MGT::ImmClassifierApp::ImmClassifierApp Class Reference

Inheritance diagram for MGT::ImmClassifierApp::ImmClassifierApp:

List of all members.

Public Member Functions
def	makeOptionParserArgs
def	parseCmdLinePost
def	initWork
def	doWork
def	mapSeqToTree
def	pickSeqOnTree
def	train
def	predict
def	reduceScores
Static Public Attributes
tuple	batchDepModes = ("predict","train")
	Derived classes should set this to a list of opt.mode values that can result in submision of new batch jobs.

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Detailed Description

App-derived class for building and using IMM-based taxonomic classifier in the spirit of Phymm.
The main difference with Phymm is that we build IMMs for higher-level clades by pulling sequence
data for subnodes.
This class can be mostly viewed as imposing a TaxaTree structure onto ImmApp.

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Member Function Documentation

def MGT::ImmClassifierApp::ImmClassifierApp::doWork	(		self,
			kw
	)

Do the actual work.
Must be redefined in the derived classes.
Should not be called directly by the user except from doWork() in a derived class.
Should work with empty keyword dict, using only self.opt.
If doing batch submision of other App instances, must return a list of sink (final) BatchJob objects.

Reimplemented from MGT::App::App.

def MGT::ImmClassifierApp::ImmClassifierApp::initWork	(		self,
			kw
	)

Perform common initialization right before doing the actual work in doWork().
Must be redefined in the derived classes.
Should not be called directly by the user except from initWork() in a derived class.
This one can create large objects because they are not passed through the batch submission,
but immediately used within the same process.

Reimplemented from MGT::App::App.

def MGT::ImmClassifierApp::ImmClassifierApp::makeOptionParserArgs

(

klass )

Return a Struct with optparse.OptionParser constructor arguments specific to the application.
The "option_list" attribute must be obtained with a sequence of calls to optparse.make_option.
Other possible attributes can be e.g. "usage".
This method will be called by parseCmdLine() and the returned "option_list" concatenated with the default
one provided by the parseCmdLine().
Must be redefined in the derived class only if there are any application specific command-line options.

Reimplemented from MGT::App::App.

def MGT::ImmClassifierApp::ImmClassifierApp::mapSeqToTree

(

self )

Assign list of SeqDB IDs to corresponding taxonomy tree nodes.
In the current SeqDB version, each ID is a unique taxonomy id, so
a one-element list will be assigned.
@post Attribute 'leafSeqDbIds' is assigned to EVERY node and contains a list of IDs, possibly empty.
The empty list will be a reference to a single shared object, so it should be treated as immutable

def MGT::ImmClassifierApp::ImmClassifierApp::parseCmdLinePost	(		klass,
			options,
			args,
			parser
	)

Optionally modify options and args in-place.
Called at the end of parseCmdLine to allow the derived classes customizing the option processing.
@param options options returned by OptionParser and converted to Struct object
@param args args returned by OptionParser
@param parser OptionParser object used to parse the command line - needed here to call its error() method
if necessary.
options should be modified in place by this method

Reimplemented from MGT::App::App.

def MGT::ImmClassifierApp::ImmClassifierApp::pickSeqOnTree	(		self,
			maxSeqIdCnt
	)

Assign to each node of the taxonomy tree the list of SeqDB IDs in the subtree under that node.
It picks a medium count of IDs from each child node and itself, clipped by maxSeqIdCnt.

def MGT::ImmClassifierApp::ImmClassifierApp::predict	(		self,
			kw
	)

Score with all IMMs and predict the taxonomy.
Parameters are taken from self.opt
@param inpSeq Name of the input multi-FASTA file to score
@param outDir Directory name for output score files
@param outScoreComb name for output file with combined scores

def MGT::ImmClassifierApp::ImmClassifierApp::reduceScores	(		self,
			kw
	)

Reduce a matrix of combined scores to best positions on the taxonomic tree.
Parameters are taken from self.opt
@param outScoreComb name for file with combined scores
@param outTaxaPred name for output file with predicted taxonomy

def MGT::ImmClassifierApp::ImmClassifierApp::train	(		self,
			kw
	)

Train all IMMs.
Parameters are taken from self.opt

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Member Data Documentation

tuple MGT::ImmClassifierApp::ImmClassifierApp::batchDepModes = ("predict","train") [static]

Derived classes should set this to a list of opt.mode values that can result in submision of new batch jobs.

Reimplemented from MGT::App::App.

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The documentation for this class was generated from the following file:

• mgtaxa/MGT/ImmClassifierApp.py