Edit Sequence.py

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