dbaln_fungalbt.cpp File Reference

#include "mysql++.h"
#include "Evolution.h"
#include <string>
#include "bioseq.h"
#include "dynaln.h"
#include <math.h>
#include <fstream>
#include "dbinfo.h"
#include <map>
#include <ctime>
#include <algorithm>
#include <numeric>
#include <iterator>
#include <boost/random.hpp>
#include "strformat.h"
#include "dbalnhelper.h"

Defines
#define	MYSQLPLUS2
Functions
void	alignProtein (const string &alnfile, const StoreQueryResult &res, Connection &conn1, Connection &conn2, vector< double > &btres, vector< double > &btres_ns)
bool	createBootTable (Connection &conn, const string &tab)
void	usage ()
void	bufferProtein (map< int, string > &store, Connection &conn)
vector< double >	bootstrap (const vector< int > &marr, int numtry)
int	main (int argc, char *argv[])
Variables
string	user
string	passwd
bool	DEBUG = false

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Detailed Description

This is for bootstrap of fungal alignments.

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Define Documentation

#define MYSQLPLUS2

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Function Documentation

void alignProtein	(	const string &	alnfile,
		const StoreQueryResult &	res,
		Connection &	conn1,
		Connection &	conn2,
		vector< double > &	btres,
		vector< double > &	btres_ns
	)

References bootstrap(), bufferProtein(), Dynaln::getNgMatchArray(), itos(), length, Dynaln::printAlign(), and Dynaln::runlocal().

vector< double > bootstrap	(	const vector< int > &	marr,
		int	numtry
	)

Referenced by alignProtein().

void bufferProtein	(	map< int, string > &	store,
		Connection &	conn
	)

this method will use protein_jgi for non-JGI databases

taken the protein sequence from the JGI protein table this table has column (proteinId, seq) Non-JGI database protein table has a view protein_jgi.

References DEBUG, string(), and tableExists().

bool createBootTable	(	Connection &	conn,
		const string &	tab
	)

only create the tab if it is not in the database

References tableExists().

Referenced by main().

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

References alignProtein(), createBootTable(), MysqlDBInfo::getAuthenInfo(), MysqlDBInfo::getPassword(), MysqlDBInfo::getUser(), GrishinDistance(), passwd, usage, and user.

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.

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Variable Documentation

bool DEBUG = false

string passwd

string user

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.

format I am adding a format for bootstrap where a vector of 0,1,2 are output that stands for mismatch, similar, and match respectively.

I will use the view protein_jgi as standard that has two columns: (proteinId, seq), this requires minimal amount of manual work.

All non-JGI database have a protein_jgi view that has (proteinId,description,seq) columns.