4 files changed, 60 insertions, 14 deletions

diff --git a/src/assign/assign_protein_type.c b/src/assign/assign_protein_type.c
index 065880f..52a0b70 100644
--- a/src/assign/assign_protein_type.c
+++ b/src/assign/assign_protein_type.c
@@ -19,18 +19,26 @@
 /*
  * BLAST database containing all of the influenza protein sequences.
  */
-#define SEQDB "/u/ac/dpellegr/Documents/exp004/influenzadb/influenzadb"
+#define SEQDB "/influenzadb/influenzadb"
 
 /*
  * BLAST reference database of prototypical protein types.
  */
-#define REFDB "/u/ac/dpellegr/Documents/exp004/influenzadb/proteinnames"
+#define REFDB "/influenzadb/proteinnames"
 
 #define BUFFER_LEN 50
 
 void
 assign_protein_type (hid_t file_id)
 {
+  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);
+    }
+
   /*
    * Iterate through the records for which no protein type has been
    * assigned.  Create a BioSeq Pointer to the data and then use this
@@ -47,7 +55,12 @@ assign_protein_type (hid_t file_id)
   /*
    * Open the BLAST sequence database.
    */
-  ReadDBFILEPtr seqdb = readdb_new (SEQDB, true);
+  char* loc1 = malloc (strlen (exp004) + strlen (SEQDB) + 1);
+  loc1[0] = '\0';
+  strcat (loc1, exp004);
+  strcat (loc1, SEQDB);
+  ReadDBFILEPtr seqdb = readdb_new (loc1, true);
+  free (loc1);
 
   /*
    * Get default BLAST options.
@@ -215,14 +228,19 @@ assign_protein_type (hid_t file_id)
                              "record set.  See the BLAST formatdb.log file "
                              "for details.\n", faa_buf[i].gi);
             }
-
+          
+          char* loc2 = malloc (strlen (exp004) + strlen (REFDB) + 1);
+          loc2[0] = '\0';
+          strcat (loc2, exp004);
+          strcat (loc2, REFDB);
           SeqAlignPtr seqalign = BioseqBlastEngine (bsp,
                                                     "blastp",
-                                                    REFDB,
+                                                    loc2,
                                                     options,
                                                     NULL,
                                                     &error_returns,
                                                     NULL);
+          free (loc2);
 
           /*
            * BLAST reported an error.  Write it out and continue processing.