dnastring.py

#gc_content
#base_count('G')
#reverse_complement

#G to C
#T to A
# this code allows to calculate the GC content of a sequence from a given fasta file
class NucleotideString:
    base_complement = {'G': 'C', 'C':'G',
                       'A': 'T', 'T': 'A'}
    
    def __init__(self, sequence):
        self.sequence = sequence
        self.bases = {}
    
    def base_count(self, base):
        if base in self.bases:
            return self.bases[base]
        else:
            self.bases[base] = self.sequence.count(base)
            return self.bases[base]
    def gc_content(self):
        g = self.base_count('G')
        c = self.base_count('C')
        return float(g+c)/len(self.sequence)
    def reverse_complement(self):
        complement = ''        
        for base in self.sequence:
            complement = self.base_complement[base] + complement
        
        return complement
class DNAString(NucleotideString):
    pass
class RNAString(NucleotideString):
    base_complement = {'G': 'C', 'C':'G',
                       'A': 'U', 'U': 'A'}