view release on metacpan or  search on metacpan

lib/App/Fasops/Command/xlsx.pm  view on Meta::CPAN

        27,    # Lite Turquoise
        44,    # Pale Blue          0b100
        46,    # Lavender
        47,    # Tan
        24,    # Periwinkle
        49,    # Aqua
        51,    # Gold
        45,    # Rose
        52,    # Light Orange
        26,    # Ivory
        29,    # Coral
        31,    # Ice Blue

        #        30,    # Ocean Blue
        #        41,    # Light Turquoise, again
        #        48,    # Light Blue
        #        50,    # Lime
        #        54,    # Blue-Gray
        #        62,    # Indigo
    );

    for my $i ( 0 .. $#colors ) {
        $bg_of->{$i}{bg_color} = $colors[$i];

    }
    $bg_of->{unknown}{bg_color} = 9;    # White

    # snp base
    my $snp_fg_of = {
        'A' => { color => 58, },        # Dark Green
        'C' => { color => 18, },        # Dark Blue
        'G' => { color => 28, },        # Dark Purple
        'T' => { color => 16, },        # Dark Red
        'N' => { color => 8, },         # Black
        '-' => { color => 8, },         # Black
    };

    for my $fg ( keys %{$snp_fg_of} ) {
        for my $bg ( keys %{$bg_of} ) {
            $format_of->{snp}{"$fg$bg"} = $workbook->add_format(
                font   => 'Courier New',
                size   => 10,
                align  => 'center',
                valign => 'vcenter',
                %{ $snp_fg_of->{$fg} },
                %{ $bg_of->{$bg} },
            );
        }
    }
    $format_of->{snp}{'-'} = $workbook->add_format(
        font   => 'Courier New',
        size   => 10,
        align  => 'center',
        valign => 'vcenter',
    );

    for my $bg ( keys %{$bg_of} ) {
        $format_of->{indel}->{$bg} = $workbook->add_format(
            font   => 'Courier New',
            size   => 10,
            bold   => 1,
            align  => 'center',
            valign => 'vcenter',
            %{ $bg_of->{$bg} },
        );
    }

    return $format_of;
}

# store all variations
sub get_vars {
    my $seq_refs = shift;
    my $opt      = shift;

    # outgroup
    my $out_seq;
    if ( $opt->{outgroup} ) {
        $out_seq = pop @{$seq_refs};
    }

    my $seq_count = scalar @{$seq_refs};
    if ( $seq_count < 2 ) {
        Carp::confess "Too few sequences [$seq_count]\n";
    }

    my $indel_sites = App::Fasops::Common::get_indels($seq_refs);
    if ( $opt->{outgroup} ) {
        App::Fasops::Common::polarize_indel( $indel_sites, $out_seq );
    }

    my $snp_sites = App::Fasops::Common::get_snps($seq_refs);
    if ( $opt->{outgroup} ) {
        App::Fasops::Common::polarize_snp( $snp_sites, $out_seq );
    }

    my %variations;
    for my $site ( @{$indel_sites} ) {
        if ( $opt->{nocomplex} and $site->{indel_freq} == -1 ) {
            next;
        }

        if ( $opt->{nosingle} and $site->{indel_freq} <= 1 ) {
            next;
        }

        if ( $opt->{noindel} ) {
            next;
        }

        if ( defined $opt->{min} and $site->{indel_freq} / $seq_count < $opt->{min} ) {
            next;
        }
        if ( defined $opt->{max} and $site->{indel_freq} / $seq_count > $opt->{max} ) {
            next;
        }

        $site->{var_type} = 'indel';
        $variations{ $site->{indel_start} } = $site;
    }