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/*
* Aggregate the collected influenza data into a single HDF5
* container.
*/
#include "error/check_h5_error.h"
#include "load/load_asn.h"
#include "load/load_blast_scores.h"
#include "load/load_features.h"
#include "load/load_influenza_aa_dat.h"
#include "load/load_influenza_faa.h"
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#define BLASTFILE "run20090807.del"
#define H5FILE "influenza.h5"
#define INFLUENZA_AA_DAT "/genomes/INFLUENZA/influenza_aa.dat"
#define INFLUENZA_FAA "/genomes/INFLUENZA/influenza.faa"
int
main ()
{
char* exp004 = getenv ("EXP004");
if (exp004 == NULL)
{
printf ("EXP004 environment variable not set. This should be set to the "
"directory containing the genomes/INFLUENZA data.\n");
exit (0);
}
/*
* Create a new HDF5 file if it does not already exist. If an
* existing file is found then open it.
*/
hid_t file_id = 0;
FILE *f = fopen (H5FILE, "r+");
if (f == NULL)
{
file_id = H5Fcreate (H5FILE, H5F_ACC_EXCL, H5P_DEFAULT, H5P_DEFAULT);
if (file_id < 0)
check_h5_error (__FILE__, __LINE__);
}
else
{
fclose (f);
file_id = H5Fopen (H5FILE, H5F_ACC_RDWR, H5P_DEFAULT);
if (file_id < 0)
check_h5_error (__FILE__, __LINE__);
}
/*
* Load the supplementary protein data file.
*/
/*
char* loc1 = malloc (strlen (exp004) + strlen (INFLUENZA_AA_DAT) + 1);
loc1[0] = '\0';
strcat (loc1, exp004);
strcat (loc1, INFLUENZA_AA_DAT);
printf ("Loading \"influenza_aa.dat\" with contents of %s.\n",
loc1);
load_influenza_aa_dat (file_id, loc1);
free (loc1);
*/
/*
* Load the FASTA protein sequence data file.
*/
/*
char* loc2 = malloc (strlen (exp004) + strlen (INFLUENZA_FAA) + 1);
loc2[0] = '\0';
strcat (loc2, exp004);
strcat (loc2, INFLUENZA_FAA);
printf ("Loading \"influenza.faa\" with contents of %s.\n",
loc2);
load_influenza_faa (file_id, loc2);
free (loc2);
*/
/*
* Load the Entrez features.
*/
// load_features (file_id, "efetch-protein-0.xml");
load_asn (file_id, "453644.asn");
/*
* Load the BLAST scores.
*/
/*
printf ("Loading \"blast\" with contents of %s.\n",
BLASTFILE);
load_blast_scores (file_id, BLASTFILE);
*/
/*
* Close the HDF5 file.
*/
herr_t status = H5Fclose (file_id);
if (status < 0)
check_h5_error (__FILE__, __LINE__);
return 0;
}
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