intronstop.cpp File Reference

#include <iostream>
#include <fstream>
#include "RNAModel.h"
#include <mysql++.h>
#include "dbinfo.h"
#include <iomanip>

Classes
struct	instopres
Functions
void	countStop (Connection &conn, const string &file, const map< string, string > &genostore)
void	cacheGenomic (Connection &conn, map< string, string > &gstore, const string &host, const string &database)
void	stopsInIntrons (const Noschain &ch, const string &gseq, map< Range, instopres > &res)
int	numberOfStops (const string &seq)
void	countIntronN (Connection &conn, const string &file, const map< string, string > &genostore)
void	countNInIntrons (const Noschain &ch, const string &gseq, map< Range, int > &res, int bs[4])
void	writeBaseCount (ostream &ous, int base[4])
void	usage ()
int	main (int argc, char *argv[])

---

Function Documentation

void cacheGenomic	(	Connection &	conn,
		map< string, string > &	gstore,
		const string &	host,
		const string &	database
	)

the schema for genomic sequence in JGI is not staightforward, This function may not work well. It is usually better to make a genomic table from the subtables There are three tables: scaffold, scaffoldSeq, scaffoldInfo scaffold, is a JGI track table scaffoldInfo is a table describing the internal structure of scaffold in terms of contigs. This table also have a sequnce column but are left un populated. scaffoldSeq is the actual sequence. if genomic sequence is long you cannot use scaffoldSeq table, you have to use my kzgenomic table for this.

Referenced by main().

void countIntronN	(	Connection &	conn,
		const string &	file,
		const map< string, string > &	genostore
	)

count N in all intron sequences. Both coding and non-coding introns are counted. count 4 bases plust N and derive frequency.

References countNInIntrons(), and writeBaseCount().

Referenced by main().

void countNInIntrons	(	const Noschain &	ch,
		const string &	gseq,
		map< Range, int > &	res,
		int	bs[4]
	)

Parameters:

	bs[]	is a vector of 4 elements: A,C,G,T count from the intron sequences. This is an accumulator.
	res	is a intron b,e => number_of_N bases map.

References Range::begin(), Range::direction(), Range::end(), Noschain::numberOfRanges(), and reverseComplement().

Referenced by countIntronN().

void countStop	(	Connection &	conn,
		const string &	file,
		const map< string, string > &	genostore
	)

count stop in coding introns in the frame of the preceeding exon

References stopsInIntrons(), and Noschain::subchain().

Referenced by main().

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

References cacheGenomic(), countIntronN(), countStop(), MysqlDBInfo::getAuthenInfo(), MysqlDBInfo::getPassword(), MysqlDBInfo::getUser(), and usage.

int numberOfStops

(

const string &

seq

)

count stop codon in frame 0, which is inframe with the preceding exon.

Referenced by stopsInIntrons().

void stopsInIntrons	(	const Noschain &	ch,
		const string &	gseq,
		map< Range, instopres > &	res
	)

Parameters:

res.

Is the accumulator for each genomic sequence. The Range only make sense within this genomic sequence.

References Range::begin(), Range::direction(), Range::end(), Range::length(), Noschain::numberOfRanges(), numberOfStops(), and reverseComplement().

Referenced by countStop().

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.

void writeBaseCount	(	ostream &	ous,
		int	base[4]
	)

Parameters:

	base	input array of frequenies of four bases
	ous	write result in the format of Base Character <TAB> Count <TAB> Frequence Also write expected stop frequency in isolation.

Referenced by countIntronN().