nrep.cpp File Reference

#include "GenModel.h"
#include "TranscriptExon.h"
#include <mysql++.h>
#include <dbinfo.h>
#include <fstream>
#include <map>
#include <set>
#include "hatrees.h"
#include "ModelFactory.h"
#include "strformat.h"
#include <cstdio>


Classes
class	Progparam
Functions
vector< GenModel * >	removePregnantModels (vector< GenModel * > &mds, ostream &ous, vector< GenModel * > &preg)
vector< GenModel * >	removeChimeraModels (vector< GenModel * > &mds, ostream &ous, vector< GenModel * > &chim, const Progparam &par)
vector< GenModel * >	removeLowCDSModels (vector< GenModel * > &mds, ostream &ous, vector< GenModel * > &lwcds)
vector< GenModel * >	pickGoodModel (vector< GenModel * > &mds, ostream &ouslog, vector< GenModel * > &bad, const Progparam &par)
vector< GenModel * >	removeIdentical (const vector< GenModel * > &mds)
void	showRow (const Row &row, ostream &ous)
vector< GenModel * >	buildGeneCluster (const vector< GenModel * > &mds, map< int, int > &memrep, ostream &logos)
void	checkUTRChimera (const GenModel i, const GenModel j, RangeChain &uc)
void	memoryRelease (vector< GenModel * > &m)
void	writeModel (vector< GenModel * > &srcmod, ostream &model, ostream &exon)
void	storeModel (const vector< GenModel * > &mod, Query &mq, const string &modtab, const string &extab)
void	createModelTable (Query &q, const string &tab)
void	createGenericTable (Query &q, const string &tab)
void	createExonTable (Query &q, const string &tab)
void	constructJGIModel (const string &jmod, const string &mod, const string &ex, Connection &conn, const string &label, const string &allmod, int version, map< string, string > &trackfeat)
void	storeModelCluster (const string &modcltab, Connection &conn, const map< int, int > &modcl, const string &modtab)
void	colorRepModels (Connection &conn, const string &mod, const string &gen)
void	constructJGIGene (Connection &conn, const string &tab, const string &jgimodel, const string &modcltab, int version)
void	checkAndBuildInput (const Progparam &par, Connection &conn)
void	writeResultToFile (Progparam &par, ModelFactory &modfac, ostream &ouslog)
void	writeResultToDatabase (Progparam &par, ModelFactory &modfac, Connection &conn2, ostream &OU)
void	createModelClusterTable (Connection &conn, const string &tabname)
void	createModelAndExonTables (Connection &conn, Progparam &par)
void	constructDerivedTables (Connection &conn, Progparam &par)
void	loadPrimaryTables (Connection &conn, const Progparam &par)
void	file2table (const string &file, const string &table, const Progparam &par)
void	addSingletonGene (Connection &conn, const Progparam &par)
void	removeDoneFile ()
void	usage (const Progparam &par)
string	getlinktab (Connection &conn)
int	main (int argc, char *argv[])
Variables
const int	chimera_intron_len = 500
const int	minutr_len = 120
const int	min_CDS_len = 1200
const int	commonex_len = 170
int	exonid = 1

Function Documentation

void addSingletonGene	(	Connection &	conn,
		const Progparam &	par
	)

References Progparam::getGoodModelTable(), and Progparam::getModelClusterTable().

Referenced by main().

vector< GenModel * > buildGeneCluster	(	const vector< GenModel * > &	mds,
		map< int, int > &	memrep,
		ostream &	logos
	)

member => rep with the longest CDS if CDS are identical, then use the longest exon length

Only genes with more than one models are outputed. The rest are single exon genes. The user need to figure it out with set operations.

Parameters:

	mds	input vector of model pointers
	memrep	output. map of member -> rep. Rep has the longest CDS.

Returns:: vector of pointer to good gene models. Models that are missing are those that are contained in good models.

1. Discard contained models 2. Build overlap relationship 3. Cluster into member => rep relationship 4. Picke the longest models, longest CDS as rep. So rep should have most of the information.

Parameters:

memrep

is the output or result of this funciton. It contains member => rep relationship.

References Noschain::exonLength(), hatrees< T >::getCluster(), good, Noschain::numberOfRanges(), and hatrees< T >::readFromMap().

Referenced by writeResultToDatabase(), and writeResultToFile().

void checkAndBuildInput	(	const Progparam &	par,
		Connection &	conn
	)

ideally, the input table should be made before hand If not available, it will generate a table from all existing tracks.

References Progparam::database, Progparam::getAllmodelTable(), and Progparam::host.

