tabaln_same.cpp File Reference

#include "mlocalS_str.h"
#include "../../../cadbc/cadbc.h"
#include "libpq++.h"
#include <string>
#include <iostream>
#include <fstream>
#include "dbinfo.h"
#include "strformat.h"

Functions
void	usage ()
void	getPep (cadbc *ace, char *&seqstr, int &seqlen, char *seq1name)
int	main (int argc, char *argv[])

---

Function Documentation

void getPep	(	cadbc *	ace,
		char *&	seqstr,
		int &	seqlen,
		char *	seq1name
	)

References cadbc::getPeptideString().

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

References ace, dyaln::align(), dyaln::freeTrace(), getPep(), itoa(), dyaln::outputAln(), dyaln::outputTab(), dyaln::setGapCost(), dyaln::setMatrix(), dyaln::setNaligns(), and usage.

void usage

(

)

to use this program the ENVIRONMENT Variable MATDIR needs ot be set that contains the matrix directory for the seqaln programs Do tabaln taken input Portein sequence from the same database, such as SwissProt locally installed.

Relational tab output will be put into a file: use -o file to specify this file. If not specified, the default file is alnresult.tab and alignment result will be output to the stdout.

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.