diff --git a/alignement.py b/alignement.py index c209192f4f357ee3b5153017249c0680f04191fc..44d3ff01bdaacbef1c09d4919b4c413c68694efb 100644 --- a/alignement.py +++ b/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)