Like this:   s/(?<=[^n])n|n(?=[^n])/^/ig

Hey, thanks for quick reply! where do I put this line? I mean how do I use it? Thanks

shell$ perl -pi.bak -le 's/(?<=[^n])n|n(?=[^n])/^/ig' yourfile.txt
[download]

will do the substitution and leave a backup file named yourfile.txt.bak

UPDATE: it will not work, because your file has newlines (somehow I missed it). Try this instead:

perl -pi.bak -0377 -e 's/n([n\n]*)n/^$1^/ig' yourfile.txt
[download]

[]s, HTH, Massa

What does "large file" mean in your context? Of what file sizes are you speaking?

I think this could be a solution for files less than 100 MB. Didn't test it... (with large files)

#!/usr/bin/perl
use strict;
use warnings;

{
    local $/;
    my $data = <DATA>;

    $data =~ s/((?:n+\n?)+n+)/replace($1)/gme;

    print $data, "\n";

    sub replace {
        my $s = shift;

        substr( $s, 0, 1, '^' );
        substr( $s, -1, 1, '^' );

        return $s;
    }
}
__DATA__
acacccacacacaccacacccacacaccacacccacacccacacaccaca
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
cccacaccacacccacacaccacacaccacacccacacccacacacacca
cacccacacaccacacccacacacaccctaaccctaacccctaaccccta
accctaacccnnnnnnnnnnnnnnnnnnnnnnnnnnnccctaaccctaac
ccctaaccctaaccctaaccgtaaccctaaccctttaccctaacccgaac
ccctaacnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnggggg
gaccctgaccgtgaccctgaccctaacccgaacccgaacccgaaccccga
accccgaaccccgaaccccaaccccaaccccaaccccaaccctaacccct
caccctcaccctcgacccccgacccccgacccccgacccccaccccgaac
ggnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnaccctaaccctaaaaccctaaccctagcc
ctagccctagccctagccctaacccctaacccctaaccctaagccgaagc
[download]

Thanks, The files are up to 1G...

Ok, what about newlines? Are there newlines in your datafiles? Or are they just one long string consisting of character class [a-zA-Z]?

update:
I know that for DNA information the character class can be much smaller ;o))

massa's post made me think about my script. I wonder why I got stuck to the idea to let an extra subroutine do the replacement... and why I forgot everything about character classes...

Here's an updated version of my script without an extra subroutine. All work is done by the regex. And the DNA data is now read from a file (so if your system has enough memory this might hopefully work for you).

#!/usr/bin/perl
use strict;
use warnings;

my $file = shift @ARGV;

die "no dna file specified!\n" if !defined $file;

open my $fh, '<', $file or die "$file: $!\n";
my $data = do { local $/; <$fh> };
close $fh;

$data =~ s/n([nN\n]+)n/^$1^/gm;

print $data, "\n";

__END__
[download]

Never forget the edge cases.

No!, all n sequences are > 30

#!/usr/bin/perl -w

use strict;
use warnings;

my $filename = shift;

open my $fh,'<',$filename or die "No input file\n";
open my $ofh, '>', "$filename.new" or die "Can't open output file\n";

my $previousline= undef;

while (<$fh>) {
    chomp;
    s/(?<=[^n])n|n(?=[^n])/^/ig; #borrowed from jwkrahn
    if (defined $previousline) {
    ($previousline=~/[^n]$/i) and (s/^n/^/i);  
    (/^[^n]/i) and ($previousline=~s/n$/^/i);  
    print $ofh $previousline,"\n";
    }
    $previousline= $_;
}

print $ofh $previousline,"\n" if (defined $previousline);

close $fh; close $ofh;

rename "$filename.new",$filename;
[download]

This replaces the first and last n in each n run with ^ (rather than quoting the n run). It also "quotes" all n runs, not just the first and last as required by the OP.

---

Perl is environmentally friendly - it saves trees

Read again. The OP wanted a replacement and not a quote.

I made sure now by making a diff between the output of my program and what he gave as wanted. Absolutely identical.

use strict;
use warnings;

open my $dnaFH, q{<}, \ <<'EOD' or die qq{open: HEREDOC: $!\n};
acacccacacacaccacacccacacaccacacccacacccacacaccaca
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
cccacaccacacccacacaccacacaccacacccacacccacacacacca
cacccacacaccacacccacacacaccctaaccctaacccctaaccccta
accctaacccnnnnnnnnnnnnnnnnnnnnnnnnnnnccctaaccctaac
ccctaaccctaaccctaaccgtaaccctaaccctttaccctaacccgaac
ccctaacnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnggggg
gaccctgaccgtgaccctgaccctaacccgaacccgaacccgaaccccga
accccgaaccccgaaccccaaccccaaccccaaccccaaccctaacccct
caccctcaccctcgacccccgacccccgacccccgacccccaccccgaac
ggnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnaccctaaccctaaaaccctaaccctagcc
ctagccctagccctagccctaacccctaacccctaaccctaagccgaagc
gaccctgannnnnnncccccgaccccnnnnnnngccctaaccctaaccct
gaccctgannnnnnnnnnnnnnctaacccgaacccgaacccgaaccnnnn
EOD

my $rxReplaceN = qr
   {(?xi)
       (?<![nN\n])n
       |
       n(?![nN\n])
       |
       n(?=\n[^nN])
       |
       n(?=\n\z)
   };

my $outFile = q{spw697207.out};
open my $outFH, q{>}, $outFile
   or die qq{open: > $outFile: $!\n};

my $acc = q{};

while ( 1 )
{
    emitAcc(), last if eof $dnaFH;
    $acc .= <$dnaFH>;
    emitAcc() unless $acc =~ m{[nN]$};
}

close $dnaFH or die qq{close: HEREDOC: $!\n};
close $outFH or die qq{close: > $outFile: $!\n};

sub emitAcc
{
    $acc =~ s{$rxReplaceN}{^}g;
    print $outFH $acc;
    $acc = q{};
}
[download]

