Review RNF34

RNF34.py

@@ -0,0 +1,134 @@
+from abc import ABC, abstractmethod
+
+
+class BiologicalSequence(ABC):
+    @abstractmethod
+    def __init__(self, sequence):
+        pass
+
+    @abstractmethod
+    def __len__(self):
+        pass
+
+    @abstractmethod
+    def __getitem__(self, slc):
+        pass
+
+    @abstractmethod
+    def __str__(self):
+        pass
+
+    @abstractmethod
+    def __repr__(self):
+        pass
+
+    @abstractmethod
+    def is_valid_alphabet(self):
+        pass
+
+
+class NucleicAcid(BiologicalSequence):
+    def __init__(self, sequence):
+        self.sequence = sequence
+
+    def __len__(self):
+        return len(self.sequence)
+
+    def __getitem__(self, slc):
+        return self.sequence[slc]
+
+    def __str__(self):
+        return str(self.sequence)
+
+    def __repr__(self):
+        return self.sequence
+
+    def is_valid_alphabet(self):
+        alphabet = type(self).ALPHABET
+        if set(self.sequence).issubset(alphabet):
+            return True
+        else:
+            return False
+
+    def complement(self):
+        if type(self) == NucleicAcid:
+            raise NotImplementedError("Cannot complement NucleicAcid instance")
+
+        map_dict = type(self).MAP
+        comp_seq = "".join([map_dict[base] for base in self.sequence])
+
+        return type(self)(comp_seq)
+
+    def gc_content(self):
+        if type(self) == NucleicAcid:
+            raise NotImplementedError("Cannot gc_content NucleicAcid instance")
+        gc_count = sum([1 for base in self.sequence if base in ["C", "G"]])
+        gc_content = (gc_count / len(self)) * 100
+
+        return gc_content
+
+
+class DNASequence(NucleicAcid):
+    ALPHABET = set("ATGC")
+    MAP = {"A": "T", "T": "A", "C": "G", "G": "C"}
+
+    def transcribe(self):
+        transcribed = self.sequence.replace("T", "U")
+
+        return RNASequence(transcribed)
+
+
+class RNASequence(NucleicAcid):
+    ALPHABET = set("AUGC")
+    MAP = {"A": "U", "U": "A", "C": "G", "G": "C"}
+
+
+class AminoAcidSequence(BiologicalSequence):
+    ALPHABET = set("ACDEFGHIKLMNPQRSTVWY")
+
+    def __init__(self, sequence):
+        self.sequence = sequence
+
+    def __len__(self):
+        return len(self.sequence)
+
+    def __getitem__(self, slc):
+        return self.sequence[slc]
+
+    def __str__(self):
+        return str(self.sequence)
+
+    def __repr__(self):
+        return self.sequence
+
+    def is_valid_alphabet(self):
+        alphabet = type(self).ALPHABET
+        if set(self.sequence).issubset(alphabet):
+            return True
+        else:
+            return False
+
+    amino_acid_frequency = {}
+
+    def calculate_aa_freq(self):
+        """
+        Calculates the frequency of each amino acid in a protein sequence or sequences.
+
+        :param sequences: protein sequence or sequences
+        :type sequences: str or list of str
+        :return: dictionary with the frequency of each amino acid
+        :rtype: dict
+        """
+
+        # Creating a dictionary with aminoacid frequencies:
+        amino_acid_frequency = {}
+
+        for amino_acid in self.sequence:
+            # If the aminoacid has been already in:
+            if amino_acid in amino_acid_frequency:
+                amino_acid_frequency[amino_acid] += 1
+            # If the aminoacid hasn't been already in:
+            else:
+                amino_acid_frequency[amino_acid] = 1
+
+        return amino_acid_frequency