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.

-- Ken

In reply to Re: add letters to the begin of the sentence by kcott
in thread add letters to the begin of the sentence by intect

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.