问模拟RNA合成的Perl程序

EN

use warnings; use strict;
use feature 'state';


# read_codon works by using the new [state][1] feature in Perl 5.10
# both @buffer and $handle represent 'state' on this function:
# Both permits abstracting reading codons from processing the file
# line-by-line.
# Once read_colon is called for the first time, both are initialized.
# Since $handle is a state variable, the current file handle position
# is never reset. Similarly, @buffer always holds whatever was left
# from the previous call.
# The base case is that @buffer contains less than 3bp, in which case
# we need to read a new line, remove the "\n" character,
# split it and push the resulting list to the end of the @buffer.
# If we encounter EOF on the $handle, then we have exhausted the file,
# and the @buffer as well, so we 'return' undef.
# otherwise we pick the first 3bp of the @buffer, join them into a string,
# transcribe it and return it.

sub read_codon {
    my ($file) = @_;

    state @buffer;
    open state $handle, '<', $file or die $!;

    if (@buffer < 3) {
        my $new_line = scalar <$handle> or return;
        chomp $new_line;
        push @buffer, split //, $new_line;
    }

    return transcribe(
                       join '', 
                       shift @buffer,
                       shift @buffer,
                       shift @buffer
                     );
}

sub transcribe {
    my ($codon) = @_;
    $codon =~ tr/T/U/;
    return $codon;
}


# translate works by using the new [state][1] feature in Perl 5.10
# the $TRANSLATE state is initialized to 0
# as codons are passed to it, 
# the sub updates the state according to start and stop codons.
# Since $TRANSLATE is a state variable, it is only initialized once,
# (the first time the sub is called)
# If the current state is 'translating',
# then the sub returns the appropriate amino-acid from the %codes table, if any.
# Thus this provides a logical way to the caller of this sub to determine whether
# it should print an amino-acid or not: if not, the sub will return undef.
# %codes could also be a state variable, but since it is not actually a 'state',
# it is initialized once, in a code block visible form the sub,
# but separate from the rest of the program, since it is 'private' to the sub

{
    our %codes = (
        AUG => 'M',
        ...
    );

    sub translate {
        my ($codon) = @_ or return;

        state $TRANSLATE = 0;

        $TRANSLATE = 1 if $codon =~ m/AUG/i;
        $TRANSLATE = 0 if $codon =~ m/U(AA|GA|AG)/i;

        return $codes{$codon} if $TRANSLATE;
    }
}