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package Pheno::Ranker; |
2
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3
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3
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3
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166844
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use strict; |
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3
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25
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3
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89
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4
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3
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3
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15
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use warnings; |
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3
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3
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3
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68
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5
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3
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3
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1017
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use autodie; |
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3
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32153
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3
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14
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6
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3
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3
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19265
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use feature qw(say); |
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6
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3
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398
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7
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3
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3
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2076
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use Data::Dumper; |
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3
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21532
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3
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192
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8
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3
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3
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23
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use File::Basename qw(dirname); |
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5
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3
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273
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9
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3
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3
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20
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use Cwd qw(abs_path); |
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6
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3
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133
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10
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3
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501
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use File::Spec::Functions qw(catdir catfile); |
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979
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3
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153
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3
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3
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3181
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use Moo; |
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26376
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3
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3
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3
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10437
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use Types::Standard qw(Str Int Num Enum ArrayRef HashRef Undef Bool); |
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394683
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3
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44
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13
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3
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3
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14659
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use File::ShareDir::ProjectDistDir qw(dist_dir); |
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3
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115941
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3
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26
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14
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3
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3
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1109
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use List::Util qw(all); |
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7
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3
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307
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15
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3
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2068
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use Pheno::Ranker::IO; |
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8
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3
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282
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3
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2752
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use Pheno::Ranker::Align; |
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15
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3
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250
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17
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3
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3
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21
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use Pheno::Ranker::Stats; |
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5
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3
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181
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18
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19
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3
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3
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19
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use Exporter 'import'; |
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5
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3
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225
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20
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our @EXPORT_OK = qw($VERSION write_json); |
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22
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# Global variables: |
23
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$Data::Dumper::Sortkeys = 1; |
24
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our $VERSION = '0.00_2'; |
25
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our $share_dir = dist_dir('Pheno-Ranker'); |
26
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3
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3
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15
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use constant DEVEL_MODE => 0; |
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3
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6
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3
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6674
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27
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28
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# Misc variables |
29
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my ( |
30
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$config_sort_by, $config_max_out, $config_max_number_var, |
31
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$config_seed, @config_allowed_terms |
32
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); |
33
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my $default_config_file = catfile( $share_dir, 'conf', 'config.yaml' ); |
34
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35
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############################################ |
36
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# Start declaring attributes for the class # |
37
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############################################ |
38
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39
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# Complex defaults here |
40
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has 'config_file' => ( |
41
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default => $default_config_file, |
42
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coerce => sub { |
43
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$_[0] // $default_config_file; |
44
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}, |
45
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is => 'ro', |
46
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isa => sub { die "$_[0] is not a valid file" unless -e $_[0] }, |
47
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trigger => sub { |
48
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my ( $self, $config_file ) = @_; |
49
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my $config = read_yaml($config_file); |
50
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51
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##################### |
52
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# Set config params # |
53
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##################### |
54
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55
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$config_sort_by = $config->{sort_by} // 'hamming'; |
56
