Upload New File : reads

reads.py

+import gzip
+from Bio import SeqIO
+
+
+class Read_file:
+    """
+    Represente un fichier compressé fasta ou fastq, contenant un ou plusieurs reads
+    """
+    def __init__(self, file: str):
+        """
+        constructeur d'un objet Read
+        :param file: str, le chemin vers un fichier compressé fastq ou fasta
+        """
+        self.it = None
+        self.file = file
+        self.extension = "rt"
+        if 'fastq.gz' in self.file:
+            self. method = "fastq"
+        if '.fna.gz' in self.file or '.fasta' in self.file:
+            self.method = "fasta"
+
+    def __len__(self) -> int:
+        """
+        permet de compter le nombre de reads dans un objet Read
+        :return: int
+        """
+        count = 0
+        with gzip.open(self.file, self.extension) as fichier:
+            for _ in SeqIO.parse(fichier, self.method):
+                count += 1
+        return count
+
+    def next(self):
+        """
+        appelle l'itérateur
+        :return: it
+        """
+        with gzip.open(self.file, self.extension):
+            return next(self.it)
+
+    def get_read(self, nb: int) -> str:
+        """
+        renvoie la sequence du read voulue selon sa position dans le fichier
+        :param nb: int, une position
+        :return:
+        """
+        with gzip.open(self.file, self.extension) as fichier:
+            record = SeqIO.parse(fichier, self.method)
+            for _ in range(0, (nb - 1)):
+                record.__next__()
+            return str(record.__next__().seq)
+
+    def fin(self):
+        count = 0
+        while count < len(self.file):
+            seq = self.next()
+            kmer = seq.kmers()
+
+    def concat_fasta(self, output):
+        """
+
+        :param output:
+        :return:
+        """
+        with open(output, "w") as out_fasta:
+            with gzip.open(self.file, self.extension) as fichier:
+                record = SeqIO.parse(fichier, self.method)
+                for n in range(0, self.__len__()):
+                    out_fasta.write(str(record.__next__().seq))
+        print(f"fin, resultat dans {output}")
+
+
+if __name__ == "__main__":
+    G = "/home/m1miso/pacome.riobe.etu/PycharmProjects/pythonProject_petitebete/petitgenome.fna.gz"
+    Q = "/home/m1miso/pacome.riobe.etu/PycharmProjects/pythonProject_petitebete/petitquery.fastq.gz"
+    genome = Read_file(G)
+    query = Read_file(Q)
+
+    print("___")
+    print("len")
+    print("___")
+    print(query.__len__())
+