CPAN::Groonga

er::Metrics;
use Pheno::Ranker::Graph;

use Exporter 'import';
our @EXPORT_OK = qw($VERSION write_json);

# Personalize warn and die functions
$SIG{__WARN__} = sub { warn BOLD YELLOW "Warn: ", @_ };
$

as hpo_file => (
    default => catfile( $share_dir, 'db', 'hp.json' ),
    coerce  => sub { $_[0] // catfile( $share_dir, 'db', 'hp.json' ) },
    is      => 'ro',
    isa     => sub { die "Error <$_

ed_phenotypicFeatures align align_basename export export_basename
      log verbose age cytoscape_json graph_stats/
] => ( is => 'ro' );

has [qw/append_prefixes reference_files patients_of_interest/]

#!/usr/bin/perl
#
#   A script that creates a disease-based 
#   BFF/PXF JSON array from HPO CSV data
#
#   Last Modified: Jan/15/2024
#
#   $VERSION taken from Pheno::Ranker
#
#   Copyright (C) 2023-

program helps you in your research, please cite.

use strict;
use warnings;
use Text::CSV_XS;
use JSON::XS;
use Getopt::Long qw(:config no_ignore_case);

# Command-line arguments
GetOptions(
    'i|in

 to arrays for JSON encoding
my %output_data;
foreach my $type (keys %diseases) {
    $output_data{$type} = [ values %{ $diseases{$type} } ];
}

# Initialize JSON encoder
my $json = JSON::XS->new->utf

nk create_glob_and_ref_hashes randomize_variables remap_hash create_binary_digit_string parse_hpo_json);

use constant DEVEL_MODE => 0;

our %nomenclature = ();

sub check_format {

    my $data = shi

weight hamming-distance json-path label/;

    # The dataframe will have two header lines
    # *** IMPORTANT ***
    # nsort does not yield same results as canonical from JSON::XS
    # NB: we're sor

tamic Pyruvic Transaminase, CTCAE'
    my @dataframe = join ';', 'Id', @labels;

    # Variables (json path)
    push @dataframe, join ';', 'Id', @sort_keys_glob_hash;

    # 0/1
    push @dataframe, 

package Pheno::Ranker::Graph;

use strict;
use warnings;
use autodie;
use feature qw(say);
use JSON::XS;
use Pheno::Ranker::IO;
use Exporter 'import';
our @EXPORT = qw(matrix2graph cytoscape2graph);
u

    my $arg         = shift;
    my $input       = $arg->{matrix};
    my $output      = $arg->{json};
    my $verbose     = $arg->{verbose};
    my $graph_stats = $arg->{graph_stats};

    # Open t

edges => \@edges,
        }
    );

    # Open a file to write JSON output
    say "Writting <$output> file " if $verbose;
    write_json( { filepath => $output, data => \%graph } );

    return defin

nk create_glob_and_ref_hashes randomize_variables remap_hash create_binary_digit_string parse_hpo_json);

use constant DEVEL_MODE => 0;

our %nomenclature = ();

sub check_format {
    my $data = shif

weight hamming-distance json-path label/;

    # The dataframe will have two header lines
    # *** IMPORTANT ***
    # nsort does not yield same results as canonical from JSON::XS
    # NB: we're sor

tamic Pyruvic Transaminase, CTCAE'
    my @dataframe = join ';', 'Id', @labels;

    # Variables (json path)
    push @dataframe, join ';', 'Id', @sort_keys_glob_hash;

    # 0/1
    push @dataframe, 

e);
use JSON::XS;

#use Data::Dumper;

#use Sort::Naturally qw(nsort);
use Exporter 'import';
our @EXPORT =
  qw(serialize_hashes write_alignment io_yaml_or_json read_json read_yaml write_json write_a

rray2txt array2object validate_json write_poi coverage_stats check_existence_of_include_terms append_and_rename_primary_key restructure_pxf_interpretations);
use constant DEVEL_MODE => 0;

###########

    my $export_basename = $arg->{export_basename};
    write_json(
        { data => $data->{$_}, filepath => qq/$export_basename.$_.json/ } )
      for keys %{$data};
    return 1;
}

sub write_alig