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DNA-RNAclasses.py

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+
+# coding: utf-8
+
+# In[ ]:
+
+
+# Dna class. Inherited from str class.
+class Dna(str):
+    def __init__(self, sequence):
+        DNAcharlist = ('A', 'C', 'G', 'T', 'S', 'W', 'R', 
+                       'Y', 'K', 'M', 'B', 'D', 'H', 'V', 'N')
+        badseq = False
+        trueseq = ''
+        for char in sequence:
+            if char.upper() in DNAcharlist:
+                trueseq += char
+            else:
+                badseq = True
+                continue
+        self.sequence = trueseq
+        if badseq:
+            print ('While initializing Dna object non-DNA characters were omitted')
+        if len (sequence) == 0:
+            print ('Empty DNA sequence was created. Using gc() function will return None')
+
+    def __repr__(self):
+        return (self.sequence)
+
+    def __str__(self):
+        return (self.sequence)
+
+# transcribe function returns transcription 
+# in coordinates [transcr_start : transcr_end] 
+# as an Rna class object
+# whole sequence is transcribed by default
+    def transcribe(self, transcr_start = 1, transcr_end = None): 
+        if transcr_end == None:
+            transcr_end = len(self)
+        Rnatext = self.sequence[(transcr_start-1):transcr_end].replace('T', 'U').replace('t', 'u')
+        return Rna(Rnatext)
+
+# gc() function returns None if sequence length is 0 
+# or all characters are ambiguous
+    def gc(self):
+        DNAgcdict = {'A': 0, 'C': 1, 'G': 1, 'T': 0, 'S': 1, 'W': 0}
+        notforgc = ['R', 'Y', 'K', 'M', 'B', 'D', 'H', 'V', 'N']
+        gcs = 0
+        definedbps = len(self.sequence)
+        if len(self.sequence) == 0:
+            return None
+        for char in self.sequence:
+            if char in notforgc:
+                definedbps -= 1
+            else:
+                gcs += DNAgcdict[char.upper()]
+        if definedbps == 0:
+            return None
+        else:
+            return (round(gcs / definedbps, 2))
+
+# reverse_complement() function returns Dna object 
+# of complementary strand in 5' - 3' orientation
+    def reverse_complement(self):
+        DNArcdict = {'A': 'T', 'C': 'G', 'G': 'C', 'T': 'A', 
+                     'S': 'W', 'W': 'S', 'R': 'Y', 'Y': 'R', 
+                     'K': 'M', 'M': 'K', 'B': 'V', 'D': 'H', 
+                     'H': 'D', 'V': 'B', 'N': 'N'}
+        rcseq = ''
+        for char in self.sequence:
+            if char.isupper():
+                rcseq = DNArcdict[char] + rcseq
+            else:
+                rcseq = DNArcdict[char.upper()].lower() + rcseq
+        return Dna(rcseq)
+
+
+# Rna class. Inherited from str class. Same as Dna, 
+# except transcribe() function is impossible
+class Rna(str):
+    def __init__(self, sequence):
+        RNAcharlist = ('A', 'C', 'G', 'U', 'S', 'W', 'R', 
+                       'Y', 'K', 'M', 'B', 'D', 'H', 'V', 'N')
+        badseq = False
+        trueseq = ''
+        for char in sequence:
+            if char.upper() in RNAcharlist:
+                trueseq += char
+            else:
+                badseq = True
+                continue
+        self.sequence = trueseq
+        if badseq:
+            print ('While initializing Rna object non-RNA characters were omitted')
+        if len (sequence) == 0:
+            print ('Empty RNA sequence was created. Using gc() function will return None')
+
+    def __repr__(self):
+        return (self.sequence)
+
+    def __str__(self):
+        return (self.sequence)
+
+# gc() function returns None if sequence length is 0 
+# or all characters are ambiguous
+    def gc(self):
+        RNAgcdict = {'A': 0, 'C': 1, 'G': 1, 'U': 0, 'S': 1, 'W': 0}
+        notforgc = ['R', 'Y', 'K', 'M', 'B', 'D', 'H', 'V', 'N']
+        gcs = 0
+        definedbps = len(self.sequence)
+        if len(self.sequence) == 0:
+            return None
+        for char in self.sequence:
+            if char in notforgc:
+                definedbps -= 1
+            else:
+                gcs += RNAgcdict[char.upper()]
+        if definedbps == 0:
+            return None
+        else:
+            return (round(gcs / definedbps, 2))
+
+# reverse_complement() function returns Rna object 
+# of complementary sequence in 5' - 3' orientation
+    def reverse_complement(self):
+        RNArcdict = {'A': 'U', 'C': 'G', 'G': 'C', 'U': 'A', 
+                     'S': 'W', 'W': 'S', 'R': 'Y', 'Y': 'R', 
+                     'K': 'M', 'M': 'K', 'B': 'V', 'D': 'H', 
+                     'H': 'D', 'V': 'B', 'N': 'N'}
+        rcseq = ''
+        for char in self.sequence:
+            if char.isupper():
+                rcseq = RNArcdict[char] + rcseq
+            else:
+                rcseq = RNArcdict[char.upper()].lower() + rcseq
+        return Rna(rcseq)
+