dumpcds.cpp File Reference

#include <mysql++.h>
#include <iostream>
#include <fstream>
#include "bioseq.h"
#include <iomanip>
#include "strformat.h"

Functions
void	updownnumbers (const vector< pair< int, int > > &nums, int delta, ostream &OU, int fwidth)
void	dumpIntronExon (Connection &conn, Connection &conn2, int maxintron, const string &genomictab)
void	dumpFromModel (Connection &conn1, Connection &conn2, const string &mod, const string &gtab, ostream &ous)
vector< int >	tonumber (const vector< string > &vos)
void	usage (ostream &ous, int intergenic)
int	main (int argc, char *argv[])

---

Function Documentation

void dumpFromModel	(	Connection &	conn1,
		Connection &	conn2,
		const string &	mod,
		const string &	gtab,
		ostream &	ous
	)

References dissect(), DNA::GCContent(), bioseq::getName(), bioseq::getTitle(), itos(), bioseq::length(), bioseq::printFasta(), bioseq::setName(), string(), DNA::subseq(), and tonumber().

Referenced by main().

void dumpIntronExon	(	Connection &	conn,
		Connection &	conn2,
		int	maxintron,
		const string &	genomictab
	)

References DNA::GCContent(), bioseq::getName(), bioseq::getTitle(), bioseq::setName(), bioseq::setTitle(), and DNA::subseq().

Referenced by main().

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

References delta(), dumpFromModel(), dumpIntronExon(), bioseq::getTitle(), bioseq::length(), bioseq::printFasta(), bioseq::setName(), usage, and user.

vector< int > tonumber

(

const vector< string > &

vos

)

Referenced by dumpFromModel().

void updownnumbers	(	const vector< pair< int, int > > &	nums,
		int	delta,
		ostream &	OU,
		int	fwidth
	)

@ dumpcds a C++ program to generate input file for Fgenesh training.

This program takes a table as input. The default table is fgtraining. and produces a sequences with information about intron locations and start and end of coding regions. It also dump the file with spliced the CDS, and Introns.

void usage	(	ostream &	ous,
		int	intergenic
	)