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example.c
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example.c
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/* example.c libabpoa usage example
To compile:
gcc -g example.c -I ./include -L ./lib -labpoa -lz -lm -o example
or:
gcc -g example.c -I ./include ./lib/libabpoa.a -lz -lm -o example
*/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <stdint.h>
#include "include/abpoa.h"
// for nt
// AaCcGgTtNn ==> 0,1,2,3,4
unsigned char nt4_table[256] = {
0, 1, 2, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 /*'-'*/, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4
};
// 65,97=>A, 67,99=>C, 71,103=>G, 84,85,116,117=>T, else=>N
const char nt256_table[256] = {
'A', 'C', 'G', 'T', 'N', '-', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', '-', 'N', 'N', 'N', 'N',
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
'N', 'A', 'N', 'C', 'N', 'N', 'N', 'G', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
'N', 'N', 'N', 'N', 'T', 'T', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
'N', 'A', 'N', 'C', 'N', 'N', 'N', 'G', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
'N', 'N', 'N', 'N', 'T', 'T', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N'
};
int main(void) {
int i, j, n_seqs = 10;
// char seqs[10][100] = {
// "CGTCAATCTATCGAAGCATACGCGGGCAGAGCCGAAGACCTCGGCAATCCA",
// "CCACGTCAATCTATCGAAGCATACGCGGCAGCCGAACTCGACCTCGGCAATCAC",
// "CGTCAATCTATCGAAGCATACGCGGCAGAGCCCGGAAGACCTCGGCAATCAC",
// "CGTCAATGCTAGTCGAAGCAGCTGCGGCAGAGCCGAAGACCTCGGCAATCAC",
// "CGTCAATCTATCGAAGCATTCTACGCGGCAGAGCCGACCTCGGCAATCAC",
// "CGTCAATCTAGAAGCATACGCGGCAAGAGCCGAAGACCTCGGCCAATCAC",
// "CGTCAATCTATCGGTAAAGCATACGCTCTGTAGCCGAAGACCTCGGCAATCAC",
// "CGTCAATCTATCTTCAAGCATACGCGGCAGAGCCGAAGACCTCGGCAATC",
// "CGTCAATGGATCGAGTACGCGGCAGAGCCGAAGACCTCGGCAATCAC",
// "CGTCAATCTAATCGAAGCATACGCGGCAGAGCCGTCTACCTCGGCAATCACGT"
// };
char seqs[10][100] = {
"CGATCGATCGATCGATGCATGCATCGATGCATCGATCGATGCATGCAT",
"CGATCGATCGATAAAAAAAAAAAAAAAAAAACGATGCATGCATCGATGCATCGATCGATGCATGCAT",
"CGATCGATCGATCGATGCATGCATCGATGCATCGATCGATGCATGCAT",
"CGATCGATCGATCGATGCATGCATCGATGCATCGATCGATGCATGCAT",
"CGATCGATCGATAAAAAAAAAAAAAAAAAAACGATGCATGCATCGATGCATCGATCGATGCATGCAT",
"CGATCGATCGATAAAAAAAAAAAAAAAAAAACGATGCATGCATCGATGCATCGATCGATGCATGCAT",
"CGATCGATCGATAAAAAAAAAAAAAAAAAAACGATGCATGCATCGATGCATCGATCGATGCATGCAT",
"CGATCGATCGATCGATGCATGCATCGATGCATCGATCGATGCATGCAT",
"CGATCGATCGATCGATGCATGCATCGATGCATCGATCGATGCATGCAT",
"CGATCGATCGATCGATGCATGCATCGATGCATCGATCGATGCATGCAT"
};
// initialize variables
abpoa_t *ab = abpoa_init();
abpoa_para_t *abpt = abpoa_init_para();
// alignment parameters
// abpt->align_mode = 0; // 0:global 1:local, 2:extension
// abpt->mat_fn = strdup("HOXD70.mtx"); abpt->use_score_matrix = 1; // score matrix instead of constant match/mismatch score
// abpt->match = 2; // match score
