reverse-complement description

Background

… by knowing the sequence of bases of one strand of DNA we immediately know the sequence of the DNA strand which will bind to it, this strand is called the reverse complement …

HN discussion

How to implement

We ask that contributed programs not only give the correct result, but also use the same algorithm to calculate that result.

Each program should:

• read line-by-line a redirected FASTA format file from stdin

  (grow the data, buffered-read by buffered-read; don't get the size and make a single allocation.)

• for each sequence:

  • write the id, description, and the reverse-complement sequence in FASTA format to stdout

Use these code complements:

code  meaning   complement
A    A                   T
C    C                   G
G    G                   C
T/U  T                   A
M    A or C              K
R    A or G              Y
W    A or T              W
S    C or G              S
Y    C or T              R
K    G or T              M
V    A or C or G         B
H    A or C or T         D
D    A or G or T         H
B    C or G or T         V
N    G or A or T or C    N

diff program output for this 10KB input file (generated with the fasta program N = 1000) with this output file to check your program output has the correct format, before you contribute your program.

Generate a larger input file (using one of the fasta programs with command line arguments: 25000000 > input25000000.txt) to check program performance.