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

package App::Fasops::Command::xlsx;
use strict;
use warnings;
use autodie;

use Excel::Writer::XLSX;

use App::Fasops -command;
use App::Fasops::Common;

sub abstract {
    return 'paint substitutions and indels to an excel file';
}

sub opt_spec {
    return (
        [ "outfile|o=s", "Output filename" ],
        [ "length|l=i", "the threshold of alignment length", { default => 1 }, ],
        [ 'wrap=i',     'wrap length',                       { default => 50 }, ],
        [ 'spacing=i',  'wrapped line spacing',              { default => 1 }, ],
        [ 'colors=i',   'number of colors',                  { default => 15 }, ],
        [ 'section=i', 'start section', { default => 1, hidden => 1 }, ],
        [ 'outgroup',  'alignments have an outgroup', ],
        [ 'noindel',   'omit indels', ],
        [ 'nosingle',  'omit singleton SNPs and indels', ],
        [ 'nocomplex', 'omit complex SNPs and indels', ],
        [ 'min=f',     'minimal frequency', ],
        [ 'max=f',     'maximal frequency', ],
        { show_defaults => 1, }
    );
}

sub usage_desc {
    return "fasops xlsx [options] <infile>";
}

sub description {
    my $desc;
    $desc .= ucfirst(abstract) . ".\n";
    $desc .= <<'MARKDOWN';

* <infiles> are paths to axt files, .fas.gz is supported
* infile == stdin means reading from STDIN

MARKDOWN

    return $desc;
}

sub validate_args {
    my ( $self, $opt, $args ) = @_;

    if ( @{$args} != 1 ) {
        my $message = "This command need one input file.\n\tIt found";
        $message .= sprintf " [%s]", $_ for @{$args};
        $message .= ".\n";
        $self->usage_error($message);
    }
    for ( @{$args} ) {
        next if lc $_ eq "stdin";
        if ( !Path::Tiny::path($_)->is_file ) {
            $self->usage_error("The input file [$_] doesn't exist.");
        }
    }

    if ( !exists $opt->{outfile} ) {
        $opt->{outfile} = Path::Tiny::path( $args->[0] )->absolute . ".xlsx";
    }

    if ( $opt->{colors} ) {
        $opt->{colors} = List::Util::min( $opt->{colors}, 15 );
    }
}

sub execute {
    my ( $self, $opt, $args ) = @_;

    #@type IO::Handle
    my $in_fh;
    if ( lc $args->[0] eq "stdin" ) {
        $in_fh = *STDIN{IO};
    }
    else {
        $in_fh = IO::Zlib->new( $args->[0], "rb" );
    }

    # Create workbook and worksheet objects
    #@type Excel::Writer::XLSX
    my $workbook = Excel::Writer::XLSX->new( $opt->{outfile} );

    #@type Excel::Writer::XLSX::Worksheet
    my $worksheet = $workbook->add_worksheet;

    my $format_of       = create_formats($workbook);
    my $max_name_length = 1;

    my $content = '';    # content of one block
    while (1) {
        last if $in_fh->eof and $content eq '';
        my $line = '';
        if ( !$in_fh->eof ) {
            $line = $in_fh->getline;
        }
        next if substr( $line, 0, 1 ) eq "#";

        if ( ( $line eq '' or $line =~ /^\s+$/ ) and $content ne '' ) {
            my $info_of = App::Fasops::Common::parse_block( $content, 1 );
            $content = '';

            my @full_names;