Edit alignement.py

alignement.py

@@ -27,8 +27,17 @@ class Alignement:
         """
         cherche aussi les hits
         :param kmer_list:
-        :param genome:
-        :return:
+        :param genome: genome obj
+        :return: position kmer dans la sequence query avec la position de la correspondance dans le genome
+
+        exemple :
+        >>> query = "ATGGAT"
+        >>> genome = "ATGATGATGATG"
+        >>> kmer = 3
+        >>> alignement = Alignement(query_objet, genome_objet, kmer)
+        >>> seeds = alignement.search_seed()
+        >>> print(seeds)
+        [[0, 6], [0, 3], [0, 0]]
         """
         k = self.get_taille_kmer()
         liste = []
@@ -57,21 +66,6 @@ class Alignement:
         :param query:
         :param genome:
         :return:
-
-        liste = []
-        seeds = self.search_seed()
-        # alignement semi-global
-        for seed in seeds:
-            genome = self.genome[seed:self.taille_kmer + seed]
-            align_sg = parasail.sg_dx_trace_scan_sat(query, genome, 5, 1, parasail.dnafull)
-            score = align_sg.score
-            traceback = align_sg.get_traceback()
-
-        # seq align (query = read, ref = génome)
-            align_seq_query = traceback.query
-            align_seq_genome = traceback.ref
-            liste.append(score, align_seq_query, align_seq_genome)
-
         """
         seeds = self.search_seed()
         print(seeds)