Routines to load the results of a BLAST run into the HDF5 file.

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;
+}
diff --git a/src/load/load_blast_scores.h b/src/load/load_blast_scores.h
new file mode 100644
index 0000000..e41968d
--- a/dev/null
+++ b/src/load/load_blast_scores.h
@@ -0,0 +1,11 @@
+#ifndef LOAD_BLAST_SCORES_H
+#define LOAD_BLAST_SCORES_H
+
+#include <hdf5.h>
+
+/*
+ * Load the results of a BLAST run into the HDF5 container.
+ */
+void load_blast_scores (hid_t file_id, const char *file_name);
+
+#endif // LOAD_BLAST_SCORES_H
diff --git a/src/model/blast_scores_data.h b/src/model/blast_scores_data.h
new file mode 100644
index 0000000..8c4aaef
--- a/dev/null
+++ b/src/model/blast_scores_data.h
@@ -0,0 +1,21 @@
+#ifndef BLAST_SCORES_DATA_H
+#define BLAST_SCORES_DATA_H
+
+#define BLAST_SCORES_DATA_FIELD_NUM 9
+
+#define BLAST_SCORES_DATA_FIELD_NAMES { "Source GI", "Source Start", "Source End", "Target GI", "Target Start", "Target End", "Score", "Bit Score", "Evalue" }
+
+typedef struct
+{
+  int source_gi;
+  int source_start;
+  int source_end;
+  int target_gi;
+  int target_start;
+  int target_end;
+  int score;
+  double bit_score;
+  double evalue;
+} blast_scores_data;
+
+#endif // BLAST_SCORES_DATA_H
diff --git a/src/model/blast_scores_data_init.c b/src/model/blast_scores_data_init.c
new file mode 100644
index 0000000..14fa6f0
--- a/dev/null
+++ b/src/model/blast_scores_data_init.c
@@ -0,0 +1,43 @@
+#include "blast_scores_data_init.h"
+#include "blast_scores_data.h"
+
+void
+blast_scores_data_init (size_t *dst_size, size_t *dst_offset, size_t *dst_sizes,
+                        hid_t *field_type)
+{
+  *dst_size = sizeof (blast_scores_data);
+
+  dst_offset[0] = HOFFSET (blast_scores_data, source_gi);
+  dst_offset[1] = HOFFSET (blast_scores_data, source_start);
+  dst_offset[2] = HOFFSET (blast_scores_data, source_end);
+  dst_offset[3] = HOFFSET (blast_scores_data, target_gi);
+  dst_offset[4] = HOFFSET (blast_scores_data, target_start);
+  dst_offset[5] = HOFFSET (blast_scores_data, target_end);
+  dst_offset[6] = HOFFSET (blast_scores_data, score);
+  dst_offset[7] = HOFFSET (blast_scores_data, bit_score);
+  dst_offset[8] = HOFFSET (blast_scores_data, evalue);
+
+  blast_scores_data dst_buf[1];
+
+  dst_sizes[0] = sizeof (dst_buf[0].source_gi);
+  dst_sizes[1] = sizeof (dst_buf[0].source_start);
+  dst_sizes[2] = sizeof (dst_buf[0].source_end);
+  dst_sizes[3] = sizeof (dst_buf[0].target_gi);
+  dst_sizes[4] = sizeof (dst_buf[0].target_start);
+  dst_sizes[5] = sizeof (dst_buf[0].target_end);
+  dst_sizes[6] = sizeof (dst_buf[0].score);
+  dst_sizes[7] = sizeof (dst_buf[0].bit_score);
+  dst_sizes[8] = sizeof (dst_buf[0].evalue);
+
+  field_type[0] = H5T_NATIVE_INT;
+  field_type[1] = H5T_NATIVE_INT;
+  field_type[2] = H5T_NATIVE_INT;
+  field_type[3] = H5T_NATIVE_INT;
+  field_type[4] = H5T_NATIVE_INT;
+  field_type[5] = H5T_NATIVE_INT;
+  field_type[6] = H5T_NATIVE_INT;
+  field_type[7] = H5T_NATIVE_DOUBLE;
+  field_type[8] = H5T_NATIVE_DOUBLE;
+
+  return;
+}
diff --git a/src/model/blast_scores_data_init.h b/src/model/blast_scores_data_init.h
new file mode 100644
index 0000000..cae6edd
--- a/dev/null
+++ b/src/model/blast_scores_data_init.h
@@ -0,0 +1,14 @@
+#ifndef BLAST_SCORES_DATA_INIT_H
+#define BLAST_SCORES_DATA_INIT_H
+
+#include <hdf5.h>
+
+/*
+ * Initialize the structures describing the struct.  These descriptive
+ * structures are used by the HDF5 API.
+ */
+void
+blast_scores_data_init (size_t *dst_size, size_t *dst_offset, size_t *dst_sizes,
+                        hid_t *field_type);
+
+#endif // BLAST_SCORES_DATA_INIT_H