// abpt->mismatch = 4; // mismatch penalty
// abpt->gap_mode = ABPOA_CONVEX_GAP; // gap penalty mode
// abpt->gap_open1 = 4; // gap open penalty #1
// abpt->gap_ext1 = 2; // gap extension penalty #1
// abpt->gap_open2 = 24; // gap open penalty #2
// abpt->gap_ext2 = 1; // gap extension penalty #2
// gap_penalty = min{gap_open1 + gap_len * gap_ext1, gap_open2 + gap_len * gap_ext2}
// abpt->bw = 10; // extra band used in adaptive banded DP
// abpt->bf = 0.01;
// output options
abpt->out_msa = 1; // generate Row-Column multiple sequence alignment(RC-MSA), set 0 to disable
abpt->out_cons = 1; // generate consensus sequence, set 0 to disable
abpt->w = 6, abpt->k = 9; abpt->min_w = 10; // minimizer-based seeding and partition
abpt->progressive_poa = 1;
abpt->max_n_cons = 2; // to generate 2 consensus sequences
abpoa_post_set_para(abpt);
// collect sequence length, trasform ACGT to 0123
int *seq_lens = (int*)malloc(sizeof(int) * n_seqs);
uint8_t **bseqs = (uint8_t**)malloc(sizeof(uint8_t*) * n_seqs);
int **weights = (int**)malloc(sizeof(int*) * n_seqs);
for (i = 0; i < n_seqs; ++i) {
seq_lens[i] = strlen(seqs[i]);
bseqs[i] = (uint8_t*)malloc(sizeof(uint8_t) * seq_lens[i]);
weights[i] = (int*)malloc(sizeof(int) * seq_lens[i]);
for (j = 0; j < seq_lens[i]; ++j) {
bseqs[i][j] = nt4_table[(int)seqs[i][j]];
if (j >= 12) weights[i][j] = 2;
else weights[i][j] = 0;
}
}
// 1. directly output to stdout
fprintf(stdout, "=== output to stdout ===\n");
abpt->use_qv = 1;
// perform abpoa-msa
// set weights as NULL if no quality score weights are used
abpoa_msa(ab, abpt, n_seqs, NULL, seq_lens, bseqs, weights, stdout);
// 2. output MSA alignment and consensus sequence stored in (abpoa_cons_t *)
abpoa_cons_t *abc = ab->abc;
fprintf(stdout, "=== stored in variables ===\n");
fprintf(stdout, ">Multiple_sequence_alignment\n");
for (i = 0; i < abc->n_seq; ++i) {
for (j = 0; j < abc->msa_len; ++j) {
fprintf(stdout, "%c", nt256_table[abc->msa_base[i][j]]);
}
fprintf(stdout, "\n");
}
for (i = 0; i < abc->n_cons; ++i) {
fprintf(stdout, ">Consensus_sequence");
if (abc->n_cons > 1) {
fprintf(stdout, "_%d ", i+1);
for (j = 0; j < abc->clu_n_seq[i]; ++j) { // output read ids for each cluster/group
fprintf(stdout, "%d", abc->clu_read_ids[i][j]);
if (j != abc->clu_n_seq[i]-1) fprintf(stdout, ",");
}
}
fprintf(stdout, "\n");
for (j = 0; j < abc->cons_len[i]; ++j)
fprintf(stdout, "%c", nt256_table[abc->cons_base[i][j]]);
fprintf(stdout, "\n");
}
/* generate DOT partial order graph plot */
abpt->out_pog = strdup("example.png"); // dump parital order graph to file
if (abpt->out_pog != NULL) abpoa_dump_pog(ab, abpt);
// free seq-related variables
for (i = 0; i < n_seqs; ++i) { free(bseqs[i]); free(weights[i]); }
free(bseqs); free(seq_lens); free(weights);
// free abpoa-related variables
abpoa_free(ab); abpoa_free_para(abpt);
return 0;
}