class DNA:
"""Class representing DNA as a string sequence."""
basecomplement = {'A': 'T', 'C': 'G', 'T': 'A', 'G': 'C'}
codon2aa = {"TTT":"F","TTC":"F","TTA":"L","TTG":"L","TCT":"S","TCC":"S",
"TCA":"S","TCG":"S","TAT":"Y","TAC":"Y","TAA":"*","TAG":"*",
"TGT":"C","TGC":"C","TGA":"*","TGG":"W","CTT":"L","CTC":"L",
"CTA":"L","CTG":"L","CCT":"P","CCC":"P","CCA":"P","CCG":"P",
"CAT":"H","CAC":"H","CAA":"Q","CAG":"Q","CGT":"R","CGC":"R",
"CGA":"R","CGG":"R","ATT":"I","ATC":"I","ATA":"I","ATG":"M",
"ACT":"T","ACC":"T","ACA":"T","ACG":"T","AAT":"N","AAC":"N",
"AAA":"K","AAG":"K","AGT":"S","AGC":"S","AGA":"R","AGG":"R",
"GTT":"V","GTC":"V","GTA":"V","GTG":"V","GCT":"A","GCC":"A",
"GCA":"A","GCG":"A","GAT":"D","GAC":"D","GAA":"E","GAG":"E",
"GGT":"G","GGC":"G","GGA":"G","GGG":"G"}
def __init__(self, s):
"""Create DNA instance initialized to string s."""
self.seq = s
def transcribe(self):
"""Return as rna string."""
return self.seq.replace('T', 'U')
def reverse(self):
"""Return dna string in reverse order."""
letters = list(self.seq)
letters.reverse()
return ''.join(letters)
def complement(self):
"""Return the complementary dna string."""
letters = list(self.seq)
letters = [self.basecomplement[base] for base in letters]
return ''.join(letters)
def reversecomplement(self):
"""Return the reverse of complement of the dna string."""
letters = list(self.seq)
letters.reverse()
letters = [self.basecomplement[base] for base in letters]
return ''.join(letters)
def gc(self):
"""Return the % of dna composed of G+C."""
s = self.seq
gc = s.count('G') + s.count('C')
return gc * 100.0 / len(s)
def codons(self):
"""Return list of codons for the dna string,"""
s = self.seq
end = len(s) - (len(s) % 3) - 1
codons = [s[i:i+3] for i in range(0, end, 3)]
return codons
def translate(self):
"""Return amino acid sequence translating dna seq."""
s = self.seq
codons = self.codons()
aa = [self.codon2aa[aa] for aa in codons]
return ''.join(aa)
"""
How to use this code...
save this code in a file name as bio.py
then open python terminal and use this as a module
for example...
>>> from bio import *
>>> S = DNA('ATGTGCGTGCTC')
>>> S
<bio.DNA instance at 0x02A09B48>
>>> S.translate()
'MCVL'
>>> S.transcribe()
'AUGUGCGUGCUC'
>>> S.reverse()
'CTCGTGCGTGTA'
>>> S.complement()
'TACACGCACGAG'
>>> S.codons()
['ATG', 'TGC', 'GTG', 'CTC']
>>>
"""
