| -rw-r--r-- | src/aggregator.c | 33 | ||||
| -rw-r--r-- | src/assign/assign_blast_scores.c | 11 | ||||
| -rw-r--r-- | src/assign/assign_protein_type.c | 28 | ||||
| -rw-r--r-- | src/updator.c | 2 |
4 files changed, 60 insertions, 14 deletions
diff --git a/src/aggregator.c b/src/aggregator.c index c789502..8057bb3 100644 --- a/src/aggregator.c +++ b/src/aggregator.c @@ -8,15 +8,25 @@ #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 "/u/ac/dpellegr/Documents/exp004/genomes/INFLUENZA/influenza_aa.dat" -#define INFLUENZA_FAA "/u/ac/dpellegr/Documents/exp004/genomes/INFLUENZA/influenza.faa" +#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."); + exit (0); + } + /* * Create a new HDF5 file if it does not already exist. If an * existing file is found then open it. @@ -40,15 +50,26 @@ main () /* * 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", - INFLUENZA_AA_DAT); - load_influenza_aa_dat (file_id, INFLUENZA_AA_DAT); + loc1); + load_influenza_aa_dat (file_id, loc1); + free (loc1); /* * Load the FASTA protein sequence data file. */ - printf ("Loading \"influenza.faa\" with contents of %s.\n", INFLUENZA_FAA); - load_influenza_faa (file_id, INFLUENZA_FAA); + 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 BLAST scores. |
