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#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>
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[1000];
FILE *dat = fopen (file_name, "r");
if (dat == NULL)
check_error (__FILE__, __LINE__);
char *line = NULL;
size_t len = 0;
int current_line = 0;
int i = -1;
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 (current_line == 1)
{
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__);
}
if ((i % 1000 == 0) && (i > 0))
{
herr_t status =
H5TBappend_records (file_id, "blast", 1000,
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 of records.\n", current_line);
i = -1;
}
if (running)
free (running);
} // End for each line of the input file.
if (line)
free (line);
fclose (dat);
return;
}
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