| -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 @@ #include "assign_protein_type.h" #include "check_ncbi_error.h" +#include "check_h5_error.h" #include <ncbi.h> #include <readdb.h> #include <blast.h> #include <salpacc.h> #include <stdbool.h> +#include <hdf5_hl.h> /* * BLAST database containing all of the influenza protein sequences. @@ -45,6 +47,33 @@ assign_protein_type (hid_t file_id) ValNodePtr error_returns = NULL; /* + * Read the data from HDF5 file. + */ + hsize_t nfields; + hsize_t nrecords; + herr_t status = H5TBget_table_info (file_id, "influenza.faa", &nfields, + &nrecords); + if (status < 0) + check_h5_error (status, __FILE__, __LINE__); + + /* + * todo: Allocate memory of nrecords for dst_buf. + * + * todo: Refactor code to share structres in read and write HDF5 + * calls. + */ + + status = H5TBread_table (file_id, "influenza.faa", dst_size, dst_offset, + dst_sizes, dst_buf); + if (status < 0) + check_h5_error (status, __FILE__, __LINE__); + + for (int i = 0; i < nrecords; i++) + { + + } + + /* * Read the sequence from the database by GI. */ Int4 sequence_number = readdb_gi2seq (seqdb, 453644, NULL); |
