CPAN::Groonga

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

aResources => { x_IRC => $irc }]);
	}
	
	my @from_build = qw(INSTALL LICENSE CONTRIBUTING.md META.json);
	push @from_build, $install_with_makemaker ? 'Makefile.PL' : 'Build.PL';
	my @ignore_files = qw

);
	# @Basic, with some modifications
	$self->add_plugins(qw/PruneCruft ManifestSkip MetaYAML MetaJSON
		License ReadmeAnyFromPod ExecDir ShareDir/);
	$self->add_plugins([ExecDir => 'ScriptDir' => { d

FromRelease]
 filename = INSTALL
 filename = LICENSE
 filename = CONTRIBUTING.md
 filename = META.json
 filename = Makefile.PL
 [Git::Commit]
 add_files_in = /
 allow_dirty = dist.ini
 allow_dirty = C

, 
		track_version_result 	=> $version,
	);
	scalar @results > 1 
		and warn ("more than one EffectChain matching query!, found", 
			map{ json_out($_->as_hash) } @results);
	$results[-1]
}
1;
__END__

  $$column{type} //= 'TEXT';

        $$column{sql_type} = 'TEXT'
          if $$column{type} eq 'JSON';

        $$column{sql_type} = 'INTEGER'
          if $$column{type} eq 'Time::Moment';

       

registration data from an EPP server.
use base qw(Net::RDAP::Server);
use List::Util qw(any);
use JSON::PP;
use Net::EPP::Simple;
use Net::RDAP::EPPStatusMap;
use Net::EPP::ResponseCodes;
use vars qw(

igned => $JSON::PP::true,
            dsData => $self->generate_dnssec_dsdata($info->{DS}),
        };

    } elsif ($info->{DNSKEY}) {
        return {
            delegationSigned => $JSON::PP::true

data($info->{DNSKEY}),
        };

    } else {
        return {
            delegationSigned => $JSON::PP::false,
        };

    }
}

#
# Convert dsData info from an <info> response.
#
sub generate_

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, 

ub load_project {
	logsub((caller(0))[3]);
	my %args = @_;
	logpkg(__FILE__,__LINE__,'debug', sub{json_out \%args});
	
	$project->{name} = $args{name};
	if (not $project->{name} or not -d project_dir(

}	
sub restore_state {
	logsub((caller(0))[3]);
		my $name = shift;

		if( ! $name  or $name =~ /.json$/ or !  $config->{use_git})
		{
			restore_state_from_file($name)
		}
		else { restore_state_from

t();

	# save current project status to temp state file 
	
	my $previous_state = '_previous_state.json';
	save_state($previous_state);

	# edit current project into a template
	
	# No tracks are recor

ng);
use Carp qw(carp cluck croak confess);
use Data::Dumper::Concise;
use Audio::Nama::Assign qw(json_out);
use Audio::Nama::Log qw(logsub logpkg);
use Audio::Nama::Util qw(timer start_event stop_eve

ss grep { $id eq $_ } @$owns;

		logpkg(__FILE__,__LINE__,'debug',sub{join " ", "my attributes:", json_out($self->as_hash)});
		# find position of parent id in the track ops array 
 		# and insert chi

p->{before} )
	{
		$p->{chain} = fxn($p->{before})->chain;
	}
	#logpkg(__FILE__,__LINE__,'debug',(json_out($p));

}

#		How effect chains are added (by default before fader)
#		user command: add_effec

lone);
use Audio::Nama::Util qw(signal_format input_node output_node);
use Audio::Nama::Assign qw(json_out);
no warnings 'uninitialized';

our (

	$g,  # routing graph object - 

		# based on project 

, $chain_setup;
	wantarray() ? @files : scalar @files;
}
	
sub show_io {
	my $output = json_out( \%inputs ). json_out( \%outputs ); 
	Audio::Nama::pager( $output );
}

sub warn_missing_jack_clients {

und edge attributes: ",json_out($eattr)) if $eattr;

	my $vattr = $g->get_vertex_attributes($edge->[0]) // {};
	logpkg(__FILE__,__LINE__,'debug',"found vertex attributes: ",json_out($vattr)) if $vattr

#!/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

Effect  qw(fxn append_effect);
use Audio::Nama::Log qw(logpkg logsub);
use Audio::Nama::Assign qw(json_out);

use Audio::Nama::Globals qw($fx_cache %tn $fx);

our $AUTOLOAD;
our $VERSION = 0.001;
no w

} xor $vals{attrib}{project});

		logpkg(__FILE__,__LINE__,'debug','constructor arguments ', sub{ json_out(\%vals) });

		my $ops_data = {};
		# ops data is taken preferentially 
		# from ops_data arg

t_chain => ec_index,
					
					$hash
				} @{$vals{inserts_data}}
			];
		}

		#say Audio::Nama::json_out($vals{inserts_data}) if $vals{inserts_data};
	}
	my $object = bless { %vals }, $class;
	$by_i

