Delete sequence

sequence

-import parasail
-
-
-class Sequence:
-    """
-    represente une sequence ADN
-    """
-    def __init__(self, sequence: str):
-        """
-        constructeur d'un objet Sequence
-        :param sequence: str, une sequence ADN
-        """
-        self.sequence = sequence
-        self.taille_kmer = 0
-
-    def __len__(self) -> int:
-        """
-        renvoie la taille de l'objet Sequence
-        :return: int
-        """
-        return len(self.sequence)
-
-    def suffix_array(self) -> list:
-        """
-        construit la table des suffixes
-        :return: list, la table des suffixes
-        """
-        return sorted(range(len(self.sequence)), key=lambda i: self.sequence[i:])
-
-    def kmers(self, k) -> list:
-        """
-        renvoie la liste des kmers ; les kmers chevauchants sont filtrés
-        :param k: int, la taille des kmers
-        :return: list, les kmers
-        """
-        self.taille_kmer = k
-        kmers = []  # dict
-        for i in range(0, (len(self.sequence) - k), int(k/2)):
-            kmers.append(i)
-        return kmers
-
-    def get_kmer(self, kmer):
-        """
-        renvoie le kmer correspondant à sa position entree en parametre
-        :param kmer: int, position du kmer
-        :return:
-        """
-        sequence = self.sequence
-        return sequence[kmer:self.taille_kmer]
-
-    def get_sequence(self) -> str:
-        """
-        renvoie la sequencede l'objet Sequence
-        :return: str, la sequence
-        """
-        return self.sequence
-
-
-def search_kmer(kmer: list, genome: str) -> list:
-    """
-    recherche les hits entre la liste de kmers et le genome
-    :param kmer: list, liste de kmers
-    :param genome: str, une sequence adn
-    :return: list, la liste des positions des hits
-    """
-    liste_positions = []
-    n = 0
-    table_suffixes = genome.suffix_array()
-    valeur_suffixe = int(len(table_suffixes) / 2)
-    while kmer != genome.sequence[valeur_suffixe:valeur_suffixe+len(kmer)]:
-        if kmer < genome.sequence[valeur_suffixe:valeur_suffixe+len(kmer)]:
-            valeur_suffixe = int(valeur_suffixe/2)
-        if kmer > genome.sequence[valeur_suffixe:valeur_suffixe+len(kmer)]:
-            valeur_suffixe += int((len(table_suffixes) - valeur_suffixe)/2)
-        if kmer == genome.sequence[valeur_suffixe:valeur_suffixe+len(kmer)]:
-            val_egale = valeur_suffixe
-            liste_positions.append(valeur_suffixe)
-            if val_egale > 0 and kmer == genome.sequence[valeur_suffixe:valeur_suffixe+len(kmer)]:
-                valeur_suffixe = valeur_suffixe - 1
-                if kmer == genome.sequence[valeur_suffixe:valeur_suffixe+len(kmer)]:
-                    liste_positions.append(valeur_suffixe)
-            if val_egale < len(genome):
-                val_egale = val_egale + 1
-                if kmer == genome.sequence[val_egale:val_egale+len(kmer)]:
-                    liste_positions.append(val_egale)
-    return liste_positions
-
-
-def align_sequences(query: str, genome: str):
-    """
-    realise l'alignement
-    :param query: str,
-    :param genome: str,
-    :return: le score, l'alignement
-    """
-    # alignement semi-global
-    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
-    return score, align_seq_query, align_seq_genome
-
-
-if __name__ == "__main__":
-    query = "ATGACCA"
-    genome = "ATTCATGACCAGGTGCTGTCCAGGCTGAATGACCAGGTCGGATTATAGGCTATGACCAGGATGC"
-    genome_objet = Sequence(genome)
-    query_objet = Sequence(query)
-    suffixe_array = genome_objet.suffix_array()
-    for value in suffixe_array:
-        print(genome[value:])