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package App::RL::Command::stat; |
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14
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9243
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use strict; |
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406
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70
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use warnings; |
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14
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331
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66
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use autodie; |
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79
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14
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83213
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use App::RL -command; |
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145
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7
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14
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4751
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use App::RL::Common; |
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14
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351
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8
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71
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use constant abstract => 'coverage statistics on chromosomes for runlists'; |
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14
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13604
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10
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11
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sub opt_spec { |
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return ( |
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7
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7
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1
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59
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[ "outfile|o=s", "Output filename. [stdout] for screen." ], |
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[ "size|s=s", "chr.sizes", { required => 1 } ], |
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[ "remove|r", "Remove 'chr0' from chromosome names." ], |
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[ "mk", "YAML file contains multiple sets of runlists." ], |
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[ "all", "Only write whole genome stats." ], |
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{ show_defaults => 1, } |
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); |
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} |
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22
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sub usage_desc { |
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7
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1
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52272
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return "runlist stat [options] "; |
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} |
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26
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sub description { |
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1
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1
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1
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1280
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my $desc; |
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1
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3
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$desc .= ucfirst(abstract) . ".\n"; |
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1
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return $desc; |
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} |
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32
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sub validate_args { |
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5
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7161
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my ( $self, $opt, $args ) = @_; |
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5
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100
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if ( @{$args} != 1 ) { |
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21
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1
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my $message = "This command need one input file.\n\tIt found"; |
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1
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$message .= sprintf " [%s]", $_ for @{$args}; |
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3
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38
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1
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$message .= ".\n"; |
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1
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$self->usage_error($message); |
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} |
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4
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for ( @{$args} ) { |
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42
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4
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50
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next if lc $_ eq "stdin"; |
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4
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100
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if ( !Path::Tiny::path($_)->is_file ) { |
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1
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129
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$self->usage_error("The input file [$_] doesn't exist."); |
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} |
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} |
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48
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3
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245
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if ( !exists $opt->{outfile} ) { |
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0
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0
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$opt->{outfile} = Path::Tiny::path( $args->[0] )->absolute . ".csv"; |
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} |
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} |
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53
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sub execute { |
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3
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3
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1
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my ( $self, $opt, $args ) = @_; |
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56
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#----------------------------# |
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# Loading |
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#----------------------------# |
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3
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my $infile; # YAML::Syck::LoadFile handles IO::* |
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3
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50
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14
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if ( lc $args->[0] eq 'stdin' ) { |
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0
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0
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$infile = *STDIN; |
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} |
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else { |
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3
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$infile = $args->[0]; |
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} |
66
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67
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3
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18
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my $length_of = App::RL::Common::read_sizes( $opt->{size}, $opt->{remove} ); |
68
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69
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3
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10
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my $s_of = {}; |
70
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3
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7
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my @keys; |
71
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3
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100
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10
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if ( $opt->{mk} ) { |
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1
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6
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my $yml = YAML::Syck::LoadFile($infile); |
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1
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140
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@keys = sort keys %{$yml}; |
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1
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7
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74
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75
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1
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4
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for my $key (@keys) { |
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$s_of->{$key} |
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5
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= App::RL::Common::runlist2set( $yml->{$key}, $opt->{remove} ); |
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} |
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} |
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else { |
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2
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@keys = ("__single"); |
82
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$s_of->{__single} |
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2
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= App::RL::Common::runlist2set( YAML::Syck::LoadFile($infile), $opt->{remove} ); |
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} |
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86
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#----------------------------# |
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# Calcing |
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#----------------------------# |
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3
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24
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my $out_fh; |
90
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3
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50
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19
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if ( lc( $opt->{outfile} ) eq "stdout" ) { |
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3
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18
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$out_fh = *STDOUT; |
92
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} |
93
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else { |
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0
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0
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open $out_fh, ">", $opt->{outfile}; |
95
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} |
96
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97
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3
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10
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my $header = sprintf "key,chr,chr_length,size,coverage\n"; |
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3
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100
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11
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if ( $opt->{mk} ) { |
99
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1
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50
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5
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if ( $opt->{all} ) { |
100
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1
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5
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$header =~ s/chr\,//; |
101
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} |
102
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1
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4
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my @lines = ($header); |
103
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104
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1
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3
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for my $key (@keys) { |
105
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5
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14
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my @key_lines = csv_lines( $s_of->{$key}, $length_of, $opt->{all} ); |
106
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5
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14
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$_ = "$key,$_" for @key_lines; |
107
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5
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54
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push @lines, @key_lines; |
108
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} |
109
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110
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1
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3
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print {$out_fh} $_ for @lines; |
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6
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74
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111
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} |
112
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else { |
113
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2
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16
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$header =~ s/key\,//; |
114
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2
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100
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13
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if ( $opt->{all} ) { |
115
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1
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5
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$header =~ s/chr\,//; |
116
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} |
117
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2
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11
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my @lines = ($header); |
118
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119
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2
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16
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push @lines, csv_lines( $s_of->{__single}, $length_of, $opt->{all} ); |
120
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2
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30
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print {$out_fh} $_ for @lines; |
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20
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305
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121
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} |
122
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123
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3
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46
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close $out_fh; |
124
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} |
125
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126
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sub csv_lines { |
127
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7
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7
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0
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18
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my $set_of = shift; |
128
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7
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13
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my $length_of = shift; |
129
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7
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20
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my $all = shift; |
130
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131
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7
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13
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my @lines; |
132
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7
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16
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my ( $all_length, $all_size, $all_coverage ); |
133
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7
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11
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for my $chr ( sort keys %{$set_of} ) { |
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7
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40
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134
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37
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72
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my $length = $length_of->{$chr}; |
135
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37
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103
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my $size = $set_of->{$chr}->size; |
136
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37
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10267
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my $coverage = sprintf "%.4f", $size / $length; |
137
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138
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37
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60
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$all_length += $length; |
139
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37
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56
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$all_size += $size; |
140
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141
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37
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121
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push @lines, "$chr,$length,$size,$coverage\n"; |
142
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} |
143
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7
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27
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$all_coverage = sprintf "%.4f", $all_size / $all_length; |
144
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145
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# only keep whole genome |
146
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7
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23
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my $all_line = "all,$all_length,$all_size,$all_coverage\n"; |
147
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7
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100
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19
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if ($all) { |
148
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6
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16
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@lines = (); |
149
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6
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22
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$all_line =~ s/all,//; |
150
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} |
151
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7
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17
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push @lines, $all_line; |
152
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153
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7
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25
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return @lines; |
154
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} |
155
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156
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1; |