Another Reverse Complement Question...

[lkenefic]

This node falls below the community's threshold of quality. You may see it by logging in.

[johngg]

It might be that tr (see Quote and Quote like Operators) will perform your reverse complement.

knoppix@Microknoppix:~$ perl -E '
> $seq = q{ACTGTGGCGTCAACTG};
> say $seq;
> ( $revSeq = $seq ) =~ tr{ATCG}{TAGC};
> say $revSeq;'
ACTGTGGCGTCAACTG
TGACACCGCAGTTGAC
knoppix@Microknoppix:~$

I hope this is helpful.

[Cristoforo]

I don't work with BioPerl, but they do have a reverse complement method, revcom and it can be used like this example:

#!/usr/bin/perl
use strict;
use warnings;
use 5.014;
use Bio::PrimarySeq;

my $seqobj = Bio::PrimarySeq->new(-seq      => 'ACTGTGGCGTCAACTG',
                                  -alphabet => 'dna',
                                  -id       => 'test');

say $seqobj->seq;
say $seqobj->revcom->seq;

__END__
*** print out

ACTGTGGCGTCAACTG
CAGTTGACGCCACAGT

But this doesn't do the translation you want: A => T, C => G, G => C and T => A. So, I don't know if this is any help.

Update: After examining the reversed complement sequence, I see indeed it performs the complement as you stated but it also reverses the sequence with the first letter in the original being complemented and last in the reversed sequence, the second in the original complemented and being next to last in the reversed complement sequence, etc.

[snape]

You haven't use while loop to read the file line by line after opening the file. You don't have to use <STDIN> when you have initialized $infile before. You use <STDIN> when you want the input from the user/keyboard. Also, you haven't defined your file handler. It should be :

my $infile = "xxx_capillary_SNPs.txt\n"; 
open IN, $infile or die "open infile failed\n";
while(<IN>){

## do your reverse complement
}
close(IN);

[snape]

Please refer to the following link before posting your code