local $/ = "";
while (<>) {
    # should have a whole record
    # split up 4 line record
    my (@line) = split( "\n");
    # change if necessary to check we have a valid record
    if ($line[0] =~ /^@/) {
       $line[1] =~ s/([ACGT]{5})$//;
       $line[3] =~ s/(\w{5})$//;
       print join("\n", @line);
    }
}

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If you spot any bugs in my solutions, it's because I've deliberately left them in as an exercise for the reader! :-)

In reply to Re^2: Removing nucleotide frm sequence by space_monk
in thread Removing nucleotide frm sequence by bingalee

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