t/CXGN/Genomic/clonenameparser.t

   1 #!/usr/bin/env perl
   2 use strict;
   3 no strict 'refs';
   4 #use UNIVERSAL qw/isa/;
   5
   6 BEGIN {
   7   our %tests = ( clone_name_with_chromosome => [
   8                                                [ 'SGN12H032K07',
   9                                                  { lib       => 'LE_HBa',
  10                                                    plate     => 32,
  11                                                    chr       => 12,
  12                                                    row       => 'K',
  13                                                    col       => 7,
  14                                                    clonetype => 'bac',
  15                                                    match     => 'SGN12H032K07',
  16                                                    version   => undef,
  17                                                    fragment  => undef,
  18                                                  },
  19                                                ],
  20                                                [ 'C11HBa119D16',
  21                                                  { lib       => 'LE_HBa',
  22                                                    plate     => 119,
  23                                                    chr       => 11,
  24                                                    row       => 'D',
  25                                                    col       => 16,
  26                                                    clonetype => 'bac',
  27                                                    match     => 'C11HBa119D16',
  28                                                    version   => undef,
  29                                                    fragment  => undef,
  30                                                  },
  31                                                ],
  32                                                [ 'C02HBa0155C04',
  33                                                  { lib       => 'LE_HBa',
  34                                                    plate     => 155,
  35                                                    chr       => 2,
  36                                                    row       => 'C',
  37                                                    col       => 4,
  38                                                    clonetype => 'bac',
  39                                                    match     => 'C02HBa0155C04',
  40                                                    version   => undef,
  41                                                    fragment  => undef,
  42                                                  },
  43                                                ],
  44                                                [ 'C02HBa0155C04.3-87',
  45                                                  { lib       => 'LE_HBa',
  46                                                    plate     => 155,
  47                                                    chr       => 2,
  48                                                    row       => 'C',
  49                                                    col       => 4,
  50                                                    clonetype => 'bac',
  51                                                    match     => 'C02HBa0155C04.3-87',
  52                                                    version   => 3,
  53                                                    fragment  => 87,
  54                                                  },
  55                                                ],
  56                                                [ 'C02HBa0155C04-87',
  57                                                  undef,
  58                                                ],
  59
  60                                                [ 'LE_HBa0034B23',
  61                                                  undef,
  62                                                ],
  63                                                [ '002C17',
  64                                                  undef,
  65                                                ],
  66                                               ],
  67                 seqwright_bac_chromat_file => [
  68                                                [ 'tomato_genome/bac_ends/Le-HBa001_A01-T7.ab1.gz',
  69                                                  { lib       => 'LE_HBa',
  70                                                    plate     => 1,
  71                                                    row       => 'A',
  72                                                    col       => 1,
  73                                                    clonetype => 'bac',
  74                                                    path      => 'tomato_genome/bac_ends/',
  75                                                    suffix    => '.ab1.gz',
  76                                                    primer    => 'T7',
  77                                                    filename  => 'Le-HBa001_A01-T7',
  78                                                    match     => 'Le-HBa001_A01-T7',
  79                                                  },
  80                                                ],
  81                                                [ '/bac_ends/SL_MboI_1_A05-SP6.g',
  82                                                  { lib       => 'SL_MboI',
  83                                                    plate     => 1,
  84                                                    col       => 5,
  85                                                    row       => 'A',
  86                                                    clonetype => 'bac',
  87                                                    path      => '/bac_ends/',
  88                                                    suffix    => '',
  89                                                    primer    => 'SP6',
  90                                                    filename  => 'SL_MboI_1_A05-SP6.g',
  91                                                    match     => 'SL_MboI_1_A05-SP6',
  92                                                  },
  93                                                ],
  94                                               ],
  95                  genbank_accession         => [
  96                                                [ 'CT990638.3' =>
  97                                                  {
  98                                                   lib       => 'LE_HBa',
  99                                                   plate     => 6,
 100                                                   row       => 'E',
 101                                                   col       => 18,
 102                                                   clonetype => 'bac',
 103                                                   match     => 'CT990638',
 104                                                  }
 105                                                ],
 106                                                [ 'CT990624' =>
 107                                                  {
 108                                                   lib       => 'LE_HBa',
 109                                                   plate     => 27,
 110                                                   row       => 'G',
 111                                                   col       => 19,
 112                                                   clonetype => 'bac',
 113                                                   match     => 'CT990624',
 114                                                  }
 115                                                ],
 116                                                [ CT990637 =>
 117                                                  {
 118                                                   lib       => 'LE_HBa',
 119                                                   plate     => 36,
 120                                                   row       => 'C',
 121                                                   col       => 23,
 122                                                   clonetype => 'bac',
 123                                                   match     => 'CT990637',
 124                                                  }
 125                                                ],
 126                                                #[ NE999999 => undef ],
 127                                               ],
 128               );
 129 }
 130 use Test::More qw/no_plan/;
 131
 132 use_ok('CXGN::Genomic::CloneNameParser');
 133
 134 my $parser = CXGN::Genomic::CloneNameParser->new;
 135 isa_ok($parser,'CXGN::Genomic::CloneNameParser' ,'CloneNameParser constructor works');
 136
 137 #test each clone name parser function jimmy
 138 foreach my $funcname (keys our %tests) {
 139   foreach my $test (@{$tests{$funcname}}) {
 140     #pretty-print the expected return value
 141     my $exp_str = hashref_to_str($test->[1]);
 142
 143     my $ret = $parser->$funcname( $test->[0] );
 144
 145     ok( eq_hash( $ret, $test->[1] ),"$funcname('$test->[0]')")
 146       or diag "expected $exp_str\ngot      ".hashref_to_str($ret)."\n";
 147   }
 148 }
 149
 150 sub hashref_to_str {
 151   my $ref = shift;
 152
 153   if ( defined($ref) ) {
 154     ref $ref eq 'HASH' or die 'not a hash ref';
 155
 156     my @strs;
 157     foreach my $key (sort keys %$ref) {
 158       my $val = $ref->{$key};
 159       $val = 'undef' unless defined($val);
 160       push @strs, "$key => $val";
 161     }
 162     return join(', ',@strs);
 163   } else {
 164     return 'undef';
 165   }
 166 }