diff --git a/Sequence.py b/Sequence.py index 16e832e4213220f16536e8f19a89593d5004fb40..15f48ecd251798eee7aa27cd51df8b684b58bb45 100644 --- a/Sequence.py +++ b/Sequence.py @@ -24,6 +24,12 @@ class Sequence: """ construit la table des suffixes :return: list, la table des suffixes + + exemple : + >>> genome = "ATTCATGACCAGGTGCTGTCCAGGCTGAATGACCAGGTCGGATTATAGGCTATGACCAGGATGC" + >>> genome_obj = Sequence(genome) + >>> genome_obj.suffix_array() + [27, 54, 31, 7, 57, 46, 21, 34, 10, 44, 51, 28, 4, 60, 41, 0, 63, 56, 20, 33, 9, 3, 55, 19, 32, 8, 38, 49, 24, 15, 26, 53, 30, 6, 59, 40, 62, 48, 23, 14, 58, 39, 47, 22, 35, 11, 17, 36, 12, 45, 43, 50, 2, 18, 37, 25, 52, 29, 5, 61, 13, 16, 42, 1] """ return sorted(range(len(self.sequence)), key=lambda i: self.sequence[i:]) @@ -32,6 +38,12 @@ class Sequence: renvoie la liste des kmers ; les kmers chevauchants sont filtrés :param k: int, la taille des kmers :return: list, les kmers + + exemple : + >>> query = "ATGACCAATTCATGACCAGGTGCTGTCCAGGCTGAATG" + >>> query_obj = Sequence(query) + >>> query_obj.kmers(11) + [0, 5, 10, 15, 20, 25, 27] """ self.taille_kmer = k kmers = [] # dict @@ -52,6 +64,12 @@ class Sequence: """ renvoie la sequencede l'objet Sequence :return: str, la sequence + + exemple : + >>> seq = "ATGACCAATTCATGACCAGGTGCTGTCCAGGCTGAATG" + >>> seq_obj = Sequence(seq) + >>> seq_obj.get_sequence() + ATGACCAATTCATGACCAGGTGCTGTCCAGGCTGAATG """ return self.sequence