The output.

acacccacacacaccacacccacacaccacacccacacccacacaccaca
^nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn^
cccacaccacacccacacaccacacaccacacccacacccacacacacca
cacccacacaccacacccacacacaccctaaccctaacccctaaccccta
accctaaccc^nnnnnnnnnnnnnnnnnnnnnnnnn^ccctaaccctaac
ccctaaccctaaccctaaccgtaaccctaaccctttaccctaacccgaac
ccctaac^nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn^ggggg
gaccctgaccgtgaccctgaccctaacccgaacccgaacccgaaccccga
accccgaaccccgaaccccaaccccaaccccaaccccaaccctaacccct
caccctcaccctcgacccccgacccccgacccccgacccccaccccgaac
gg^nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnn^accctaaccctaaaaccctaaccctagcc
ctagccctagccctagccctaacccctaacccctaaccctaagccgaagc
gaccctga^nnnnn^cccccgacccc^nnnnn^gccctaaccctaaccct
gaccctga^nnnnnnnnnnnn^ctaacccgaacccgaacccgaacc^nn^
[download]

I hope this is of interest.

Cheers,

JohnGG

Well, if you've got enough memory you could read the entire file into memory and use a regex. Alternatively, you could read the file a character at a time (read the documentation for $/), and change the current character if it's /n/i and the previous one wasn't, or the previous character if it's /n/i and the current one isn't. I've got to run some errands, so I'll try to post some code later.

Update: this is an answer to the wrong question! It solves the problem of quoting only the first and last n/N runs. The OP wants to replace the first and last N/n in each run with ^.

The following (rather fussy because of special cases) code remembers where the last N/n run started then rewrites the last part of the output file with the markers inserted.

use strict;
use warnings;

my $data = <<DATA;
acacccacacacaccacacccacacaccacacccacacccacacaccaca
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
cccacaccacacccacacaccacacaccacacccacacccacacacacca
cacccacacaccacacccacacacaccctaaccctaacccctaaccccta
accctaacccnnnnnnnnnnnnnnnnnnnnnnnnnnnccctaaccctaac
ccctaaccctaaccctaaccgtaaccctaaccctttaccctaacccgaac
ccctaacnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnggggg
gaccctgaccgtgaccctgaccctaacccgaacccgaacccgaaccccga
accccgaaccccgaaccccaaccccaaccccaaccccaaccctaacccct
caccctcaccctcgacccccgacccccgacccccgacccccaccccgaac
ggnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnaccctaaccctaaaaccctaaccctagcc
ctagccctagccctagccctaacccctaacccctaaccctaagccgaagc
DATA

my $result;

open my $inFile,  '<', \$data or die "Unable to open input fille: $!\n
+";
open my $outFile, '>', \$result or die "Unable to create output file: 
+$1\n";

my $currStartN;
my $lastStartN;
my $lastEndN;
my $prevLineEnd = 0;

while (<$inFile>) {
    my $runEnd;

    if (defined $currStartN) {
        # Looking for an end N/n
        next unless /([^nN\n])/; # Continue if full line of N/n

        $runEnd = $-[0];
        # Insert ^ for first run
        if ($runEnd == 0) {
            # Need to insert ^ at end of previous line
            seek $outFile, $prevLineEnd, 0;
            print $outFile "^\n";
        } else {
            substr $_, $runEnd, 0, '^' unless defined $lastStartN;
        }

    } else {
        # Looking for a start N/n
        next unless /([nN]+)/;

        $runEnd = $+[0];
        $currStartN = tell ($inFile) - length ($_) + $-[0];
        s/([nN])/^$1/ unless defined $lastStartN; # Insert ^ for first
+ run
        next unless $runEnd < length ($_) - 2; # Continue if full line
+ of N/n
    }

    $lastStartN = $currStartN;
    $lastEndN = tell ($inFile) - length ($_) + $runEnd;
    $currStartN = undef;

} continue {
    $prevLineEnd = tell $outFile;
    print $outFile $_;
    chomp;
    $prevLineEnd += length;
}

# Insert ^ around last run of N/n
seek $outFile, $lastStartN + 2, 0;
print $outFile '^';

seek $inFile, $lastStartN, 0;
read $inFile, my $nRun, ($lastEndN - $lastStartN - 1);
print $outFile $nRun, '^';
print $outFile $_ while <$inFile>;

close $inFile;
close $outFile;

print $result;
[download]

Prints:

acacccacacacaccacacccacacaccacacccacacccacacaccaca
^nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn^
cccacaccacacccacacaccacacaccacacccacacccacacacacca
cacccacacaccacacccacacacaccctaaccctaacccctaaccccta
accctaacccnnnnnnnnnnnnnnnnnnnnnnnnnnnccctaaccctaac
ccctaaccctaaccctaaccgtaaccctaaccctttaccctaacccgaac
ccctaacnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnggggg
gaccctgaccgtgaccctgaccctaacccgaacccgaacccgaaccccga
accccgaaccccgaaccccaaccccaaccccaaccccaaccctaacccct
caccctcaccctcgacccccgacccccgacccccgacccccaccccgaac
gg^nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnn^naccctaaccctaaaaccctaaccctagcc
ctagccctagccctagccctaacccctaacccctaaccctaagccgaagc
[download]