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

    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" );
    }

    my $out_fh;
    if ( lc( $opt->{outfile} ) eq "stdout" ) {
        $out_fh = *STDOUT{IO};
    }
    else {
        open $out_fh, ">", $opt->{outfile};
    }

    # csv object
    my $csv = Text::CSV_XS->new( { eol => $/, } );

    # headers
    my @headers = qw{
        first legnth comparables identities differences gaps ns errors D indel
    };
    $csv->print( $out_fh, \@headers );

    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;
            my $seq_refs = [];

            for my $key ( keys %{$info_of} ) {
                push @full_names, $key;
                push @{$seq_refs}, $info_of->{$key}{seq};
            }

            if ( $opt->{length} ) {
                next if length $info_of->{ $full_names[0] }{seq} < $opt->{length};
            }

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

            my $first_name  = $full_names[0];
            my $result      = App::Fasops::Common::multi_seq_stat($seq_refs);
            my $indel_sites = App::Fasops::Common::get_indels($seq_refs);

            $csv->print( $out_fh, [ $first_name, @{$result}, scalar( @{$indel_sites} ) ] );
        }
        else {
            $content .= $line;
        }
    }

    close $out_fh;
    $in_fh->close;
}

1;