dbaln.cpp File Reference

#include "mysql++.h"
#include <string>
#include "bioseq.h"
#include "dynaln.h"
#include <math.h>
#include <fstream>
#include "dbalnhelper.h"
#include "dbinfo.h"

Classes
class	Sourceprt
Defines
#define	MYSQLPLUS2
Functions
void	readConfig (const string &confile, Sourceprt &input)
void	getPrt (mysqlpp::Query &q, const string &id, string &prt)
void	alignProtein (const string &alnfile, const string &alntabfile, const string &pairtab, mysqlpp::Connection &conn, mysqlpp::Connection &conn1, mysqlpp::Connection &conn2)
void	alignProtein (const string &alnfile, const string &alntabfile, mysqlpp::Connection &conn, const string &pairtab, const string &column, const map< string, string > &pstore1, const map< string, string > &pstore2)
void	alignDNA (const string &alnfile, const string &alntabfile, const string &pairtab, mysqlpp::Connection &conn, mysqlpp::Connection &conn1, mysqlpp::Connection &conn2)
void	bufferGenomic (mysqlpp::Connection &conn, const string &sqlstr, map< string, DNA > &id2seq)
void	loadProtein (Connection &conn, const string &table, const string &column, map< string, string > &pstore)
bool	fileExists (const string &file)
void	usage ()
int	main (int argc, char *argv[])

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Define Documentation

#define MYSQLPLUS2

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Function Documentation

void alignDNA	(	const string &	alnfile,
		const string &	alntabfile,
		const string &	pairtab,
		mysqlpp::Connection &	conn,
		mysqlpp::Connection &	conn1,
		mysqlpp::Connection &	conn2
	)

References bufferGenomic(), LSDynaln::buildResult(), LSDynaln::global(), Dynaln::headers(), Dynaln::printAlign(), Dynaln::setGapExtend(), Dynaln::setGapInsert(), string(), and Dynaln::toDelimitedString().

Referenced by main().

void alignProtein	(	const string &	alnfile,
		const string &	alntabfile,
		mysqlpp::Connection &	conn,
		const string &	pairtab,
		const string &	column,
		const map< string, string > &	pstore1,
		const map< string, string > &	pstore2
	)

this is version using protein sequences that are stored in maps instead of fetching one by one that is too slow.

References Dynaln::headers(), Dynaln::printAlign(), Dynaln::runlocal(), string(), and Dynaln::toDelimitedString().

void alignProtein	(	const string &	alnfile,
		const string &	alntabfile,
		const string &	pairtab,
		mysqlpp::Connection &	conn,
		mysqlpp::Connection &	conn1,
		mysqlpp::Connection &	conn2
	)

References getPrt(), Dynaln::headers(), Dynaln::printAlign(), Dynaln::runlocal(), string(), and Dynaln::toDelimitedString().

Referenced by main().

void bufferGenomic	(	mysqlpp::Connection &	conn,
		const string &	sqlstr,
		map< string, DNA > &	id2seq
	)

References bioseq::length(), string(), DNA::subseq(), tableExists(), and bioseq::toLowerCase().

Referenced by alignDNA().

bool fileExists

(

const string &

file

)

References ifstream().

Referenced by main().

void getPrt	(	mysqlpp::Query &	q,
		const string &	id,
		string &	prt
	)

DESCRIPTION use three connections, the first connection provide the alignment pairs. the second and the third provided the raw sequences All three connections can be the same. each connection provide a table. the tab must have id and seq column

References string().

Referenced by alignProtein().

void loadProtein	(	Connection &	conn,
		const string &	table,
		const string &	column,
		map< string, string > &	pstore
	)

Parameters:

pstore

is a pid => pepseq map

Referenced by main(), and writeJobInstruction().

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

References alignDNA(), alignProtein(), Sourceprt::column, Sourceprt::column1, Sourceprt::column2, Sourceprt::db, Sourceprt::db1, Sourceprt::db2, fileExists(), MysqlDBInfo::getAuthenInfo(), MysqlDBInfo::getPassword(), MysqlDBInfo::getUser(), Dynaln::headers(), Sourceprt::host, Sourceprt::host1, Sourceprt::host2, input, loadProtein(), passwd, readConfig(), Sourceprt::readFile(), Sourceprt::sufficient(), Sourceprt::table, Sourceprt::table1, Sourceprt::table2, usage, and user.

void readConfig	(	const string &	confile,
		Sourceprt &	input
	)

References Sourceprt::column, Sourceprt::column1, Sourceprt::column2, Sourceprt::db, Sourceprt::db1, Sourceprt::db2, Sourceprt::host, Sourceprt::host1, Sourceprt::host2, ifstream(), Sourceprt::table, Sourceprt::table1, and Sourceprt::table2.

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.