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#include "load_influenza_faa.h"
#include "check_error.h"
#include "check_h5_error.h"
#include "hdf5_hl.h"
#include <string.h>
#include <stdlib.h>
#define SEQUENCE_DATA_FIELD_NUM 4
void
load_influenza_faa (hid_t file_id)
{
typedef struct
{
int gi;
char gb[9];
char description[196];
char protein_type[7];
} sequence_data;
size_t dst_size = sizeof (sequence_data);
size_t dst_offset[SEQUENCE_DATA_FIELD_NUM] =
{ HOFFSET (sequence_data, gi),
HOFFSET (sequence_data, gb),
HOFFSET (sequence_data, description),
HOFFSET (sequence_data, protein_type)
};
sequence_data dst_buf[1];
size_t dst_sizes[SEQUENCE_DATA_FIELD_NUM] = {
sizeof (dst_buf[0].gi),
sizeof (dst_buf[0].gb),
sizeof (dst_buf[0].description),
sizeof (dst_buf[0].protein_type)
};
hid_t field_type[SEQUENCE_DATA_FIELD_NUM];
field_type[0] = H5T_NATIVE_INT;
hid_t gb_type = H5Tcopy (H5T_C_S1);
H5Tset_size (gb_type, 9);
field_type[1] = gb_type;
hid_t description_type = H5Tcopy (H5T_C_S1);
H5Tset_size (description_type, 196);
field_type[2] = description_type;
hid_t protein_type_type = H5Tcopy (H5T_C_S1);
H5Tset_size (protein_type_type, 7);
field_type[3] = protein_type_type;
const char *field_names[SEQUENCE_DATA_FIELD_NUM] =
{ "GI",
"GB",
"Description",
"Protein Type" };
hsize_t chunk_size = 10;
int *fill_data = NULL;
int compress = 0;
sequence_data p_data;
FILE *dat = fopen ("/home/don/exp004/genomes/INFLUENZA/influenza.faa",
"r");
if (dat == NULL)
check_error (__FILE__, __LINE__);
char *line = NULL;
size_t len = 0;
int current_line = 0;
while (getline (&line, &len, dat) != -1)
{
current_line++;
// Header line.
if (line[0] == '>')
{
char *running = strdup (line);
char *token = NULL;
// Eat the ">gi".
strsep (&running, "|");
// GI value.
token = strsep (&running, "|");
p_data.gi = atoi (token);
// Eat the "gb"
strsep (&running, "|");
// GB value.
strncpy (p_data.gb, strsep(&running, "|"), sizeof (p_data.gb));
// Description value.
strncpy (p_data.description, strsep (&running, "|"),
sizeof (p_data.description));
strncpy (p_data.protein_type, "", sizeof (p_data.protein_type));
if (current_line == 1)
{
herr_t status = H5TBmake_table ("influenza.faa", file_id,
"influenza.faa",
SEQUENCE_DATA_FIELD_NUM, 1,
dst_size, field_names,
dst_offset, field_type,
chunk_size, fill_data, compress,
&p_data);
if (status < 0)
check_h5_error (status, __FILE__, __LINE__);
}
else
{
herr_t status =
H5TBappend_records (file_id, "influenza.faa", 1, dst_size,
dst_offset, dst_sizes, &p_data);
if (status < 0)
check_h5_error (status, __FILE__, __LINE__);
}
if (running)
free (running);
}
}
if (line)
free (line);
fclose (dat);
H5Tclose (gb_type);
H5Tclose (description_type);
H5Tclose (protein_type_type);
return;
}
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