141 lines
5.4 KiB
C
141 lines
5.4 KiB
C
/*********************************************************************************************
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Description: Some useful functions
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Copyright : All right reserved by NCIC.ICT
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Author : Zhang Zhonghai
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Date : 2023/08/25
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***********************************************************************************************/
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#include <string.h>
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#include <stdint.h>
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#include <stdio.h>
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#include <string.h>
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#include "utils.h"
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#include "debug.h"
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unsigned char nst_nt4_table[256] = {
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4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
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4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
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4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5 /*'-'*/, 4, 4,
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4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
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4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
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4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
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4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
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4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
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4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
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4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
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4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
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4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
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4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
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4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
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4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
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4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4};
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const char *BASE = "ACGTN";
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// 将碱基字符转成2位编码
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void base_char_to_int(char *str)
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{
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int i;
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const int slen = strlen(str);
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for (i = 0; i < slen; ++i)
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{
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str[i] = nst_nt4_table[(uint8_t)str[i]];
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}
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}
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/* read row_num_to_read lines of query-target info */
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/**
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* info_num: numbers of int value in one line of info file (2: qlen, tlen or 3: qlen, tlen, init_score)
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*/
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int read_qt_info(qti_v *qti_arr, buf_t *buf, int row_num_to_read, int info_num, FILE *fp)
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{
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if (!qti_arr || !buf || !fp) return -1;
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if (info_num !=2 && info_num != 3) return -1;
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if (buf->m == 0) { buf->m = BUF_SIZE; buf->addr = malloc(buf->m); }
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int read_row_num = 0;
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while (row_num_to_read > 0 && fgets((char *)buf->addr, buf->m, fp) != NULL)
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{
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// if (strlen((char *)buf->addr) == 1) continue; // skip null line
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if (qti_arr->m <= read_row_num) { // expend the seq array
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int old_m = qti_arr->m;
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kv_resize(qti_t, *qti_arr, old_m == 0 ? 128 : old_m * 2);
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memset(&qti_arr->a[old_m], 0, (qti_arr->m - old_m) * sizeof(qti_t)); // set the newly allocated mem to zero
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}
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qti_t *qti = &kv_A(*qti_arr, qti_arr->n++); // get a new query-target info
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if (qti->m < info_num) { kv_resize(int, *qti, info_num); }
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if (info_num == 2) sscanf((char *)buf->addr, "%d %d", &qti->a[0], &qti->a[1]);
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else sscanf((char *)buf->addr, "%d %d %d", &qti->a[0], &qti->a[1], &qti->a[2]);
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// test output
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// int i; for (i = 0; i < info_num; ++i) { fprintf(stderr, "%d\t", kv_A(*qti, i)); } fprintf(stderr, "\n");
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--row_num_to_read;
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++read_row_num;
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}
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return read_row_num;
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}
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/* read row_num_to_read lines of query or target sequence */
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int read_seq(seq_v *seq_arr, buf_t *buf, int row_num_to_read, FILE *fp)
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{
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if (!seq_arr || !buf || !fp) return -1;
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if (buf->m == 0) { buf->m = BUF_SIZE; buf->addr = malloc(buf->m); }
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int read_row_num = 0;
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while (row_num_to_read > 0 && fgets((char*)buf->addr, buf->m, fp) != NULL)
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{
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int base_size = strlen((char *)buf->addr);
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// trim the '\n' char
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if ((char)buf->addr[base_size - 1] == '\n') {
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buf->addr[base_size - 1] = (uint8_t)'\0';
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--base_size;
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}
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// if (base_size == 0) continue; // skip null line
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// fprintf(stderr, "%d %s\n", base_size, (char *) buf->addr);
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// test output
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// fprintf(stderr, "%s\n", (char *)buf->addr);
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if (seq_arr->m <= read_row_num) { // expend the seq array
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int old_m = seq_arr->m;
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kv_resize(seq_t, *seq_arr, old_m == 0 ? 128 : old_m * 2);
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memset(&seq_arr->a[old_m], 0, (seq_arr->m - old_m) * sizeof(seq_t)); // set the newly allocated mem to zero
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}
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seq_t *seq = &kv_A(*seq_arr, seq_arr->n++); // get a new query-target sequence
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if (seq->m < base_size) { kv_resize(uint8_t, *seq, base_size + 16); }
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base_char_to_int((char*)buf->addr);
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memcpy(seq->a, buf->addr, base_size);
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seq->n = base_size;
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// test output
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// int i; for (i = 0; i < seq->n; ++i) fprintf(stderr, "%d", kv_A(*seq, i)); fprintf(stderr, "\n");
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--row_num_to_read;
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++read_row_num;
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}
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return read_row_num;
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}
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void write_query_target_sequence(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int h0, int fnum)
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{
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#ifdef DEBUG_FILE_OUTPUT
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// 写到三个文件里，query.fa，target.fa，每行一个序列，info.txt，包含前缀得分h0，和长度信息qlen，tlen
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FILE *query_f = gfq[fnum],
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*target_f = gft[fnum],
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*info_f = gfi[fnum];
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const char seq_map[5] = {'A', 'C', 'G', 'T', 'N'};
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int i;
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// 处理query
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for (i = 0; i < qlen; ++i)
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fprintf(query_f, "%c", seq_map[query[i]]);
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fprintf(query_f, "\n");
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// 处理target
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for (i = 0; i < tlen; ++i)
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fprintf(target_f, "%c", seq_map[target[i]]);
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fprintf(target_f, "\n");
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// 处理其他信息
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if (h0 > 0)
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fprintf(info_f, "%-8d%-8d%-8d\n", qlen, tlen, h0);
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else
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fprintf(info_f, "%-8d%-8d\n", qlen, tlen);
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#endif
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} |