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$config_max_out = $config->{max_out} // 50; |
57
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$config_max_number_var = $config->{max_number_var} // 10_000; |
58
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59
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# Validate $config->{allowed_terms} |
60
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unless ( exists $config->{allowed_terms} |
61
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&& ArrayRef->check( $config->{allowed_terms} ) |
62
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&& @{ $config->{allowed_terms} } ) |
63
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{ |
64
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die |
65
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"No <allowed terms> provided or not an array ref at\n$config_file\n"; |
66
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} |
67
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@config_allowed_terms = @{ $config->{allowed_terms} }; |
68
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69
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############################### |
70
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# Set config exclusive params # |
71
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############################### |
72
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$config_seed = |
73
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( defined $config->{seed} && Int->check( $config->{seed} ) ) |
74
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? $config->{seed} |
75
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: 123456789; |
76
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77
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# Set on $self |
78
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$self->{primary_key} = $config->{primary_key} // 'id'; # setter; |
79
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$self->{exclude_properties_regex} = $config->{exclude_properties_regex} |
80
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// ''; # setter |
81
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$self->{array_terms} = $config->{array_terms} // ['foo']; # setter - To validate |
82
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$self->{array_regex} = $config->{array_regex} // '^(\w+):(\d+)'; # setter - To validate |
83
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$self->{format} = $config->{format}; # setter |
84
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85
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# Validate $config->{id_correspondence} if we have "real" array_terms |
86
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if ( $self->{array_terms}[0] ne 'foo' ) { |
87
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unless ( exists $config->{id_correspondence} |
88
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&& HashRef->check( $config->{id_correspondence} ) ) |
89
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{ |
90
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die |
91
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"No <id_correspondence> provided or not a hash ref at\n$config_file\n"; |
92
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} |
93
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$self->{id_correspondence} = $config->{id_correspondence}; # setter |
94
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95
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# Validate format if exists and check that has a match in config->{id_correspondence} |
96
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if ( exists $config->{format} && Str->check( $config->{format} ) ) { |
97
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die |
98
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"<$config->{format}> does not match any key from <id_correspondence>\n" |
99
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unless |
100
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exists $config->{id_correspondence}{ $config->{format} }; |
101
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} |
102
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} |
103
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} |
104
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); |
105
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106
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has sort_by => ( |
107
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default => $config_sort_by, |
108
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is => 'ro', |
109
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coerce => sub { $_[0] // $config_sort_by }, |
110
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lazy => 1, |
111
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isa => Enum [qw(hamming jaccard)] |
112
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); |
113
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114
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has max_out => ( |
115
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default => $config_max_out, # Limit to speed up runtime |
116
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is => 'ro', |
117
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coerce => sub { $_[0] // $config_max_out }, |
118
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lazy => 1, |
119
