MGT::ImmApp::ImmApp Class Reference

Inheritance diagram for MGT::ImmApp::ImmApp:

List of all members.

Public Member Functions
def	parseCmdLinePost
def	initWork
def	doWork
def	trainOne
def	trainMany
def	scoreBatch
def	scoreMany
def	combineScores
Static Public Attributes
tuple	batchDepModes = ("score","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 collections of IMMs/ICMs and scoring against them

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Member Function Documentation

def MGT::ImmApp::ImmApp::combineScores	(		self,
			kw
	)

Combine scores as a final stage of scoreMany().
Parameters are taken from self.opt
@param immIds List of IMM IDs to score with
@param inpSeq Name of the input multi-FASTA file that was scored (to pull seq lengths here)
@param outDir Directory name for output score files
@param outScoreComb name for output file with combined scores

def MGT::ImmApp::ImmApp::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::ImmApp::ImmApp::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::ImmApp::ImmApp::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::ImmApp::ImmApp::scoreBatch	(		self,
			kw
	)

Score with a batch of several IMM.
Parameters are taken from self.opt
@param immIds Score with these IMMs (in memory list)
@param inpSeq Name of the input multi-FASTA file to score
@param outDir Directory name for output score files

def MGT::ImmApp::ImmApp::scoreMany	(		self,
			kw
	)

Score with many IMMs.
Parameters are taken from self.opt
@param immIds List of IMM IDs to score with
@param inpSeq Name of the input multi-FASTA file to score
@param nImmBatches Number of IMM batches (determines number of batch jobs)
@param outDir Directory name for output score files
@param outScoreComb name for output file with combined scores

def MGT::ImmApp::ImmApp::trainMany	(		self,
			kw
	)

Train many IMMs.
Parameters are taken from self.opt
@param immIdToSeqIds File name that contains a dict (immId->immSeqIds)

def MGT::ImmApp::ImmApp::trainOne	(		self,
			kw
	)

Train and save one IMM.
Parameters are taken from self.opt
@param immId Assign this ID to the IMM
@param immSeqIds List of sequence ids from seqDb

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Member Data Documentation

tuple MGT::ImmApp::ImmApp::batchDepModes = ("score","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/ImmApp.py