5 files changed, 208 insertions, 0 deletions

diff --git a/src/load/load_blast_scores.c b/src/load/load_blast_scores.c
new file mode 100644
index 0000000..42e6bd9
--- a/dev/null
+++ b/src/load/load_blast_scores.c
@@ -0,0 +1,119 @@
+#include "error/check_error.h"
+#include "error/check_h5_error.h"
+#include "model/blast_scores_data.h"
+#include "model/blast_scores_data_init.h"
+#include "load_blast_scores.h"
+#include <hdf5_hl.h>
+#include <string.h>
+#include <stdlib.h>
+
+void
+load_blast_scores (hid_t file_id, const char *file_name)
+{
+  size_t dst_size;
+  size_t dst_offset[BLAST_SCORES_DATA_FIELD_NUM];
+  size_t dst_sizes[BLAST_SCORES_DATA_FIELD_NUM];
+  hid_t field_type[BLAST_SCORES_DATA_FIELD_NUM];
+
+  blast_scores_data_init (&dst_size, dst_offset, dst_sizes, field_type);
+
+  hsize_t chunk_size = 10;
+  int *fill_data = NULL;
+  int compress = 0;
+
+  blast_scores_data p_data[1000];
+  FILE *dat = fopen (file_name, "r");
+  if (dat == NULL)
+    check_error (__FILE__, __LINE__);
+  char *line = NULL;
+  size_t len = 0;
+  int current_line = 0;
+  int i = -1;
+
+  while (getline (&line, &len, dat) != -1)
+    {
+      current_line++;
+      i++;
+
+      char *running = strdup (line);
+      char *token = NULL;
+      
+      token = strsep (&running, ",");
+      p_data[i].source_gi = atoi (&token[4]);
+
+      token = strsep (&running, ",");
+      p_data[i].source_start = atoi (token);
+
+      token = strsep (&running, ",");
+      p_data[i].source_end = atoi (token);
+
+      token = strsep (&running, ",");
+      p_data[i].target_gi = atoi (&token[4]);
+
+      token = strsep (&running, ",");
+      p_data[i].target_start = atoi (token);
+
+      token = strsep (&running, ",");
+      p_data[i].target_end = atoi (token);
+
+      token = strsep (&running, ",");
+      p_data[i].score = atoi (token);
+
+      token = strsep (&running, ",");
+      p_data[i].bit_score = strtod (token, NULL);
+
+      token = strsep (&running, ",");
+      p_data[i].evalue = strtod (token, NULL);
+
+      if (current_line == 1)
+        {
+          
+          const char *blast_scores_data_field_names[BLAST_SCORES_DATA_FIELD_NUM] =
+            BLAST_SCORES_DATA_FIELD_NAMES;
+
+          herr_t status = H5TBmake_table ("blast", file_id,
+                                          "blast",
+                                          BLAST_SCORES_DATA_FIELD_NUM, 1,
+                                          dst_size,
+                                          blast_scores_data_field_names,
+                                          dst_offset, field_type,
+                                          chunk_size, fill_data,
+                                          compress,
+                                          &p_data);
+
+          if (status < 0)
+            check_h5_error (__FILE__, __LINE__);
+
+        }
+
+      if ((i % 1000 == 0) && (i > 0))
+        {
+
+          herr_t status =
+            H5TBappend_records (file_id, "blast", 1000,
+                                dst_size, dst_offset, dst_sizes,
+                                &p_data[0]);
+          if(status < 0)
+            check_h5_error (__FILE__, __LINE__);
+
+          status = H5Fflush (file_id, H5F_SCOPE_GLOBAL);
+          if (status < 0)
+            check_h5_error (__FILE__, __LINE__);
+
+          printf ("Processed %i of records.\n", current_line);
+
+          i = -1;
+        }
+
+      if (running)
+        free (running);
+
+    } // End for each line of the input file.
+
+  if (line)
+    free (line);
+
+  fclose (dat);
+
+  return;
+}