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isa => Int |
120
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); |
121
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122
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has max_number_var => ( |
123
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default => $config_max_number_var, |
124
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is => 'ro', |
125
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coerce => sub { $_[0] // $config_max_number_var }, |
126
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lazy => 1, |
127
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isa => Int |
128
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); |
129
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130
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has hpo_file => ( |
131
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default => catfile( $share_dir, 'db', 'hp.json' ), |
132
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coerce => sub { |
133
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$_[0] // catfile( $share_dir, 'db', 'hp.json' ); |
134
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}, |
135
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is => 'ro', |
136
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isa => sub { die "$_[0] is not a valid file" unless -e $_[0] }, |
137
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); |
138
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139
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has poi_out_dir => ( |
140
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default => catdir('./'), |
141
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coerce => sub { |
142
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$_[0] // catdir('./'); |
143
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}, |
144
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is => 'ro', |
145
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isa => sub { die "$_[0] dir does not exist" unless -d $_[0] }, |
146
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); |
147
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148
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has [qw /include_terms exclude_terms/] => ( |
149
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is => 'ro', |
150
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lazy => 1, |
151
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152
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#isa => ArrayRef [Enum $config->{allowed_terms}], # It's created at compile time and we don't have $config->{allowed_terms} |
153
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isa => sub { |
154
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my $value = shift; |
155
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die "<--include_terms> and <--exclude_terms> must be an array ref" |
156
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unless ref $value eq 'ARRAY'; |
157
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die |
158
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qq/Invalid term in <--include_terms> or <--exclude_terms>. Allowed values are:\n/, |
159
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( join ',', @config_allowed_terms ), "\n" |
160
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unless all { |
161
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my $term = $_; |
162
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grep { $_ eq $term } @config_allowed_terms |
163
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} @$value; |
164
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}, |
165
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default => sub { [] }, |
166
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); |
167
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168
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has 'cli' => ( |
169
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is => 'ro', |
170
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isa => Bool, |
171
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default => 0, # Set the default value to 0 |
172
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coerce => sub { $_[0] // 0 }, # Coerce to 0 if undefined |
173
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); |
174
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175
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# Miscellanea atributes here |
176
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has [ |
177
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qw/target_file weights_file out_file include_hpo_ascendants align align_basename export export_basename log verbose age/ |
178
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] => ( is => 'ro' ); |
179
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180
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has [qw /append_prefixes reference_files patients_of_interest/] => |
181
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( default => sub { [] }, is => 'ro' ); |
182
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183
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|
########################################## |
184
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# End declaring attributes for the class # |
185
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|