Referenced by main().

void checkUTRChimera	(	const GenModel *	i,
		const GenModel *	j,
		RangeChain &	uc
	)

References RangeChain::add(), chimera_intron_len, Range::contain(), Range::copyShrinkBothEnds(), Noschain::exonLength(), GenModel::FivePrimeUTR(), Noschain::intronsInside(), length, Range::length(), max, Noschain::maxIntron(), minutr_len, Noschain::numberOfRanges(), Range::overlay(), and GenModel::ThreePrimeUTR().

Referenced by removeChimeraModels().

void colorRepModels	(	Connection &	conn,
		const string &	mod,
		const string &	gen
	)

Referenced by constructDerivedTables().

void constructDerivedTables	(	Connection &	conn,
		Progparam &	par
	)

use primary tables produced by filtering to build JGI tracks: Good Model, Bad Model, and Gene for Good Model

References Progparam::buildgene, colorRepModels(), constructJGIGene(), constructJGIModel(), Progparam::getAllmodelTable(), Progparam::getBadExonTable(), Progparam::getBadModelTable(), Progparam::getGoodExonTable(), Progparam::getGoodModelTable(), Progparam::getJGIBadModelTable(), Progparam::getJGIGoodModelTable(), Progparam::getModelClusterTable(), and Progparam::version.

Referenced by main().

void constructJGIGene	(	Connection &	conn,
		const string &	tab,
		const string &	jgimodel,
		const string &	modcltab,
		int	version
	)

References createGenericTable().

Referenced by constructDerivedTables().

void constructJGIModel	(	const string &	jmod,
		const string &	mod,
		const string &	ex,
		Connection &	conn,
		const string &	label,
		const string &	allmod,
		int	version,
		map< string, string > &	trackfeat
	)

Right now label is good or bad

References getlinktab(), and itos().

Referenced by constructDerivedTables().

void createExonTable	(	Query &	q,
		const string &	tab
	)

Referenced by createModelAndExonTables().

void createGenericTable	(	Query &	q,
		const string &	tab
	)

Referenced by constructJGIGene().

void createModelAndExonTables	(	Connection &	conn,
		Progparam &	par
	)

References createExonTable(), createModelTable(), Progparam::getBadExonTable(), Progparam::getBadModelTable(), Progparam::getGoodExonTable(), and Progparam::getGoodModelTable().

Referenced by main().

void createModelClusterTable	(	Connection &	conn,
		const string &	tabname
	)

modelid => geneid create a table of two columns, the first one is a primary key

Referenced by loadPrimaryTables(), and storeModelCluster().

void createModelTable	(	Query &	q,
		const string &	tab
	)

create an empty table tab with the following schema:

id serial primary key, genomic varchar(48), name varchar(200), exons text, mb integer, me integer, -- model boundary cdsb integer, cdse integer, -- CDS boundary cdsphase integer -- 0,1,2 hasstart boolean hasstrop boolean

Referenced by createModelAndExonTables().

void file2table	(	const string &	file,
		const string &	table,
		const Progparam &	par
	)

References Progparam::database, and Progparam::host.

string getlinktab ( Connection & conn )

this is also defined in gathercaiwegene, in the future this function should be put into a mysql helper header Now using copy and pasting.

void loadPrimaryTables	(	Connection &	conn,
		const Progparam &	par
	)

void memoryRelease ( vector< GenModel * > & m )

Referenced by writeResultToDatabase(), and writeResultToFile().

vector< GenModel * > pickGoodModel	(	vector< GenModel * > &	mds,
		ostream &	ouslog,
		vector< GenModel * > &	bad,
		const Progparam &	par
	)

return a vector of pointers of good models But some model may be contained in other models.

Parameters:

	mds	vector of input model pointers
	bad	vector for containing the bad models This function simply append to the end of this container without any clearing action. output for detailed information why model bad This is mainly for debuggin purposes.

Given a set of overlapping models, this method tries to separate the set into good + bad models.

References commonex_len, Noschain::exonLength(), good, length, Progparam::maxintronlen, min_CDS_len, Noschain::numberOfRanges(), removeChimeraModels(), removeLowCDSModels(), and removePregnantModels().

Referenced by writeResultToDatabase(), and writeResultToFile().

vector< GenModel * > removeChimeraModels	(	vector< GenModel * > &	mds,
		ostream &	ous,
		vector< GenModel * > &	chim,
		const Progparam &	par
	)

Parameters:

	ous	debug output stream
	chim	candidate chimera

References checkUTRChimera(), Progparam::chimera_contained_cdslen, commonex_len, Noschain::exonLength(), good, Progparam::maxintronlen, min_CDS_len, and Noschain::numberOfRanges().

Referenced by pickGoodModel().

void removeDoneFile ( )

Referenced by main().

vector< GenModel * > removeIdentical ( const vector< GenModel * > & mds )

References good.

