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gapsmis.c
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gapsmis.c
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/**
GapsMis: flexible sequence alignment with a bounded number of gaps.
Copyright (C) 2013 Solon P. Pissis
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
**/
#include <stdio.h>
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include "functions.h"
#include "output.h"
int main ( int argc, char ** argv)
{
struct TSwitch sw;
char * out_file;
unsigned int MAXnumgaps; //input argument
double gap_open_pen; //input argument
double gap_extend_pen; //input argument
unsigned int scoring_matrix; //input argument
unsigned int MAXgap;
unsigned int num_mat; //input argument + 1
double MAXscore; //to be computed
unsigned int MINnumgaps; //to be computed
unsigned int istart; //where to start backtracing
unsigned int jstart; //where to start backtracing
unsigned int iend; //where to end backtracing
unsigned int jend; //where to end backtracing
unsigned int * gaps_pos; //position of the gap(s)
unsigned int * gaps_len; //len of the gap(s)
unsigned int * where; //where is the gap(s): text [1] or pattern [2]
struct TSeq * t; //text t
unsigned int n; //length of text
struct TSeq * p; //pattern p
unsigned int m; //length of pattern
unsigned int L; //local alignment
double *** G; //dynamic programming matrix
int *** H; //backtracing matrix
unsigned int swap; //swap the text and the pattern in case m < n
unsigned int i, j;
/* checks the arguments */
i = decode_switches ( argc, argv, &sw );
if ( i < 5 || ! sw . seq_a || ! sw . seq_b )
{
usage ();
return ( 1 );
}
else
{
gap_open_pen = - sw . gap_open_pen; //the penalties should have a negative value
gap_extend_pen = - sw . gap_extend_pen;
out_file = sw . out_file;
L = sw . L;
if ( ! strcmp ( "EDNAFULL", sw . matrix ) ) scoring_matrix = 0;
else if ( ! strcmp ( "EBLOSUM62", sw . matrix ) ) scoring_matrix = 1;
else
{
fprintf ( stderr, "Error: scoring matrix argument should be `EDNAFULL' for nucleotide sequences or `EBLOSUM62' for protein sequences!!!\n" );
return ( 1 );
}
if ( L > 1 )
{
fprintf (stderr, "Error: wrong argument with L: should be either 0 (semi-global) or 1 (local)\n" );
return ( 1 );
}
}
/* reads the text */
t = read_fasta_file ( sw . seq_a );
if ( ! t )
{
fprintf (stderr, "Error: cannot read file %s!!!\n", sw . seq_a );
return ( 1 );
}
if ( ! t -> header ) t -> header = strdup ( "Seq A" );
/* reads the pattern */
p = read_fasta_file ( sw . seq_b );
if ( ! p )
{
fprintf( stderr, "Error: cannot read file %s!!!\n", sw . seq_b );
return ( 1 );
}
if ( ! p -> header ) p -> header = strdup ( "Seq B" );
/* calculate text's and pattern's length */
n = strlen ( t -> data );
m = strlen ( p -> data );
/* checks the lengths of text and pattern and swaps if needed */
if ( m > n )
{
swap_txt_pat ( &t, &n, &p, &m );
swap = 1;
}
else
swap = 0;
/* checks the max num of gaps: MAXnumgaps < n */
MAXnumgaps = ( sw . max_num_gaps <= -1 ) ? 2 : sw . max_num_gaps;
if( MAXnumgaps >= n )
{
fprintf ( stderr, "Error: the max gap length should be less than the length of the text!!!\n" );
return ( 1 );
}
if ( L == 1 ) num_mat = MAXnumgaps + 1;
else num_mat = MAXnumgaps;
MAXgap = ( sw . max_gap <= -1 ) ? n - 1 : sw . max_gap;
if( MAXgap >= n )
{
fprintf ( stderr, "Error: the max gap length should be less than the length of the text!!!\n" );
return ( 1 );
}
/* 3d dynamic memory allocation for matrices G and H*/
if( ( G = ( double *** ) malloc ( ( num_mat ) * sizeof( double ** ) ) ) == NULL )
{
fprintf( stderr, "G could not be allocated\n" );
return 0;
}
for ( i = 0; i < num_mat; i ++ )
{
if( ( G[i] = ( double ** ) malloc ( ( n + 1 ) * sizeof( double * ) ) ) == NULL )
{
fprintf( stderr, "G could not be allocated\n" );
return 0;
}
if( ( G[i][0] = ( double * ) calloc ( ( n + 1 ) * ( m + 1 ), sizeof( double ) ) ) == NULL )
{