########################################## |
186
|
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|
187
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|
|
sub BUILD { |
188
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|
189
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|
# BUILD: is an instance method that is called after the object has been constructed but before it is returned to the caller. |
190
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# BUILDARGS is a class method that is responsible for processing the arguments passed to the constructor (new) and returning a hash reference of attributes that will be used to initialize the object. |
191
|
8
|
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8
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0
|
314
|
my $self = shift; |
192
|
|
|
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193
|
|
|
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|
|
#$self->{primary_key} = $config->{primary_key} // 'id'; # setter; |
194
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|
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|
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#$self->{exclude_properties_regex} = $config->{exclude_properties_regex} |
195
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# // ''; # setter |
196
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197
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# ************************ |
198
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# Start Miscellanea checks |
199
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# ************************ |
200
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201
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# APPEND_PREFIXES |
202
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# Check that we have the right numbers of array elements |
203
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8
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50
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19
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if ( @{ $self->{append_prefixes} } ) { |
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8
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33
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204
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205
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# die if used without $self->{append_prefixes} |
206
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die "<--append_prefixes> needs at least 2 cohort files!\n" |
207
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0
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0
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0
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unless @{ $self->{reference_files} } > 1; |
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0
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0
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208
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209
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# die if #cohorts and #append-prefixes don't match |
210
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die "Numbers of items in <--r> and <--append-prefixes> don't match!\n" |
211
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0
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0
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0
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unless @{ $self->{reference_files} } == @{ $self->{append_prefixes} }; |
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0
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0
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0
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0
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212
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} |
213
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214
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# PATIENTS-OF-INTEREST |
215
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8
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50
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18
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if ( @{ $self->{patients_of_interest} } ) { |
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8
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66
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216
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217
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# die if used without $self->{append_prefixes} |
218
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die "<--patients-of-interest> needs to be used with <--r>\n" |
219
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0
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0
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0
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unless @{ $self->{reference_files} }; |
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0
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0
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220
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} |
221
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222
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# ********************** |
223
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# End Miscellanea checks |
224
