dbaln_cds.cpp File Reference

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

Defines
#define	MYSQLPLUS2
Functions
void	getPrt (mysqlpp::Query &q, const string &id, string &prt)
void	alignProtein (const string &alnfile, const string &alntabfile, const string &pairtab, const string &prtsrctab, Connection &conn, const int bidx, const int rowcnt)
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	storeProteinIntoMap (Connection &conn, const string &srctab, map< string, string > &id2seq, const string &pairtab, const int bidx, const int rowcnt)
int	main (int argc, char *argv[])
Variables
string	user = "internal"
string	passwd = "w00kie"

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Define Documentation

#define MYSQLPLUS2

This is a program to do protein alignment using the cdsnr table as input protein sequence and use the selfblast table as guide for pairs. Refer to the gwcdsselfpipe program for more details. This program run and load the cds self blast results and do some clean up. After this stage, this program can be used.

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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
	)

void alignProtein	(	const string &	alnfile,
		const string &	alntabfile,
		const string &	pairtab,
		const string &	prtsrctab,
		Connection &	conn,
		const int	bidx,
		const int	rowcnt
	)

References bioseq::assign(), Dynaln::headers(), itos(), bioseq::length(), Dynaln::printAlign(), Dynaln::runlocal(), LSDynaln::runlocal(), bioseq::setName(), storeProteinIntoMap(), string(), and Dynaln::toDelimitedString().

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

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

the tab must have id and seq column

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

References alignProtein(), passwd, and user.

void storeProteinIntoMap	(	Connection &	conn,
		const string &	srctab,
		map< string, string > &	id2seq,
		const string &	pairtab,
		const int	bidx,
		const int	rowcnt
	)

Referenced by alignProtein().

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Variable Documentation

string passwd = "w00kie"

Referenced by alignProtein(), and main().

string user = "internal"

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.

Input: all from one database

Referenced by alignProtein(), connect(), LoadCDSFromAce(), main(), SimpleSelect::main(), and processAll().