buildjgitranscript.cpp File Reference

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

Defines
#define	MYSQLPLUS2
Functions
void	buildGeneInfo (mysqlpp::Connection &conn, const string &sqlstr, Connection &conn1, const string &outtab, const string &genomictab)
bool	tableExists (mysqlpp::Connection &conn, const string &tab)
void	createTranscriptTable (mysqlpp::Connection &conn, const string &tableName)
int	main (int argc, char *argv[])
Variables
string	user = "internal"
string	passwd = "w00kie"

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Define Documentation

#define MYSQLPLUS2

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Function Documentation

void buildGeneInfo	(	mysqlpp::Connection &	conn,
		const string &	sqlstr,
		Connection &	conn1,
		const string &	outtab,
		const string &	genomictab
	)

References bioseq::length(), sep, string(), DNA::subseq(), bioseq::substr(), and bioseq::toString().

Referenced by main().

void createTranscriptTable	(	mysqlpp::Connection &	conn,
		const string &	tableName
	)

References tableExists().

Referenced by main().

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

References buildGeneInfo(), createTranscriptTable(), passwd, and user.

bool tableExists	(	mysqlpp::Connection &	conn,
		const string &	tab
	)

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Variable Documentation

string passwd = "w00kie"

string user = "internal"

This program use the information from the Genewise pipeline to build the transcript table defined by jgi database. input: genomic sequence table, Aniger_genomic SQL string containing cdsnrgood and exonsrelgood output: the transcript table, the CDS part, the transcript part is identical to the CDS, make a copy after the table is done!