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# ********************** |
225
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} |
226
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227
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sub run { |
228
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229
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8
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8
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0
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159
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my $self = shift; |
230
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231
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#print Dumper $self and die; |
232
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233
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# Load variables |
234
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8
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18
|
my $reference_files = $self->{reference_files}; |
235
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8
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15
|
my $target_file = $self->{target_file}; |
236
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8
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15
|
my $weights_file = $self->{weights_file}; |
237
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8
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16
|
my $export = $self->{export}; |
238
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8
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19
|
my $export_basename = $self->{export_basename}; |
239
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8
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14
|
my $include_hpo_ascendants = $self->{include_hpo_ascendants}; |
240
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8
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17
|
my $hpo_file = $self->{hpo_file}; |
241
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8
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13
|
my $align = $self->{align}; |
242
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8
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16
|
my $align_basename = $self->{align_basename}; |
243
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8
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20
|
my $out_file = $self->{out_file}; |
244
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8
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16
|
my $cohort_files = $self->{cohort_files}; |
245
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8
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16
|
my $append_prefixes = $self->{append_prefixes}; |
246
|
8
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15
|
my $max_out = $self->{max_out}; |
247
|
8
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15
|
my $sort_by = $self->{sort_by}; |
248
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8
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19
|
my $primary_key = $self->{primary_key}; |
249
|
8
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15
|
my $poi = $self->{patients_of_interest}; |
250
|
8
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16
|
my $poi_out_dir = $self->{poi_out_dir}; |
251
|
8
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13
|
my $cli = $self->{cli}; |
252
|
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253
|
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|
# die if --align dir does not exist |
254
|
8
|
100
|
|
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|
174
|
my $align_dir = defined $align ? dirname($align) : '.'; |
255
|
8
|
50
|
|
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|
132
|
die "Directory <$align_dir> does not exist (used with --align)\n" |
256
|
|
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|
|
|
|
unless -d $align_dir; |
257
|
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258
|
8
|
50
|
|
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|
41
|
my $export_dir = defined $export ? dirname($export) : '.'; |
259
|
8
|
50
|
|
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|
83
|
die "Directory <$export_dir> does not exist (used with --export)\n" |
260
|
|
|
|
|
|
|
unless -d $export_dir; |
261
|
|
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|
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|
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|
262
|
|
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|
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|
|
# We assing weights if <--w> |
263
|
|
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|
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|
|
# NB: The user can exclude variables by using variable: 0 |
264
|
8
|
|
|
|
|
55
|
my $weight = validate_json($weights_file); |
265
|
|
|
|
|
|
|
|
266
|
|
|
|
|
|
|
# Now we load $hpo_nodes, $hpo_edges if --include_hpo_ascendants |
267
|
|
|
|
|
|
|
# NB: we load them within $self to minimize the #args |
268
|
6
|
|
|
|
|
27
|
my $nodes = my $edges = undef; |
269
|
6
|
50
|
|
|
|
18
|
( $nodes, $edges ) = parse_hpo_json( read_json($hpo_file) ) |
270
|
|
|
|
|
|
|
if $include_hpo_ascendants; |
271
|
6
|
|
|
|
|
19
|
$self->{nodes} = $nodes; # setter |
272
|
6
|
|
|
|
|
16
|
$self->{edges} = $edges; # setter |
273
|
|
|
|
|
|
|
|
274
|
|
|
|
|
|
|
############################### |
275
|
|
|
|
|
|
|
