MGT::Proj::CrisprApp::CrisprApp Class Reference

Inheritance diagram for MGT::Proj::CrisprApp::CrisprApp:

List of all members.

Public Member Functions
def	parseCmdLinePost
def	getDbSql
def	delDbSql
def	initWork
def	doWork
def	findCr
def	loadCrispr
def	blastCr
def	blastCrOne
def	pilerCr
def	pilerCrOne
def	blastToCoverage
def	loadArrayBlastBin
def	parseArrayBlast
def	loadPilerArrSql
def	loadCrisprSqlArr
def	loadCrArrayRangesSql
def	loadCrArrayElemSql
Static Public Attributes
tuple	batchDepModes = ("blastcr","pilercr","findcr")
	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 base class for CRISPR array processing

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Member Function Documentation

def MGT::Proj::CrisprApp::CrisprApp::blastCr	(		self,
			kw
	)

BLAST CRISPR arrays against different DBs in parallel

def MGT::Proj::CrisprApp::CrisprApp::blastCrOne	(		self,
			kw
	)

One job launched by blastCr()

def MGT::Proj::CrisprApp::CrisprApp::blastToCoverage

(

self )

Calculate how much spacers vs repeats each BLAST match hits.
@return record array with (id_arr,id_hit,coverage_spacers,coverage_repeats)

def MGT::Proj::CrisprApp::CrisprApp::delDbSql

(

self )

Call this to free a connection to SQL server if it will not be needed for extended period of time

def MGT::Proj::CrisprApp::CrisprApp::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::Proj::CrisprApp::CrisprApp::findCr	(		self,
			kw
	)

Run full pipeline for CRISPR loci detection - from finder to SQL load and FASTA export

def MGT::Proj::CrisprApp::CrisprApp::getDbSql

(

self )

Allocate (if necessary) and return a connection to SQL server

def MGT::Proj::CrisprApp::CrisprApp::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::Proj::CrisprApp::CrisprApp::loadArrayBlastBin	(		self,
			inFile,
			minAlignLen = 20,
			minBitScore = 40,
			maxEvalue = 1000,
			maxMism = 1,
			out = None,
			debug = False
	)

Load into memory numpy record array previously created by parseArrayBlast().
The records will be filtered according to cutoff parameters.

def MGT::Proj::CrisprApp::CrisprApp::loadCrArrayElemSql	(		self,
			db
	)

Return numpy record array from SQL tables with every element of every CRISPR array.
id_seq is included, and records are sorted by (id_arr,begin).

def MGT::Proj::CrisprApp::CrisprApp::loadCrArrayRangesSql	(		self,
			db
	)

Return numpy record array from SQL tables with total coord range of every CRISPR array

def MGT::Proj::CrisprApp::CrisprApp::loadCrispr

(

self )

Import and filter original PILERCR output files and convert them into SQL tables

def MGT::Proj::CrisprApp::CrisprApp::loadCrisprSqlArr

(

self )

Load CRISPR from SQL tables into an array

def MGT::Proj::CrisprApp::CrisprApp::loadPilerArrSql	(		self,
			db,
			idGenArr,
			inserterArr,
			idGenArrElem,
			inserterArrElem,
			arr
	)

Load array dict prepared by importPiler() into SQL tables.

def MGT::Proj::CrisprApp::CrisprApp::parseArrayBlast	(		self,
			inFile,
			minAlignLen = 10,
			minBitScore = 10,
			maxEvalue = 100,
			maxMism = 100,
			out = None,
			debug = False
	)

Parse BLAST XML output and return as numpy record array.
The records will be filtered according to cutoff parameters.

def MGT::Proj::CrisprApp::CrisprApp::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::Proj::CrisprApp::CrisprApp::pilerCr	(		self,
			kw
	)

Find CRISPR arrays with PilerCr within several partitions of the input sequence in parallel

def MGT::Proj::CrisprApp::CrisprApp::pilerCrOne	(		self,
			kw
	)

One job launched by pilerCrOne()

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Member Data Documentation

tuple MGT::Proj::CrisprApp::CrisprApp::batchDepModes = ("blastcr","pilercr","findcr") [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/Proj/CrisprApp.py