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/* incre_example.c: incremental MSA example using abPOA library
To compile:
gcc -g incre_example.c -I ./include -L ./lib -labpoa -lz -lm -o incre_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, first_part = 5, second_part=3, third_part=2; // first_part: number of sequences in the first incremental MSA
// append the remaining sequences later
// 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->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);
for (i = 0; i < n_seqs; ++i) {
seq_lens[i] = strlen(seqs[i]);
bseqs[i] = (uint8_t*)malloc(sizeof(uint8_t) * seq_lens[i]);
for (j = 0; j < seq_lens[i]; ++j) {
bseqs[i][j] = nt4_table[(int)seqs[i][j]];
}
}
// abpt->verbose = ABPOA_DEBUG_VERBOSE;
// 1. align the first part of sequences
abpoa_msa(ab, abpt, first_part, NULL, seq_lens, bseqs, NULL, stdout);
// 2. clean MSA & consensus-related memory to avoid leak, always call before incremental MSA
abpoa_clean_msa_cons(ab);
// 3. append the second part of sequences one by one
printf("\nExisting graph has %d sequences, %d nodes. Now append the remaining %d sequences one by one.\n\n", ab->abs->n_seq, ab->abg->node_n, second_part);
abpt->out_msa = 0, abpt->out_cons = 0; // disable output for intermediate append
for (i = 0; i < second_part; ++i) {
abpoa_msa(ab, abpt, 1, NULL, seq_lens + first_part + i, bseqs + first_part + i, NULL, stdout);
}
printf("\nAfter appending the second part, existing graph has %d sequences, %d nodes. Now append the remaining %d sequences together.\n\n", ab->abs->n_seq, ab->abg->node_n, n_seqs - first_part - second_part);
// 4. append the third part of sequences together
abpt->out_msa = 1, abpt->out_cons = 1;
abpoa_msa(ab, abpt, third_part, NULL, seq_lens + first_part + second_part, bseqs + first_part + second_part, NULL, stdout);
printf("\nFinal graph has %d sequences, %d nodes.\n", ab->abs->n_seq, ab->abg->node_n);
// free seq-related variables
for (i = 0; i < n_seqs; ++i) { free(bseqs[i]); }
free(bseqs); free(seq_lens);
// free abpoa-related variables
abpoa_free(ab); abpoa_free_para(abpt);
return 0;
}
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