# START READING -r | -cohorts # |
276
|
|
|
|
|
|
|
############################### |
277
|
|
|
|
|
|
|
|
278
|
|
|
|
|
|
|
# *** IMPORTANT *** |
279
|
|
|
|
|
|
|
# We have three modes of operation: |
280
|
|
|
|
|
|
|
# 1 - intra-cohort (--r) a.json |
281
|
|
|
|
|
|
|
# 2 - inter-cohort (--r) a.json b.json c.json |
282
|
|
|
|
|
|
|
# 3 - patient (assigned automatically if -t) |
283
|
|
|
|
|
|
|
|
284
|
|
|
|
|
|
|
# *** IMPORTANT *** |
285
|
|
|
|
|
|
|
# $ref_data is an array array where each element is the content of the file (e.g, [] or {}) |
286
|
6
|
|
|
|
|
14
|
my $ref_data = []; |
287
|
6
|
|
|
|
|
12
|
for my $cohort_file ( @{$reference_files} ) { |
|
6
|
|
|
|
|
20
|
|
288
|
6
|
50
|
|
|
|
173
|
die "$cohort_file does not exist\n" unless -f $cohort_file; |
289
|
|
|
|
|
|
|
|
290
|
|
|
|
|
|
|
# Load JSON file as Perl data structure |
291
|
6
|
|
|
|
|
68
|
push @$ref_data, |
292
|
|
|
|
|
|
|
io_yaml_or_json( |
293
|
|
|
|
|
|
|
{ |
294
|
|
|
|
|
|
|
filepath => $cohort_file, |
295
|
|
|
|
|
|
|
mode => 'read' |
296
|
|
|
|
|
|
|
} |
297
|
|
|
|
|
|
|
); |
298
|
|
|
|
|
|
|
} |
299
|
|
|
|
|
|
|
|
300
|
|
|
|
|
|
|
# In <inter-cohort> we join --cohorts into one but we change the id |
301
|
|
|
|
|
|
|
# NB: Re-using $ref_data to save memory |
302
|
6
|
|
|
|
|
70
|
$ref_data = append_and_rename_primary_key( |
303
|
|
|
|
|
|
|
{ |
304
|
|
|
|
|
|
|
ref_data => $ref_data, |
305
|
|
|
|
|
|
|
append_prefixes => $append_prefixes, |
306
|
|
|
|
|
|
|
primary_key => $primary_key |
307
|
|
|
|
|
|
|
} |
308
|
|
|
|
|
|
|
); |
309
|
|
|
|
|
|
|
|
310
|
|
|
|
|
|
|
############################## |
311
|
|
|
|
|
|
|
# ENDT READING -r | -cohorts # |
312
|
|
|
|
|
|
|
############################## |
313
|
|
|
|
|
|
|
|
314
|
|
|
|
|
|
|
#------------------------------- |
315
|
|
|
|
|
|
|
# Write json for $poi if --poi | |
316
|
|
|
|
|
|
|
#------------------------------- |
317
|
|
|
|
|
|
|
# *** IMPORTANT *** |
318
|
|
|
|
|
|
|
# It will exit when done (dry-run) |
319
|
|
|
|
|
|
|
write_poi( |
320
|
|
|
|
|
|
|
{ |
321
|
|
|
|
|
|
|
ref_data => $ref_data, |
322
|
|
|
|
|
|
|
poi => $poi, |
323
|
|
|
|
|
|
|
poi_out_dir => $poi_out_dir, |
324
|
|
|
|
|
|
|
primary_key => $primary_key, |
325
|
|
|
|
|
|
|
verbose => $self->{verbose} |
326
|
|
|
|
|
|
|
} |
327
|
|
|
|
|
|
|
) |
328
|
6
|
50
|
0
|
|
|
27
|
and exit |
329
|
|
|
|
|
|
|
if @$poi; |
330
|
|
|
|
|
|
|
|
331
|
|
|
|
|
|
|
# We will process $ref_data to get stats on coverage |
332
|
6
|
|
|
|
|
27
|
my $coverage_stats = coverage_stats($ref_data); |
333
|
|
|
|
|
|
|
|
334
|
|
|
|
|
|
|
# We have to check if we have BFF|PXF or others unless defined at config |
335
|
|
|
|
|
|
|
add_attribute( $self, 'format', check_format($ref_data) ) |
336
|
6
|
100
|
|
|
|
45
|
unless defined $self->{format}; # setter via sub |
337
|
|
|
|
|
|
|
|
338
|
|
|
|
|
|
|
# First we create: |
339
|
|
|
|
|
|
|
# - $glob_hash => hash with all the COHORT keys possible |
340
|
|
|
|
|
|
|
# - $ref_hash => BIG hash with all individiduals' keys "flattened" |
341
|
6
|
|
|
|
|
29
|
my ( $glob_hash, $ref_hash ) = |
342
|
|
|
|
|
|
|
create_glob_and_ref_hashes( $ref_data, $weight, $self ); |
343
|
|
|
|
|
|
|
|
344
|
|
|
|
|
|
|
# Limit the number of variables if > $self-{max_number_var} |
345
|
|
|
|
|
|
|
# *** IMPORTANT *** |
346
|
|
|
|
|
|
|
# Change only performed in $glob_hash |
347
|
|
|
|
|
|
|
$glob_hash = randomize_variables( $glob_hash, $self ) |
348
|
6
|
50
|
|
|
|
36
|
if keys %$glob_hash > $self->{max_number_var}; |
349
|
|
|
|
|
|
|
|
350
|
|
|
|
|
|
|
# Second we peform one-hot encoding for each individual |
351
|
6
|
|
|
|
|
25
|
my $ref_binary_hash = create_binary_digit_string( $glob_hash, $ref_hash ); |
352
|
|
|
|
|
|
|
|
353
|
|
|
|
|
|
|
# Hases to be serialized to JSON if <--export> |
354
|
6
|
|
|
|
|
33
|
my $hash2serialize = { |
355
|
|
|
|
|
|
|
glob_hash => $glob_hash, |
356
|
|
|
|
|
|
|
ref_hash => $ref_hash, |
357
|
|
|
|
|
|
|
ref_binary_hash => $ref_binary_hash, |
358
|
|
|
|
|
|
|
coverage_stats => $coverage_stats |
359
|
|
|
|
|
|
|
}; |
360
|
|
|
|
|
|
|
|
361
|
|
|
|
|
|
|
# Perform cohort comparison |
362
|
6
|
100
|
|
|
|
46
|
cohort_comparison( $ref_binary_hash, $self ) unless $target_file; |
363
|
|
|
|
|
|
|
|
364
|
|
|
|
|
|
|
# Perform patient-to-cohort comparison and rank if (-t) |
365
|
6
|
100
|
|
|
|
20
|
if ($target_file) { |
366
|
|
|
|
|
|
|
|
367
|
|
|
|
|
|
|
#################### |
368
|
|
|
|
|
|
|
# START READING -t # |
369
|
|
|
|
|
|
|
#################### |
370
|
|
|
|
|
|
|
|
371
|
|
|
|
|
|
|
# local $tar_data is for patient |
372
|
1
|
|
|
|
|
11
|
my $tar_data = array2object( |
373
|
|
|
|
|
|
|
io_yaml_or_json( { filepath => $target_file, mode => 'read' } ) ); |
374
|
|
|
|
|
|
|
|
375
|
|
|
|
|
|
|
################## |
376
|
|
|
|
|
|
|
# END READING -t # |
377
|
|
|
|
|
|
|
################## |
378
|
|
|
|
|
|
|
|
379
|
|
|
|
|
|
|
# The target file has to have $_->{$primary_key} otherwise die |
380
|
|
|
|
|
|
|
die |
381
|
|
|
|
|
|
|
"Sorry, <$target_file> does not contain <id> term and it's mandatory\n" |
382
|
1
|
50
|
|
|
|
8
|
unless exists $tar_data->{$primary_key}; |
383
|
|
|
|
|
|
|
|
384
|
|
|
|
|
|
|
# We store {primary_key} as a variable as it might be deleted from $tar_data (--excluded-terms id) |
385
|
1
|
|
|
|
|
4
|
my $tar_data_id = $tar_data->{$primary_key}; |
386
|
|
|
|
|
|
|
|
387
|
|
|
|
|
|
|
# Now we load the rest of the hashes |
388
|
1
|
|
|
|
|
7
|
my $tar_hash = { |
389
|
|
|
|
|
|
|
$tar_data_id => remap_hash( |
390
|
|
|
|
|
|
|
{ |
