Python Programming for Biology: Bioinformatics and Beyond

Example: reverse transcribe a DNA sequence

To  illustrate  what  we  have  described  with  a  more  realistic  situation,  next  we  define  a

function  which  will  take  a  string  of  letters  representing  a  DNA  or  RNA  sequence  as  an

input argument and create the reverse complement sequence, which is the sequence of an

opposing  strand  that  will  form  a  tight  interaction  through  hydrogen-bonding  base  pairs

(see

Chapter  11

 for  further  explanation).  Naturally  we  give  the  function  an  informative

name,  and  specify  two  input  arguments,  one  which  is  mandatory  and  represents  the

sequence and the other which is optional to indicate whether we have a DNA sequence (A,

C, G and T letters) or an RNA sequence (A, C, G and U letters). This optional argument is

named isDna and defaults to True, i.e. that we have a DNA sequence, not RNA.

def reverseComplement(sequence, isDna=True):

from string import maketrans

if isDna:

sequence = sequence.replace('U','T')

transTable = maketrans('ATGC', 'TACG') else:

sequence = sequence.replace('T','U')

transTable = maketrans('AUGC', 'UACG')

complement = sequence.translate(transTable)

reverseComp = complement[::-1]

return reverseComp

Internally  this  function  relies  on  the  translate()  function  which  is  built  into  Python

strings  (like  the  input  sequence)  and  the  maketrans  function  that  is  imported  from  the

string  module;  this  makes  a  character  substitution  table  between  equivalently  positioned

letters from two strings. Also, it is notable that we use the replace() function of strings to

guard against having the wrong kinds of letter (i.e. T versus U) in the input compared to

the isDna argument. The upshot of all of this is that the input sequence has letters swapped

according  to  the  pairs  G

↔  C  and  A  ↔  T  for  DNA  or  A  ↔  U  for  RNA  to  create

complement. The reverse of this reverseComp is generated using the handy slice notation

with  a  negative  step  ([::-1]).  This  final  string  is  what  we  want  to  pass  back  from  the

function, and thus we use it with return at the end. The function is readily tested with some

example sequence strings:

seq1 = 'GATTACA'

seq2 = "AUGGUG"

print(reverseComplement(seq1)) # TGTAATC

print(reverseComplement(seq1, isDna=False)) # UGUAAUC

print(reverseComplement(seq2, False)) # CACCAU