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#include <stdio.h>
#include <stdlib.h>
#include "kalign/kalign.h"
int test_2(void);
int main(int argc, char *argv[])
{
struct msa* msa = NULL;
if(argc <= 1){
fprintf(stdout,"no inputs\n");
return EXIT_SUCCESS;
}
for(int i = 1; i < argc;i++){
fprintf(stdout,"reading from %s\n", argv[i]);
kalign_read_input(argv[i], &msa,1);
}
/* Align seqences */
kalign_run(msa,1 , -1, -1, -1 , -1);
/* write alignment in clustal format */
kalign_write_msa(msa, "test.clu", "clu");
/* write alignment in aligned fasta format */
kalign_write_msa(msa, "test.fa", "fasta");
/* cleaning up */
kalign_free_msa(msa);
test_2();
return EXIT_SUCCESS;
}
int test_2(void){
// Initialize array
char* inseq[] = {
"ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTTGCATGCATGCATGCATGCATGCATGCA",
"ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTTGCATGCATGCATGCATGCATGCATGCA",
"ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTTGCATGCATGCATGCATGCATGCATGCA",
"ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT"
};
int numseq = 4;
int L[] = {76, 76, 76, 48};
char** aln = NULL;
int aln_len = 0;
kalign(inseq, L, numseq, 4 , KALIGN_TYPE_DNA_INTERNAL, -1, -1 , -1, &aln, &aln_len);
printf("Aligned:\n");
for(int i = 0; i < numseq; i++){
printf("%s\n", aln[i]);
/* printf("%s\n", inseq[i]); */
}
for (int i = 0; i < numseq; ++i) {
int num_aligned = 0;
for (int j = 0; j < aln_len; ++j) {
if (aln[i][j] != '-' && aln[i][j] != '\0') {
num_aligned++;
}
}
if (num_aligned != L[i]) {
fprintf(stderr, "error: sequence %d is not fully aligned\n", i);
fprintf(stderr, "%s\n", inseq[i]);
fprintf(stderr, "%s\n", aln[i]);
}
}
/* Free alignment */
for(int i = 0; i < numseq;i++){
free(aln[i]);
}
free(aln);
return 0;
}
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