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lib/Bio/MUST/Core/GeneticCode/Factory.pm  view on Meta::CPAN

#  ...
# }
    my %code_for;

    for my $code (@codes) {

        # get all names and id for current code
        my ($id)      = $code =~ m/   id    \s*   (\d+)   /xms;
        my @names     = $code =~ m/ name    \s* \"(.*?)\" /xmsg;
        @names = map {       s{\n}{}xmsgr } @names;     # remove newline chars
        @names = map { split m{;\s*}xms }   @names;     # demultiplex names

        # retrieve the amino acid line
        my ($aa_line) = $code =~ m/ ncbieaa \s* \"(.*?)\" /xms;
        $aa_line =~ s{\*}{x}xmsg;               # make STOPs MUST-compliant

        # retrieve the three codon lines
        my ($b1_line) = $code =~ m/ Base1   \s* ([TACG]+) /xms;
        my ($b2_line) = $code =~ m/ Base2   \s* ([TACG]+) /xms;
        my ($b3_line) = $code =~ m/ Base3   \s* ([TACG]+) /xms;