New command and C functions: obi ecotag

src/obi_ecotag.h

@@ -0,0 +1,71 @@
+/*************************************************************************************************
+ * Header file for functions for the taxonomic assignment of sequences 							 *
+ *************************************************************************************************/
+
+/**
+ * @file obi_ecotag.h
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ * @date November 15th 2018
+ * @brief Header file for the functions for the taxonomic assignment of sequences.
+ */
+
+
+#ifndef OBI_ECOTAG_H_
+#define OBI_ECOTAG_H_
+
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <stdbool.h>
+
+
+
+#define ECOTAG_TAXID_COLUMN_NAME "TAXID"
+#define ECOTAG_NAME_COLUMN_NAME "SCIENTIFIC_NAME"
+#define ECOTAG_STATUS_COLUMN_NAME "ID_STATUS"
+#define ECOTAG_BEST_MATCH_IDS_COLUMN_NAME "BEST_MATCH"
+#define ECOTAG_SCORE_COLUMN_NAME "BEST_IDENTITY"
+
+
+/**
+ * @brief Taxonomic assignment of sequences.
+ *
+ * Note: The columns where the results are written are automatically named and created.
+ *
+ * @param dms_name The path to the DMS where the views are.
+ * @param query_view_name The name of the view containing the query sequences.
+ * @param ref_dms_name The name of the DMS containing the reference database.
+ * @param ref_view_name The name of the view corresponding to the reference database as built by build_reference_db().
+ * @param taxo_dms_name The name of the DMS containing the taxonomy associated with the reference database.
+ * @param taxonomy_name The name of the taxonomy associated with the reference database.
+ * @param output_view_name The name to give to the output view.
+ * @param output_view_comments The comments to associate to the output view.
+ * @param ecotag_threshold The threshold at which to assign.
+ *
+ * 	The algorithm works like this:
+ * 		For each query sequence:
+ *			Align with reference database
+ *			Keep the indices of all the best matches
+ *			For each kept index, get the LCA at that threshold as stored in the reference database, then the LCA of those LCAs
+ *			Write result (max score, threshold, taxid and scientific name of the LCA assigned, list of the ids of the best matches)
+ *
+ * @returns A value indicating the success of the operation.
+ * @retval 0 if the operation was successfully completed.
+ * @retval -1 if an error occurred.
+ *
+ * @since November 2018
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_ecotag(const char* dms_name,
+		       const char* query_view_name,
+			   const char* ref_dms_name,
+			   const char* ref_view_name,
+			   const char* taxo_dms_name,
+			   const char* taxonomy_name,
+			   const char* output_view_name,
+			   const char* output_view_comments,
+			   double ecotag_threshold);
+
+
+#endif /* OBI_ECOTAG_H_ */
+