-
Notifications
You must be signed in to change notification settings - Fork 1
/
find_satellite.c
74 lines (54 loc) · 1.68 KB
/
find_satellite.c
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
#include<stdio.h>
#include<stdlib.h>
#include<unistd.h>
#include"dataset.h"
#include"filter.h"
void file_error(char* path) {
printf("failed to open file %s\n",path);
_exit(1);
}
int main(int argc,char** argv) {
FILE* fasta_f;
FILE* target_f;
dataset ds, target_set;
dataset new;
size_t size,plus,minus;
unsigned int max_distance;
int n_threads;
if (argc < 7) {
printf("Arguments are: \n"
" [file] Fasta dataset to filter \n"
" [file] Fasta target sequence for Smith Waterman filter \n"
" (int) size filter size \n"
" (int) allow sequences in the range [size size+this_value] \n"
" (int) allow sequences in the tange [size-this_value size] \n"
" (int) maximum allowed Smith Waterman distance from target \n"
" (int) number of threads to use for this computation \n");
return(1);
}
sscanf(argv[3],"%lu",&size);
sscanf(argv[4],"%lu",&plus);
sscanf(argv[5],"%lu",&minus);
sscanf(argv[6],"%u",&max_distance);
sscanf(argv[7],"%i",&n_threads);
if ( NULL == (fasta_f = fopen(argv[1], "r"))) file_error(argv[1]);
ds = dataset_from_fasta(fasta_f);
fclose(fasta_f);
if ( NULL == (target_f = fopen(argv[2], "r"))) file_error(argv[2]);
target_set = dataset_from_fasta(target_f);
fclose(target_f);
new = filter_ds_by_size(ds,size,plus,minus);
free_sequences_from_dataset(ds);
ds = new;
new = filter_by_SW_distance(ds,
target_set.sequences[0],
target_set.sequence_lengths[0],
max_distance,
n_threads);
free_sequences_from_dataset(ds);
ds = new;
dataset_to_fasta(stdout,ds);
free_sequences_from_dataset(ds);
free_sequences_from_dataset(target_set);
return(0);
}