondTask = self._reader.diamondTask
diamondParams = copy.deepcopy(self._reader.params)
scoreTitle = ('Bit score' if scoreClass is HigherIsBetterScore
else '$- log_{10}(e)$')
diamondTaskParams = ReadsAlignmentsParams(
diamondTask, diamondParams,
subjectIsNucleotides=False, # DIAMOND dbs are always protein.
scoreTitle=scoreTitle)
ReadsAlignments.__init__(self, reads, diamondTaskParams,
scoreClass=scoreClass)
def testExpectedAttrs(self):
"""
A ReadsAlignmentsParams instance must have the expected attributes.
"""
applicationParams = {}
params = ReadsAlignmentsParams('application name', applicationParams,
False, 'Bit score')
self.assertEqual('application name', params.application)
self.assertIs(applicationParams, params.applicationParams)
self.assertFalse(params.subjectIsNucleotides)
self.assertEqual('Bit score', params.scoreTitle)