A more general solution is to write your regex to find the sequence ID rather than removing the '>' character. 

$pattern = qr/^(\w*)/;
if ($line =~ /$pattern/) {
    my $id = $1;
    $I++;
    print "$i: $id \n";
}

[download]

This approach would exclude the optional sequence description if it were included in the fasta file.

UPDATE: AnomalousMonk is correct. I accidentally omitted the '<' from my regex.

Bill

In reply to Re: Pattern finding and printing with regex by BillKSmith
in thread Pattern finding and printing with regex by kernelpanic@thedisco

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