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

            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;
    }

    for my $site ( @{$snp_sites} ) {
        if ( $opt->{nocomplex} and $site->{snp_freq} == -1 ) {
            next;
        }

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

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

        $site->{var_type} = 'snp';
        $variations{ $site->{snp_pos} } = $site;
    }

    return \%variations;
}

# write excel
sub paint_vars {

    #@type Excel::Writer::XLSX::Worksheet
    my $sheet     = shift;
    my $format_of = shift;
    my $opt       = shift;
    my $vars      = shift;
    my $name_refs = shift;

    my $section_start = $opt->{section};
    my $color_loop    = $opt->{colors};

    my %variations     = %{$vars};
    my $section_cur    = $section_start;
    my $col_cursor     = 1;
    my $section_height = ( scalar( @{$name_refs} ) + 1 ) + $opt->{spacing};
    my $seq_count      = scalar @{$name_refs};
    $seq_count-- if $opt->{outgroup};

    for my $pos ( sort { $a <=> $b } keys %variations ) {
        my $var = $variations{$pos};
        my $pos_row = $section_height * ( $section_cur - 1 );

        # write SNPs
        if ( $var->{var_type} eq 'snp' ) {

            # write position
            $sheet->write( $pos_row, $col_cursor, $var->{snp_pos}, $format_of->{pos} );

            for my $i ( 1 .. $seq_count ) {
                my $base = substr $var->{snp_all_bases}, $i - 1, 1;

                my $occ
                    = $var->{snp_occured} eq "unknown"
                    ? 0
                    : substr( $var->{snp_occured}, $i - 1, 1 );

                if ( $occ eq "1" ) {
                    my $bg_idx     = oct( '0b' . $var->{snp_occured} ) % $color_loop;
                    my $base_color = $base . $bg_idx;
                    $sheet->write( $pos_row + $i,
                        $col_cursor, $base, $format_of->{snp}{$base_color} );
                }
                else {
                    my $base_color = $base . "unknown";
                    $sheet->write( $pos_row + $i,
                        $col_cursor, $base, $format_of->{snp}{$base_color} );
                }
            }

            # outgroup bases with no background colors
            if ( $opt->{outgroup} ) {
                my $base_color = $var->{snp_outgroup_base} . "unknown";
                $sheet->write(
                    $pos_row + $seq_count + 1,
                    $col_cursor,
                    $var->{snp_outgroup_base},
                    $format_of->{snp}{$base_color}
                );
            }

            # increase column cursor
            $col_cursor++;
        }

        # write indels
        if ( $var->{var_type} eq 'indel' ) {

            # how many column does this indel take up
            my $col_taken = List::Util::min( $var->{indel_length}, 3 );

            # if exceed the wrap limit, start a new section
            if ( $col_cursor + $col_taken > $opt->{wrap} ) {
                $col_cursor = 1;
                $section_cur++;
                $pos_row = $section_height * ( $section_cur - 1 );
            }

            my $indel_string = "$var->{indel_type}$var->{indel_length}";

            my $bg_idx = 'unknown';
            if ( $var->{indel_occured} ne 'unknown' ) {
                $bg_idx = oct( '0b' . $var->{indel_occured} ) % $color_loop;
            }

            for my $i ( 1 .. $seq_count ) {
                my $flag = 0;
                if ( $var->{indel_occured} eq "unknown" ) {
                    $flag = 1;
                }
                else {
                    my $occ = substr $var->{indel_occured}, $i - 1, 1;
                    if ( $occ eq '1' ) {
                        $flag = 1;
                    }
                }

                if ($flag) {
                    if ( $col_taken == 1 ) {

                        # write position
                        $sheet->write( $pos_row, $col_cursor, $var->{indel_start},
                            $format_of->{pos} );

                        # write in indel occured lineage
                        $sheet->write( $pos_row + $i,
                            $col_cursor, $indel_string, $format_of->{indel}{$bg_idx} );
                    }
                    elsif ( $col_taken == 2 ) {

                        # write indel_start position
                        $sheet->write( $pos_row, $col_cursor, $var->{indel_start},
                            $format_of->{pos} );

                        # write indel_end position
                        $sheet->write( $pos_row, $col_cursor + 1,
                            $var->{indel_end}, $format_of->{pos} );

                        # merge two indel position
                        $sheet->merge_range(
                            $pos_row + $i,
                            $col_cursor,
                            $pos_row + $i,
                            $col_cursor + 1,
                            $indel_string, $format_of->{indel}{$bg_idx},
                        );
                    }
                    else {

                        # write indel_start position
                        $sheet->write( $pos_row, $col_cursor, $var->{indel_start},
                            $format_of->{pos} );

                        # write middle sign
                        $sheet->write( $pos_row, $col_cursor + 1, '|', $format_of->{pos} );

                        # write indel_end position
                        $sheet->write( $pos_row, $col_cursor + 2,
                            $var->{indel_end}, $format_of->{pos} );

                        # merge two indel position
                        $sheet->merge_range(
                            $pos_row + $i,
                            $col_cursor,
                            $pos_row + $i,
                            $col_cursor + 2,
                            $indel_string, $format_of->{indel}{$bg_idx},
                        );
                    }
                }
            }

            # increase column cursor
            $col_cursor += $col_taken;
        }

        if ( $col_cursor > $opt->{wrap} ) {
            $col_cursor = 1;
            $section_cur++;
        }
    }

    # write names
    for my $i ( $section_start .. $section_cur ) {
        my $pos_row = $section_height * ( $i - 1 );

        for my $j ( 1 .. scalar @{$name_refs} ) {
            $sheet->write( $pos_row + $j, 0, $name_refs->[ $j - 1 ], $format_of->{name} );
        }
    }

    $section_cur++;
    return $section_cur;
}

1;