test/lib/cdd_test.pm

   1 package cdd_test;
   2
   3 use Data::Dumper;
   4 use strict;
   5 use Test::More;
   6
   7 my @tests = ( 'pheno' );
   8
   9 sub test {
  10   my $self = shift;
  11   my %parms = @_;
  12   my $verbose          = $parms{'verbose'};
  13   my $debug            = $parms{'debug'};
  14   my $debug_package    = $parms{'debug_package'};
  15   my $debug_subroutine = $parms{'debug_subroutine'};
  16   my $directory        = $parms{'directory'};
  17   my $threads          = $parms{'threads'};
  18
  19   foreach my $test( @tests ){
  20     cdd_test -> $test( verbose          => $verbose,
  21                              debug            => $debug,
  22                              debug_package    => $debug_package,
  23                              debug_subroutine => $debug_subroutine,
  24                              directory        => $directory,
  25                              threads          => $threads );
  26   }
  27 }
  28
  29 sub pheno {
  30   my $self = shift;
  31   my %parms = @_;
  32   my $verbose          = $parms{'verbose'};
  33   my $debug            = $parms{'debug'};
  34   my $debug_package    = $parms{'debug_package'};
  35   my $debug_subroutine = $parms{'debug_subroutine'};
  36   my $directory        = $parms{'directory'};
  37   my $threads          = $parms{'threads'};
  38   my $bin = "$directory/../bin/cdd.pl -directory=$directory/cdd_dir2 ";
  39   my $options = "-mod=$directory/files/pheno.mod -case_column=ID -bins=10 -results_file=cdd_results.csv";
  40   $options = $options." -seed=testing";
  41   $options = $options." -debug=$debug" if defined $debug;
  42   $options = $options." -debug_package=$debug_package" if defined $debug_package;
  43   $options = $options." -debug_subroutine=$debug_subroutine" if defined $debug_subroutine;
  44   $options = $options." -threads=$threads" if defined $threads;
  45   system( $bin." ".$options );
  46   ok( -e "$directory/cdd_results.csv", 'cdd results file exist' );
  47   open( TESTRES, "$directory/cdd_results.csv" );
  48   open( ORIGRES, "$directory/files/cdd_results.csv.test" );
  49   my @test_array = <TESTRES>;
  50   my @orig_array = <ORIGRES>;
  51   close( TESTRES );
  52   close( ORIGRES );
  53   is_deeply( \@test_array,
  54              \@orig_array,
  55              'cdd results file has the correct content' );
  56 #  unlink( "$directory/cdd_results.csv" );
  57 #  system( 'rm -rf cdd_dir*' );
  58 }
  59
  60 sub mox {
  61   my $self = shift;
  62   my %parms = @_;
  63   my $verbose          = $parms{'verbose'};
  64   my $debug            = $parms{'debug'};
  65   my $debug_package    = $parms{'debug_package'};
  66   my $debug_subroutine = $parms{'debug_subroutine'};
  67   my $directory        = $parms{'directory'};
  68   my $threads          = $parms{'threads'};
  69   my $bin = "$directory/../bin/cdd.pl";
  70   my $options = "-mod=$directory/files/mox_basic.mod -case_column=ID -bins=5";
  71   $options = $options." -seed=testing";
  72   $options = $options." -debug=$debug" if defined $debug;
  73   $options = $options." -debug_package=$debug_package" if defined $debug_package;
  74   $options = $options." -debug_subroutine=$debug_subroutine" if defined $debug_subroutine;
  75   $options = $options." -threads=$threads" if defined $threads;
  76   system( $bin." ".$options );
  77   ok( -e "$directory/cdd_results.csv", 'mox cdd results file exist' );
  78   open( TESTRES, "$directory/cdd_results.csv" );
  79   open( ORIGRES, "$directory/files/cdd_results.csv.test.mox" );
  80   my @test_array = <TESTRES>;
  81   my @orig_array = <ORIGRES>;
  82   close( TESTRES );
  83   close( ORIGRES );
  84   is_deeply( \@test_array,
  85              \@orig_array,
  86              'mox cdd results file has the correct content' );
  87 #  unlink( "$directory/cdd_results.csv" );
  88   system( 'rm -rf cdd_dir*' );
  89 }
  90
  91 sub dof {
  92   my $self = shift;
  93   my %parms = @_;
  94   my $verbose          = $parms{'verbose'};
  95   my $debug            = $parms{'debug'};
  96   my $debug_package    = $parms{'debug_package'};
  97   my $debug_subroutine = $parms{'debug_subroutine'};
  98   my $directory        = $parms{'directory'};
  99   my $threads          = $parms{'threads'};
 100   my $bin = "$directory/../bin/cdd.pl";
 101   my $options = "-mod=$directory/files/dof.run51.FO.mod ".
 102     "-case_column=ID -bins=5";
 103   $options = $options." -seed=testing";
 104   $options = $options." -debug=$debug" if defined $debug;
 105   $options = $options." -debug_package=$debug_package" if defined $debug_package;
 106   $options = $options." -debug_subroutine=$debug_subroutine" if defined $debug_subroutine;
 107   $options = $options." -threads=$threads" if defined $threads;
 108   system( $bin." ".$options );
 109   ok( -e "$directory/cdd_results.csv", 'dof cdd results file exist' );
 110   open( TESTRES, "$directory/cdd_results.csv" );
 111   open( ORIGRES, "$directory/files/cdd_results.csv.test.dof" );
 112   my @test_array = <TESTRES>;
 113   my @orig_array = <ORIGRES>;
 114   close( TESTRES );
 115   close( ORIGRES );
 116   is_deeply( \@test_array,
 117              \@orig_array,
 118              'dof cdd results file has the correct content' );
 119 #  unlink( "$directory/cdd_results.csv" );
 120   system( 'rm -rf cdd_dir*' );
 121 }
 122
 123 sub war {
 124   my $self = shift;
 125   my %parms = @_;
 126   my $verbose          = $parms{'verbose'};
 127   my $debug            = $parms{'debug'};
 128   my $debug_package    = $parms{'debug_package'};
 129   my $debug_subroutine = $parms{'debug_subroutine'};
 130   my $directory        = $parms{'directory'};
 131   my $threads          = $parms{'threads'};
 132   my $bin = "$directory/../bin/cdd.pl";
 133   my $options = "-mod=$directory/files/war.mod ".
 134     "-bins=5 -case_column=ID -nm_version=6";
 135   $options = $options." -seed=testing";
 136   $options = $options." -debug=$debug" if defined $debug;
 137   $options = $options." -debug_package=$debug_package" if defined $debug_package;
 138   $options = $options." -debug_subroutine=$debug_subroutine" if defined $debug_subroutine;
 139   $options = $options." -threads=$threads" if defined $threads;
 140   system( $bin." ".$options );
 141   ok( -e "$directory/cdd_results.csv", 'war cdd results file exist' );
 142   open( TESTRES, "$directory/cdd_results.csv" );
 143   open( ORIGRES, "$directory/files/cdd_results.csv.test.war" );
 144   my @test_array = <TESTRES>;
 145   my @orig_array = <ORIGRES>;
 146   close( TESTRES );
 147   close( ORIGRES );
 148   is_deeply( \@test_array,
 149              \@orig_array,
 150              'war cdd results file has the correct content' );
 151 #  unlink( "$directory/cdd_results.csv" );
 152   system( 'rm -rf cdd_dir*' );
 153 }
 154
 155 1;