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
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
|
#define _GNU_SOURCE
#include "error/check_error.h"
#include "error/check_h5_error.h"
#include "model/blast_scores_data.h"
#include "model/blast_scores_data_init.h"
#include "load_blast_scores.h"
#include <hdf5_hl.h>
#include <string.h>
#include <stdlib.h>
#include <stdio.h>
/*
* A simple sanity check can be performed by comparing the HDF5
* content with the content of the input text file. Data block output
* from the first command should be equal to the first 5 lines of the
* input file while data block output from the second command should
* be equal to the last 5 lines of the input file.
*
* h5dump --dataset=blast --start "0" --count "5" influenza.h5
*
* h5dump --dataset=blast --start "5749892" --count "5" influenza.h5
*/
void
load_blast_scores (hid_t file_id, const char *file_name)
{
size_t dst_size;
size_t dst_offset[BLAST_SCORES_DATA_FIELD_NUM];
size_t dst_sizes[BLAST_SCORES_DATA_FIELD_NUM];
hid_t field_type[BLAST_SCORES_DATA_FIELD_NUM];
blast_scores_data_init (&dst_size, dst_offset, dst_sizes, field_type);
hsize_t chunk_size = 10;
int *fill_data = NULL;
int compress = 0;
blast_scores_data p_data[10000];
FILE *dat = fopen (file_name, "r");
if (dat == NULL)
check_error (__FILE__, __LINE__);
char *line = NULL;
size_t len = 0;
int i = -1;
int written = 0;
int current_line = 0;
while (getline (&line, &len, dat) != -1)
{
current_line++;
i++;
char *running = strdup (line);
char *token = NULL;
token = strsep (&running, ",");
p_data[i].source_gi = atoi (&token[4]);
token = strsep (&running, ",");
p_data[i].source_start = atoi (token);
token = strsep (&running, ",");
p_data[i].source_end = atoi (token);
token = strsep (&running, ",");
p_data[i].target_gi = atoi (&token[4]);
token = strsep (&running, ",");
p_data[i].target_start = atoi (token);
token = strsep (&running, ",");
p_data[i].target_end = atoi (token);
token = strsep (&running, ",");
p_data[i].score = atoi (token);
token = strsep (&running, ",");
p_data[i].bit_score = strtod (token, NULL);
token = strsep (&running, ",");
p_data[i].evalue = strtod (token, NULL);
if (written == 0)
{
printf ("Creating blast table.\n");
const char *blast_scores_data_field_names[BLAST_SCORES_DATA_FIELD_NUM] =
BLAST_SCORES_DATA_FIELD_NAMES;
herr_t status = H5TBmake_table ("blast", file_id,
"blast",
BLAST_SCORES_DATA_FIELD_NUM, 1,
dst_size,
blast_scores_data_field_names,
dst_offset, field_type,
chunk_size, fill_data,
compress,
&p_data);
if (status < 0)
check_h5_error (__FILE__, __LINE__);
written = 1;
i = -1;
current_line = 0;
}
if ((current_line % 10000 == 0) && (current_line > 0))
{
herr_t status =
H5TBappend_records (file_id, "blast", 10000,
dst_size, dst_offset, dst_sizes,
&p_data[0]);
if(status < 0)
check_h5_error (__FILE__, __LINE__);
status = H5Fflush (file_id, H5F_SCOPE_GLOBAL);
if (status < 0)
check_h5_error (__FILE__, __LINE__);
printf ("Processed %i records.\n", current_line);
written += 10000;
i = -1;
}
if (running)
free (running);
} // End for each line of the input file.
if (i >= 0)
{
herr_t status =
H5TBappend_records (file_id, "blast", i+1,
dst_size, dst_offset, dst_sizes, &p_data[0]);
if (status < 0)
check_h5_error (__FILE__, __LINE__);
printf ("Wrote %i records.\n", written + i + 1);
}
herr_t status = H5Fflush (file_id, H5F_SCOPE_GLOBAL);
if (status < 0)
check_h5_error (__FILE__, __LINE__);
if (line)
free (line);
fclose (dat);
return;
}
|