Referenced by writeResultToDatabase(), and writeResultToFile().

vector< GenModel * > removeLowCDSModels	(	vector< GenModel * > &	mds,
		ostream &	ous,
		vector< GenModel * > &	lwcds
	)

also remove models with too many non-coding exons

References good.

Referenced by pickGoodModel().

vector< GenModel * > removePregnantModels	(	vector< GenModel * > &	mds,
		ostream &	ous,
		vector< GenModel * > &	preg
	)

always return a valid model pointer, unless it run out of input from res

Returns:: a vector of pointers of good models

Parameters:

mds

input models as a vector of pointers details for logged information, for debug stage usage The output vector of pointer of pregnant models. this function will simply append to it.

Pregnant models are models whose introns contain one or more other models. Technically, we used the largest intron of the model to do this test. We also used 2 or more other models are the cutoff. We are alowing models pregnant with one models because this is could be valid situation in biology.

References Range::contain(), good, and Range::length().

Referenced by pickGoodModel().

void showRow	(	const Row &	row,
		ostream &	ous
	)

void storeModel	(	const vector< GenModel * > &	mod,
		Query &	mq,
		const string &	modtab,
		const string &	extab
	)

This is equivalent to writeModel(), directly store information into database table. This method is 100x slower than writeModel().

Parameters:

	mod	input gene model as vector of pointers
	mq	query object used to insert result
	modtab	model table name
	extab	exon table name

Columns of the table (id,genomic,name, exons, mb, me, cdsb, cdse, cdsphase, hasstart, hasstop, pep)

Referenced by writeResultToDatabase().

void storeModelCluster	(	const string &	modcltab,
		Connection &	conn,
		const map< int, int > &	modcl,
		const string &	modtab
	)

Parameters:

	modcl	is the input of member -> rep table.
	modcltab	is the output table name.
	modtab	was used to generate singleton clusters by set difference operation: modtab - modcltab (clusters with more than one member)

The model cluster implements the gene concept.

Parameters:

	modcltab	model cluster table with genes > 1 members no single ton. This is the database table name
	modcl	model cluster information, member => rep rep is one of the member's id
	modtab	model table name used to extract singleton genes by set operation. input: modcl, output modcltab

References createModelClusterTable().

Referenced by writeResultToDatabase().

void usage ( const Progparam & par )

void writeModel	(	vector< GenModel * > &	srcmod,
		ostream &	model,
		ostream &	exon
	)

this is much faster than the database interactive method storeModel()

Parameters:

	srcmod.	Input models as a vector of pointers to GenModel
	model.	The output stream for model with columns: (id,genomic,name, exons, mb, me, cdsb, cdse, cdsphase, hasstart, hasstop, pep) Should have the same column as the storeModel() method.
	exon.	Exon output stream.

References exonid.

Referenced by writeResultToFile().

void writeResultToDatabase	(	Progparam &	par,
		ModelFactory &	modfac,
		Connection &	conn2,
		ostream &	OU
	)

void writeResultToFile	(	Progparam &	par,
		ModelFactory &	modfac,
		ostream &	ouslog
	)

This is the main method through the file mechanism. It is much faster than the direct insert into database. The buffering of file system is a lot faster than the database system.

Parameters:

	ouslog	is the log file stream.
	modfac	is the model stream as input. This method first collect overlapping models (50nt or more) into a buffer. Then it calls pickGoodModels() to get good models.

In all the operations, file names are controlled by par.

References buildGeneCluster(), Range::combine(), GenModel::genomicId(), Progparam::getBadExonFile(), Progparam::getBadModelFile(), Progparam::getGoodExonFile(), Progparam::getGoodModelFile(), Progparam::getModelClusterFile(), Progparam::goodmod, memoryRelease(), GenModel::modelName(), ModelFactory::next(), Range::overlay(), pickGoodModel(), removeIdentical(), Progparam::showevery, and writeModel().

Referenced by main().

Variable Documentation

const int chimera_intron_len = 500

This is the cutoff value for checking that this intron is likely to bridge two models into on chimeric model

Referenced by checkUTRChimera().

const int commonex_len = 170

Referenced by pickGoodModel(), and removeChimeraModels().

int exonid = 1

Referenced by writeModel().

const int min_CDS_len = 1200

Referenced by pickGoodModel(), and removeChimeraModels().

const int minutr_len = 120

minimal UTR length. The UTR length that are more likely to be true. This is dependent on the organism. Some organisms have long UTRs than others. Small genomes tend to have short UTRs.

Referenced by checkUTRChimera().

nrep.cpp File Reference

Classes

Functions

Variables

Function Documentation

Variable Documentation