gathercaiwegene.cpp File Reference

#include <iostream>
#include <fstream>
#include <mysql++.h>
#include <dbinfo.h>
#include "SimpleRNAModel.h"
#include <hatrees.h>

Functions
int	groupModel (set< mRNAModelCaiwe *, lessByChainDirectionPtr > &model, ostream &ous, ostream &gous, ostream &oslog, int &chimeraCount)
int	clustergene (list< mRNAModelCaiwe * > &mod, ostream &ous, ostream &gous, ostream &oslog)
void	releaseMemory (list< mRNAModelCaiwe * > &mod)
void	updateInputTable (Connection &conn, const string &m2gtab, const string &modtab, const string &caiwetrack)
void	createGeneTable (const string &tabname, const string &modtab, const string &shortgtab, Connection &conn)
void	file2table (Connection &conn, const string &file, const string &table)
void	createTables (Connection &conn, const string &m2gtab, const string &gtab)
string	getlinktab (Connection &conn)
void	usage ()
int	main (int argc, char *argv[])
bool	isChimera (const mRNAModelCaiwe *m1, const mRNAModelCaiwe *m2, int olp)
void	writeModGeneRow (ostream &ous, ostream &gous, const mRNAModelCaiwe *mod)

---

Function Documentation

int clustergene	(	list< mRNAModelCaiwe * > &	mod,
		ostream &	ous,
		ostream &	gous,
		ostream &	oslog
	)

Returns:

number of chimeras identified will write result to ous

Parameters:

	mod	input models
	ous	result of model cluster. Two columns: modelid, repmodelid (also serve as geneid). This way we saved one column. The gene table, gene id is the same as the representative model id.
	gous	put gene info: gid, numod, begin, end, maxintron gid is the same as repmodel id.

poiter version

References Range::begin(), mRNAModelLight::CDSLength(), hatrees< T >::clusterArray(), Range::combine(), del(), mRNAModelCaiwe::getGenomicId(), mRNAModelLight::getId(), hatrees< T >::getNodeCount(), isChimera(), hatrees< T >::keyset(), Noschain::maxIntronLength(), Noschain::outerRange(), Range::output(), and writeModGeneRow().

Referenced by groupModel().

void createGeneTable	(	const string &	tabname,
		const string &	modtab,
		const string &	shortgtab,
		Connection &	conn
	)

Create a full-featured gene table from the model table Thi is just the simple stats summarized into one talbe. It is for convinience, but violates the database design principle. tabname gene table to be made

Parameters:

modtab

caiwe_model short gene table or minimal gene table.

Referenced by combestInput().

void createTables	(	Connection &	conn,
		const string &	m2gtab,
		const string &	gtab
	)

create two tables: 1. model to gene (modid -> geneid) 2. gene table

Referenced by main().

void file2table	(	Connection &	conn,
		const string &	file,
		const string &	table
	)

Referenced by loadPrimaryTables(), and main().

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.

References string().

Referenced by constructJGIModel(), and updateInputTable().

int groupModel	(	set< mRNAModelCaiwe *, lessByChainDirectionPtr > &	model,
		ostream &	ous,
		ostream &	gous,
		ostream &	oslog,
		int &	chimeraCount
	)

it will write result to ous model from one chromosome or genomic DNA gene table

References clustergene(), Range::length(), Range::merge(), min, Range::overlap(), and releaseMemory().

Referenced by combestInput(), jgiInput(), and main().

bool isChimera	(	const mRNAModelCaiwe *	m1,
		const mRNAModelCaiwe *	m2,
		int	olp
	)

the first one is more likely to be chimea

References Range::contain(), Noschain::intronLength(), Range::length(), mRNAModelCaiwe::lessESTFactor(), Noschain::maxIntronLength(), and Noschain::numberOfRanges().

Referenced by clustergene().

int main	(	int	argc,
		char *	argv[]
	)

References createTables(), file2table(), MysqlDBInfo::getAuthenInfo(), MysqlDBInfo::getPassword(), MysqlDBInfo::getUser(), groupModel(), string(), updateInputTable(), and usage.

void releaseMemory

(

list< mRNAModelCaiwe * > &

mod

)

void updateInputTable	(	Connection &	conn,
		const string &	m2gtab,
		const string &	modtab,
		const string &	caiwetrack
	)

update input table with gene table stored in files Firt load the gene table file into gene table; this gene table has only two columns modelid => geneid. We call it minimal table. This table is not very useful, so we are going to make a full-featured gene table later. Then use the table in database to update the geneid columns of the model table. This method will remove chimera models based on modelid given in file

Parameters:

	m2gtab	minimal gene table
	modtab	model table, default caiwe_model
	caiwetrack	JGI track table name

References getlinktab().

Referenced by combestInput(), and main().

void usage

(

)

given gmap summary format, this program converts it into combest archive format (*.car)

It can be used a pipe, or given specific file names.

this is a helper program to count distinct estids in the ESTId column of the combest result. So it is the actual number of ESTs mapped. This could be lower for deeply covered genome because of the coverage depth-dependent filtering.

given gmap summary format, this program converts it into combest archive format (*.car)

It can be used a pipe, or given specific file names.

this is a helper program to count distinct estids in the ESTId column of the combest result. So it is the actual number of ESTs mapped. This could be lower for deeply covered genome because of the coverage depth-dependent filtering.

void writeModGeneRow	(	ostream &	ous,
		ostream &	gous,
		const mRNAModelCaiwe *	mod
	)

helper function geneid, genomicid, begin, end, numod, maxintronlen This is one row in the gene table

Parameters:

mod

is the input model object

References mRNAModelCaiwe::getGenomicId(), mRNAModelLight::getId(), Noschain::maxIntronLength(), Noschain::outerRange(), and Range::output().

Referenced by clustergene().