-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/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 @@ | |||
19 | /* | 19 | /* |
20 | * BLAST database containing all of the influenza protein sequences. | 20 | * BLAST database containing all of the influenza protein sequences. |
21 | */ | 21 | */ |
22 | #define SEQDB "/u/ac/dpellegr/Documents/exp004/influenzadb/influenzadb" | 22 | #define SEQDB "/influenzadb/influenzadb" |
23 | 23 | ||
24 | /* | 24 | /* |
25 | * BLAST reference database of prototypical protein types. | 25 | * BLAST reference database of prototypical protein types. |
26 | */ | 26 | */ |
27 | #define REFDB "/u/ac/dpellegr/Documents/exp004/influenzadb/proteinnames" | 27 | #define REFDB "/influenzadb/proteinnames" |
28 | 28 | ||
29 | #define BUFFER_LEN 50 | 29 | #define BUFFER_LEN 50 |
30 | 30 | ||
31 | void | 31 | void |
32 | assign_protein_type (hid_t file_id) | 32 | assign_protein_type (hid_t file_id) |
33 | { | 33 | { |
34 | char* exp004 = getenv ("EXP004"); | ||
35 | if (exp004 == NULL) | ||
36 | { | ||
37 | printf ("EXP004 environment variable not set. This should be set to the " | ||
38 | "directory containing the genomes/INFLUENZA data."); | ||
39 | exit (0); | ||
40 | } | ||
41 | |||
34 | /* | 42 | /* |
35 | * Iterate through the records for which no protein type has been | 43 | * Iterate through the records for which no protein type has been |
36 | * assigned. Create a BioSeq Pointer to the data and then use this | 44 | * assigned. Create a BioSeq Pointer to the data and then use this |
@@ -47,7 +55,12 @@ assign_protein_type (hid_t file_id) | |||
47 | /* | 55 | /* |
48 | * Open the BLAST sequence database. | 56 | * Open the BLAST sequence database. |
49 | */ | 57 | */ |
50 | ReadDBFILEPtr seqdb = readdb_new (SEQDB, true); | 58 | char* loc1 = malloc (strlen (exp004) + strlen (SEQDB) + 1); |
59 | loc1[0] = '\0'; | ||
60 | strcat (loc1, exp004); | ||
61 | strcat (loc1, SEQDB); | ||
62 | ReadDBFILEPtr seqdb = readdb_new (loc1, true); | ||
63 | free (loc1); | ||
51 | 64 | ||
52 | /* | 65 | /* |
53 | * Get default BLAST options. | 66 | * Get default BLAST options. |
@@ -215,14 +228,19 @@ assign_protein_type (hid_t file_id) | |||
215 | "record set. See the BLAST formatdb.log file " | 228 | "record set. See the BLAST formatdb.log file " |
216 | "for details.\n", faa_buf[i].gi); | 229 | "for details.\n", faa_buf[i].gi); |
217 | } | 230 | } |
218 | 231 | ||
232 | char* loc2 = malloc (strlen (exp004) + strlen (REFDB) + 1); | ||
233 | loc2[0] = '\0'; | ||
234 | strcat (loc2, exp004); | ||
235 | strcat (loc2, REFDB); | ||
219 | SeqAlignPtr seqalign = BioseqBlastEngine (bsp, | 236 | SeqAlignPtr seqalign = BioseqBlastEngine (bsp, |
220 | "blastp", | 237 | "blastp", |
221 | REFDB, | 238 | loc2, |
222 | options, | 239 | options, |
223 | NULL, | 240 | NULL, |
224 | &error_returns, | 241 | &error_returns, |
225 | NULL); | 242 | NULL); |
243 | free (loc2); | ||
226 | 244 | ||
227 | /* | 245 | /* |
228 | * BLAST reported an error. Write it out and continue processing. | 246 | * BLAST reported an error. Write it out and continue processing. |