fprintf( stderr, "G could not be allocated\n" );
return 0;
}
for ( j = 1; j < n + 1; j++ )
G[i][j] = ( void * ) G[i][0] + j * ( m + 1 ) * sizeof( double );
}
if( ( H = ( int *** ) malloc ( ( num_mat ) * sizeof( int ** ) ) ) == NULL )
{
fprintf( stderr, "H could not be allocated\n" );
return 0;
}
for ( i = 0; i < num_mat; i ++ )
{
if( ( H[i] = ( int ** ) malloc ( ( n + 1 ) * sizeof( int * ) ) ) == NULL )
{
fprintf( stderr, "H could not be allocated\n" );
return 0;
}
if( ( H[i][0] = ( int * ) calloc ( ( n + 1 ) * ( m + 1 ), sizeof( int ) ) ) == NULL )
{
fprintf( stderr, "H could not be allocated\n" );
return 0;
}
for ( j = 1; j < n + 1; j++ )
H[i][j] = ( void* ) H[i][0] + j * ( m + 1 ) * sizeof( int );
}
/* dynamic programming algorithm */
if ( L == 0 )
{
if ( MAXgap == n - 1 )
{
if ( ! ( dp_algorithm( G, MAXnumgaps, H, t -> data, n, p -> data, m, scoring_matrix, gap_open_pen, gap_extend_pen ) ) )
{
fprintf ( stderr, "Error: dp_algorithm() failed!!!\n" );
return ( 1 );
}
}
else
{
if ( ! ( dp_algorithm_pruned( G, MAXnumgaps, H, t -> data, n, p -> data, m, scoring_matrix, gap_open_pen, gap_extend_pen, MAXgap ) ) )
{
fprintf ( stderr, "Error: dp_algorithm_pruned() failed!!!\n" );
return ( 1 );
}
}
}
else
{
if ( MAXgap == n - 1 )
{
if ( ! ( dp_algorithm_lcl( G, MAXnumgaps, H, t -> data, n, p -> data, m, scoring_matrix, gap_open_pen, gap_extend_pen ) ) )
{
fprintf ( stderr, "Error: dp_algorithm() failed!!!\n" );
return ( 1 );
}
}
else
{
fprintf ( stderr, "Error: option `- m' is only for global alignment!!!\n" );
return ( 1 );
}
}
MINnumgaps = 0; //to be computed
/* finds the optimal alignment based on the matrices scores */
if ( L == 0 ) opt_solution ( G, MAXnumgaps, n, m, &MAXscore, &istart, &MINnumgaps );
if ( L == 1 ) opt_solution_lcl ( G, MAXnumgaps, n, m, &MAXscore, &istart, &jstart, &MINnumgaps );
if( ( gaps_pos = ( unsigned int * ) calloc ( MINnumgaps, sizeof( unsigned int ) ) ) == NULL )
{
fprintf( stderr, "gaps_pos could not be allocated\n" );
return 0;
}
if( ( gaps_len = ( unsigned int * ) calloc ( MINnumgaps, sizeof( unsigned int ) ) ) == NULL )
{
fprintf( stderr, "gaps_pos could not be allocated\n" );
return 0;
}
if( ( where = ( unsigned int * ) calloc ( MINnumgaps, sizeof( unsigned int ) ) ) == NULL )
{
fprintf( stderr, "where could not be allocated\n" );
return 0;
}
/* computes the position of the gap */
if ( L == 0 ) backtracing ( H[MINnumgaps - 1], m, n, istart, gaps_pos, MINnumgaps, gaps_len, where );
if ( L == 1 ) backtracing_lcl ( G[MINnumgaps], m, n, H[MINnumgaps], istart, jstart, gaps_pos, MINnumgaps, gaps_len, where, &iend, &jend );
#if 0
int s;
for ( s = 0; s < num_mat; s++ )
{
for(i = 0; i < n+1; i++) //Matrix G output
{
for(j = 0; j < m+1; j++)
{
fprintf( stderr,"%d\t", (int) G[s][i][j] );
}
fprintf(stderr,"\n");
}
fprintf(stderr,"\n");
#if 1
for(i = 0; i < n+1; i++) //Matrix H output
{
for(j = 0; j < m+1; j++)
{
fprintf( stderr,"%d\t", H[s][i][j]);
}
fprintf(stderr,"\n");
}
fprintf(stderr,"\n");
#endif
}
if ( L == 1 ) fprintf( stderr,"\n[%d,%d]-->[%d,%d]\n", istart, jstart, iend, jend );
#endif
/* outputs the results */
if ( L == 0 )
if ( ! ( results ( out_file, t, n, p, m, MAXscore, gaps_pos, MINnumgaps, gaps_len, where, swap, scoring_matrix, gap_open_pen, gap_extend_pen, L ) ) )
{
fprintf(stderr, "Error: results() failed!!!\n");
return ( 1 );
}
if ( L == 1 )
if ( ! ( results_lcl ( out_file, t, n, p, m, MAXscore, gaps_pos, MINnumgaps, gaps_len, where, istart, iend, jstart, jend, swap, scoring_matrix, gap_open_pen, gap_extend_pen, L ) ) )
{
fprintf(stderr, "Error: results() failed!!!\n");
return ( 1 );
}
for ( i = 0; i < num_mat; i++ )
{
free ( G[i][0] );
free ( G[i] );
free ( H[i][0] );
free ( H[i] );
}
free ( G );
free ( H );
free ( gaps_pos );
free ( gaps_len );
free ( where );
free ( t -> header );
free ( p -> header );
free ( t );
free ( p );
free ( sw . out_file );
free ( sw . matrix );
return ( 0 );
}