	@specs = sort{ $a->[0] <=> $b->[0] } @specs;
	logpkg(__FILE__,__LINE__,'debug',sub{Audio::Nama::json_out( \@specs)});

	my @pairs = map{ spec_to_pairs($_) } @specs;

#   WEIRD message - try to figur

fects_cache.json',	\&project_root],
		gui_palette 			=> ['palette',        		\&project_root],
		state_store 			=> ['State.json',  			\&project_dir ],
		untracked_state_store 	=> ['Aux.json',				\&proj

ect_dir ],
		effect_profile 			=> ['effect_profiles.json',	\&project_root],
		chain_setup 			=> ['Setup.ecs',      		\&project_dir ],
		user_customization 		=> ['customize.pl',    		\&project_root],
	

roject_dir ],
		global_effect_chains  	=> ['global_effect_chains.json', \&project_root],
		old_effect_chains  		=> ['effect_chains.json', 		\&project_root],
		_logfile				=> ['nama.log',				\&project_

us ne OFF } grep { $_->group ne 'Temp' } Audio::Nama::all_tracks();
	\%snapshot;
}
sub status_snapshot_string { 
	my $json = json_out(status_snapshot());
	$json =~ s/: "(\d+)"/: $1/g; 
	$json
}
}
	
1;

package Audio::Nama::Sequence;
use v5.36; use Carp; 
use Audio::Nama::Assign qw(json_out);
use Audio::Nama::Log qw(logsub logpkg);
use Audio::Nama::Effect  qw(fxn modify_effect);
use Audio::Nama::Obje

ms: ",map{json_out($_->as_hash)}map{$Audio::Nama::tn{$_}}@$items) if $items;
	$items //= [];
	@_ = ($class, %args);
	my $self = super();
	logpkg(__FILE__,__LINE__,'debug',"new object: ", json_out($sel

f->as_hash));
	logpkg(__FILE__,__LINE__,'debug', "items: ",json_out($items));
	$self->{clip_counter} = $counter;
	$self->{items} = $items;
	$Audio::Nama::this_sequence = $self;
	$self;
} 
sub clip {
	

m || 'bare' } =  $match }
	}
	logpkg(__FILE__,__LINE__,'debug',sub{"get_version: " , Audio::Nama::json_out(\%versions)});
	%versions;
}

sub candidates {
	my $dir = shift;
	$dir =  File::Spec::Link->r

lete $versions{bare};
		}
	logpkg(__FILE__,__LINE__,'debug',sub{"\%versions\n================\n", json_out(\%versions)});
	\%versions;
}

sub _versions {  
#	$Audio::Nama::debug2 and print "&versions\

F )
				 );

sub bunch {
	my ($bunchname, @tracks) = @_;
	if (! $bunchname){
		Audio::Nama::pager(json_out( $project->{bunch} ));
	} elsif (! @tracks){
		$project->{bunch}->{$bunchname} 
			and pager(

package Audio::Nama::Object;
use v5.36;
our $VERSION = 1.05;
use Carp;
use Audio::Nama::Assign qw(json_out); 
use Storable qw(dclone);
use Data::Dumper::Concise;
no strict 'refs';
no strict 'subs';

B

Audio::Nama::Util qw(freq input_node dest_type dest_string join_path);
use Audio::Nama::Assign qw(json_out);
use vars qw($n %by_name @by_index %track_names %by_index);
use Audio::Nama::Object qw(
				

ess $object->hide;
	logpkg(__FILE__,__LINE__,'debug',$object->name, ": ","newly created track",$/,json_out($object->as_hash));
	$object;
}


### object methods

sub snapshot {
	my $track = shift;
	my 

= super();
	#logpkg(__FILE__,__LINE__,'debug',"new object: ", json_out($self->as_hash));
	#logpkg(__FILE__,__LINE__,'debug', "items: ",json_out($items));

	# set the args removed above
	$self->{durati

ogpkg(__FILE__,__LINE__,'debug',sub{my %q = %p; delete $q{parent}; print
		 "=============\n%p\n",json_out(\%q)});

		$vol = make_scale( \%p );
		# Mute

		$mute = $gui->{track_frame}->Button(
			-com

logpkg(__FILE__,__LINE__,'debug',sub{ my %q = %p; delete $q{parent}; print "x=============\n%p\n",json_out(\%q) });
		$pan = make_scale( \%q );

		# Center

		$center = $gui->{track_frame}->Button(
		

cts);#a ref to the object
	#logpkg(__FILE__,__LINE__,'debug', "=============$gui->{tracks}\n",sub{json_out($gui->{tracks})});
	my $independent_effects_frame 
		= ${ $gui->{tracks}->{$n}->{effects} }->