391
|
|
|
|
|
|
|
hash => $tar_data, |
392
|
|
|
|
|
|
|
weight => $weight, |
393
|
|
|
|
|
|
|
self => $self |
394
|
|
|
|
|
|
|
} |
395
|
|
|
|
|
|
|
) |
396
|
|
|
|
|
|
|
}; |
397
|
|
|
|
|
|
|
|
398
|
|
|
|
|
|
|
# *** IMPORTANT *** |
399
|
|
|
|
|
|
|
# The target binary is created from matches to $glob_hash |
400
|
|
|
|
|
|
|
# Thus, it does not include variables ONLY present in TARGET |
401
|
1
|
|
|
|
|
7
|
my $tar_binary_hash = |
402
|
|
|
|
|
|
|
create_binary_digit_string( $glob_hash, $tar_hash ); |
403
|
|
|
|
|
|
|
my ( |
404
|
1
|
|
|
|
|
9
|
$results_rank, $results_align, $alignment_ascii, |
405
|
|
|
|
|
|
|
$alignment_dataframe, $alignment_csv |
406
|
|
|
|
|
|
|
) |
407
|
|
|
|
|
|
|
= compare_and_rank( |
408
|
|
|
|
|
|
|
{ |
409
|
|
|
|
|
|
|
glob_hash => $glob_hash, |
410
|
|
|
|
|
|
|
ref_binary_hash => $ref_binary_hash, |
411
|
|
|
|
|
|
|
tar_binary_hash => $tar_binary_hash, |
412
|
|
|
|
|
|
|
weight => $weight, |
413
|
|
|
|
|
|
|
self => $self |
414
|
|
|
|
|
|
|
} |
415
|
|
|
|
|
|
|
); |
416
|
|
|
|
|
|
|
|
417
|
|
|
|
|
|
|
# Print Ranked results to STDOUT only if CLI |
418
|
1
|
50
|
|
|
|
8
|
say join "\n", @$results_rank if $cli; |
419
|
|
|
|
|
|
|
|
420
|
|
|
|
|
|
|
# Write txt ( |
421
|
1
|
|
|
|
|
11
|
write_array2txt( { filepath => $out_file, data => $results_rank } ); |
422
|
|
|
|
|
|
|
|
423
|
|
|
|
|
|
|
# Write TXT for alignment (ALWAYS!!) |
424
|
1
|
50
|
|
|
|
19
|
write_alignment( |
|
|
50
|
|
|
|
|
|
425
|
|
|
|
|
|
|
{ |
426
|
|
|
|
|
|
|
align => $align ? $align : $align_basename, # DON'T -- $align // $align_basename, |
427
|
|
|
|
|
|
|
ascii => $alignment_ascii, |
428
|
|
|
|
|
|
|
dataframe => $alignment_dataframe, |
429
|
|
|
|
|
|
|
csv => $alignment_csv |
430
|
|
|
|
|
|
|
} |
431
|
|
|
|
|
|
|
) if defined $align; |
432
|
|
|
|
|
|
|
|
433
|
|
|
|
|
|
|
# Load keys into hash if <--e> |
434
|
1
|
50
|
|
|
|
653
|
if ( defined $export ) { |
435
|
0
|
|
|
|
|
0
|
$hash2serialize->{tar_hash} = $tar_hash; |
436
|
0
|
|
|
|
|
0
|
$hash2serialize->{tar_binary_hash} = $tar_binary_hash; |
437
|
0
|
0
|
|
|
|
0
|
$hash2serialize->{alignment_hash} = $results_align |
438
|
|
|
|
|
|
|
if defined $align; |
439
|
|
|
|
|
|
|
} |
440
|
|
|
|
|
|
|
} |
441
|
|
|
|
|
|
|
|
442
|
|
|
|
|
|
|
# Dump to JSON if <--export> |
443
|
|
|
|
|
|
|
# NB: Must work for -r and -t |
444
|
|
|
|
|
|
|
serialize_hashes( |
445
|
|
|
|
|
|
|
{ |
446
|
6
|
0
|
|
|
|
25
|
data => $hash2serialize, |
|
|
50
|
|
|
|
|
|
447
|
|
|
|
|
|
|
export_basename => $export ? $export : $export_basename |
448
|
|
|
|
|
|
|
} |
449
|
|
|
|
|
|
|
) if defined $export; |
450
|
|
|
|
|
|
|
|
451
|
|
|
|
|
|
|
# Return |
452
|
6
|
|
|
|
|
5515
|
return 1; |
453
|
|
|
|
|
|
|
} |
454
|
|
|
|
|
|
|
|
455
|
|
|
|
|
|
|
sub add_attribute { |
456
|
|
|
|
|
|
|
|
457
|
|
|
|
|
|
|
# Bypassing the encapsulation provided by Moo |
458
|
3
|
|
|
3
|
0
|
14
|
my ( $self, $name, $value ) = @_; |
459
|
3
|
|
|
|
|
9
|
$self->{$name} = $value; |
460
|
3
|
|
|
|
|
6
|
return 1; |
461
|
|
|
|
|
|
|
} |
462
|
|
|
|
|
|
|
|
463
|
|
|
|
|
|
|
1; |
464
|
|
|
|
|
|
|
|
465
|
|
|
|
|
|
|
=head1 NAME |
466
|
|
|
|
|
|
|
|
467
|
|
|
|
|
|
|
Convert::Pheno - A module that performs semantic similarity in PXF/BFF data structures and beyond (JSON|YAML) |
468
|
|
|
|
|
|
|
|
469
|
|
|
|
|
|
|
=head1 SYNOPSIS |
470
|
|
|
|
|
|
|
|
471
|
|
|
|
|
|
|
use Pheno::Ranker; |
472
|
|
|
|
|
|
|
|
473
|
|
|
|
|
|
|
# Create object |
474
|
|
|
|
|
|
|
my $ranker = Pheno::Ranker->new( |
475
|
|
|
|
|
|
|
{ |
476
|
|
|
|
|
|
|
reference_files => ['individuals.json'], |
477
|
|
|
|
|
|
|
out_file => 'matrix.txt' |
478
|
|
|
|
|
|
|
} |
479
|
|
|
|
|
|
|
); |
480
|
|
|
|
|
|
|
|
481
|
|
|
|
|
|
|
# Run it (output are text files) |
482
|
|
|
|
|
|
|
$ranker->run; |
483
|
|
|
|
|
|
|
|
484
|
|
|
|
|
|
|
=head1 DESCRIPTION |
485
|
|
|
|
|
|
|
|
486
|
|
|
|
|
|
|
We recommend using the included L<command-line interface|https://metacpan.org/dist/Pheno-Ranker/view/bin/pheno-ranker>. |
487
|
|
|
|
|
|
|
|
488
|
|
|
|
|
|
|
For a better description, please read the following documentation: |
489
|
|
|
|
|
|
|
|
490
|
|
|
|
|
|
|
=over |
491
|
|
|
|
|
|
|
|
492
|
|
|
|
|
|
|
=item General: |
493
|
|
|
|
|
|
|
|
494
|
|
|
|
|
|
|
L<https://cnag-biomedical-informatics.github.io/pheno-ranker> |
495
|
|
|
|
|
|
|
|
496
|
|
|
|
|
|
|
=item Command-Line Interface: |
497
|
|
|
|
|
|
|
|
498
|
|
|
|
|
|
|
L<https://github.com/CNAG-Biomedical-Informatics/pheno-ranker#readme> |
499
|
|
|
|
|
|
|
|
500
|
|
|
|
|
|
|
=back |
501
|
|
|
|
|
|
|
|
502
|
|
|
|
|
|
|
=head1 CITATION |
503
|
|
|
|
|
|
|
|
504
|
|
|
|
|
|
|
The author requests that any published work that utilizes C<Convert-Pheno> includes a cite to the the following reference: |
505
|
|
|
|
|
|
|
|
506
|
|
|
|
|
|
|
Rueda, M. et al. "Advancing Semantic Similarity Analysis of Phenotypic Data Stored in GA4GH Standards and Beyond. (2023) I<Manuscript in preparation>. |
507
|
|
|
|
|
|
|
|
508
|
|
|
|
|
|
|
=head1 AUTHOR |
509
|
|
|
|
|
|
|
|
510
|
|
|
|
|
|
|
Written by Manuel Rueda, PhD. Info about CNAG can be found at L<https://www.cnag.eu>. |
511
|
|
|
|
|
|
|
|
512
|
|
|
|
|
|
|
=head1 METHODS |
513
|
|
|
|
|
|
|
|
514
|
|
|
|
|
|
|
See L<https://cnag-biomedical-informatics.github.io/pheno-ranker/use-as-a-module>. |
515
|
|
|
|
|
|
|
|
516
|
|
|
|
|
|
|
=head1 COPYRIGHT |
517
|
|
|
|
|
|
|
|
518
|
|
|
|
|
|
|
This PERL file is copyrighted. See the LICENSE file included in this distribution. |
519
|
|
|
|
|
|
|
|
520
|
|
|
|
|
|
|
=cut |
521
|
|
|
|
|
|
|
|