Re: add letters to the begin of the sentence

in reply to add letters to the begin of the sentence

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 Section Seekers of Perl Wisdom