By: Alexandre

Alexandre — Wed, 11 Jun 2008 01:45:30 +0000

Here is some alternative implementations of your translate function.

def translate_dna_0(sequence): proteinseq = '' for n in range(0,len(sequence),3): # "obj == True" is ugly, use the keyword 'is', as "obj is True" # for testing singleton like True, False and None, or even # better omit it completely. if gencode.has_key(sequence[n:n+3]) == True: # String concatenation is quadratic Python. Since strings are # immutable, a new string object needs to be created every time. # However, the main Python implementation does concatenation quite # efficiently, so the performance benefits are not extraordinaire. proteinseq += gencode[sequence[n:n+3]] return proteinseq


def translate_dna_1(sequence):

    # Use a list to avoid the quadratic behavior of string

    # concatenation.

    proteinseq = []

    for n in range(0, len(sequence), 3):

        # Use the idiomatic 'in' keyword to test whether a sequence

        # is in the gencode dictionary.

        if sequence[n:n+3] in gencode:

            proteinseq.append(gencode[sequence[n:n+3]])

    return ''.join(proteinseq)
def translate_dna_2(sequence):

    # Alternative implementation: use re.findall to split the sequence

    # into nucleotides.

    proteinseq = []

    for nucleo in re.findall("...", sequence):

        if nucleo in gencode:

            proteinseq.append(gencode[nucleo])

    return ''.join(proteinseq)

def translate_dna_3(sequence): # Alternative implementation: use re.sub with a callable to do the whole # translation. Short, but slow due to the function call overhead. def replace(match): return gencode[match.group(0)] return re.sub("...", replace, sequence)

Comments on: Translating DNA into proteins: second approach, now using FASTA files

By: Alexandre