-rw-r--r-- | src/assign_protein_type.c | 29 | ||||
-rw-r--r-- | src/load_influenza_aa_dat.c | 2 | ||||
-rw-r--r-- | src/load_influenza_faa.c | 42 |
3 files changed, 59 insertions, 14 deletions
diff --git a/src/assign_protein_type.c b/src/assign_protein_type.c index 54db84e..1b58f54 100644 --- a/src/assign_protein_type.c +++ b/src/assign_protein_type.c | |||
@@ -1,10 +1,12 @@ | |||
1 | #include "assign_protein_type.h" | 1 | #include "assign_protein_type.h" |
2 | #include "check_ncbi_error.h" | 2 | #include "check_ncbi_error.h" |
3 | #include "check_h5_error.h" | ||
3 | #include <ncbi.h> | 4 | #include <ncbi.h> |
4 | #include <readdb.h> | 5 | #include <readdb.h> |
5 | #include <blast.h> | 6 | #include <blast.h> |
6 | #include <salpacc.h> | 7 | #include <salpacc.h> |
7 | #include <stdbool.h> | 8 | #include <stdbool.h> |
9 | #include <hdf5_hl.h> | ||
8 | 10 | ||
9 | /* | 11 | /* |
10 | * BLAST database containing all of the influenza protein sequences. | 12 | * BLAST database containing all of the influenza protein sequences. |
@@ -45,6 +47,33 @@ assign_protein_type (hid_t file_id) | |||
45 | ValNodePtr error_returns = NULL; | 47 | ValNodePtr error_returns = NULL; |
46 | 48 | ||
47 | /* | 49 | /* |
50 | * Read the data from HDF5 file. | ||
51 | */ | ||
52 | hsize_t nfields; | ||
53 | hsize_t nrecords; | ||
54 | herr_t status = H5TBget_table_info (file_id, "influenza.faa", &nfields, | ||
55 | &nrecords); | ||
56 | if (status < 0) | ||
57 | check_h5_error (status, __FILE__, __LINE__); | ||
58 | |||
59 | /* | ||
60 | * todo: Allocate memory of nrecords for dst_buf. | ||
61 | * | ||
62 | * todo: Refactor code to share structres in read and write HDF5 | ||
63 | * calls. | ||
64 | */ | ||
65 | |||
66 | status = H5TBread_table (file_id, "influenza.faa", dst_size, dst_offset, | ||
67 | dst_sizes, dst_buf); | ||
68 | if (status < 0) | ||
69 | check_h5_error (status, __FILE__, __LINE__); | ||
70 | |||
71 | for (int i = 0; i < nrecords; i++) | ||
72 | { | ||
73 | |||
74 | } | ||
75 | |||
76 | /* | ||
48 | * Read the sequence from the database by GI. | 77 | * Read the sequence from the database by GI. |
49 | */ | 78 | */ |
50 | Int4 sequence_number = readdb_gi2seq (seqdb, 453644, NULL); | 79 | Int4 sequence_number = readdb_gi2seq (seqdb, 453644, NULL); |