Since you're working with fasta files, consider becoming familiar with Bio::SeqIO--a module that's a powerful tool for working with fasta and other such formats.

For example, to achieve your desired results using the module, you can do the following:

use strict;
use warnings;
use Bio::SeqIO;

my $in  = Bio::SeqIO->new( -file => 'file1.fasta',  -format => 'Fasta'
+ );
my $out = Bio::SeqIO->new( -file => '>file2.fasta', -format => 'Fasta'
+ );

while ( my $seq = $in->next_seq() ) {
    my $newSeq = Bio::Seq->new(
        -display_id => $seq->id,
        -seq        => 'aaaa' . $seq->seq
    );
    $out->write_seq($newSeq);
}
[download]

Output results:

>dddd
aaaaabcdef
>eeee
aaaabcdef
[download]

Notice that the module permits you to access sequences and ids as objects, using the "->" notation. For example, in the above, we prepend "aaaa" to the original sequence by doing the following:

'aaaa' . $seq->seq
[download]

Then, create a new object with the modified sequence that's written to a new file.

The module offers many more options for working with fasta (and other similarly formatted) files.

Hope this helps!

G'day intect,

This technique should do what you want:

$ perl -Mstrict -Mwarnings -e '
    my @fasta = (">dddd\n", "abcdef\n", ">eeee\n", "bcdef\n");

    for (@fasta) {
        print "aaaa" unless /^>/;
        print;
    }
'
>dddd
aaaaabcdef
>eeee
aaaabcdef
[download]

Using your filehandles, that would be:

while (<$input_fh>) {
    print $output_fh 'aaaa' unless /^>/;
    print $output_fh $_;
}
[download]

If the ACGAGTGCGT in your code is supposed to be the aaaa in your description, then just make the appropriate substitution. If it isn't, a clarification would be useful.

Thank you, Ken. It works very well. Would you help me identify the problem in my script. I moved the print after unless block but it still does not work.

"Thank you, Ken. It works very well."

You're welcome.

"Would you help me identify the problem in my script."

Happy to.

"I moved the print after unless block but it still does not work."

Unfortunately, that doesn't help me to help you. What exactly did you move? Where precisely did you move it to? What does "it still does not work" mean?

You need to provide code along with expected results, actual results, and any error or warnings messages. This is all described in more detail in the "How do I post a question effectively?" guidelines.

Here's what choroba was referring to:

$ perl -Mstrict -Mwarnings -e '
    my @fasta = (">dddd\n", "abcdef\n", ">eeee\n", "bcdef\n");

    for (@fasta) {
        unless (/^>/) {
            s/^/ACGAGTGCGT/;
        }

        print;
    }
'
>dddd
ACGAGTGCGTabcdef
>eeee
ACGAGTGCGTbcdef
[download]

That may give you your answer. If not, post the requested information so that we can provide genuine help as opposed to guesswork.

-- Ken

Hopefully choroba's post gave you the solution, but, if not or if you need more, please explain what a a connected long sequence is. Or give an example.