t/Tools/TargetP.t

   1 # -*-Perl-*- Test Harness script for Bioperl
   2 # $Id$
   3
   4 use strict;
   5
   6 BEGIN {
   7     use lib '.';
   8     use Bio::Root::Test;
   9
  10     test_begin(-tests => 124);
  11
  12         use_ok('Bio::Tools::TargetP');
  13 }
  14
  15 my $targetp = Bio::Tools::TargetP->new(
  16                                        -file => test_input_file('targetp.out')
  17                                       );
  18
  19 ok($targetp);
  20
  21 my $items = {
  22              '1' => {
  23                      'id' => 'BC1G_00001.1',
  24                      'len' => '173',
  25                      'mTP' => '0.393',
  26                      'SP'  => '0.024',
  27                      'other' => '0.683',
  28                      'loc'   => '_',
  29                      'RC'    => '4',
  30                      'tplen' => undef,
  31                     },
  32              '2' => {
  33                      'id' => 'BC1G_00002.1',
  34                      'len' => '120',
  35                      'mTP' => '0.619',
  36                      'SP'  => '0.040',
  37                      'other' => '0.458',
  38                      'loc'   => 'M',
  39                      'RC'    => '5',
  40                      'tplen' => '97',
  41                     },
  42              '3' => {
  43                      'id' => 'BC1G_00003.1',
  44                      'len' => '323',
  45                      'mTP' => '0.094',
  46                      'SP'  => '0.895',
  47                      'other' => '0.027',
  48                      'loc'   => 'S',
  49                      'RC'    => '1',
  50                      'tplen' => '21',
  51                     },
  52              '4' => {
  53                      'id' => 'BC1G_00004.1',
  54                      'len' => '361',
  55                      'mTP' => '0.402',
  56                      'SP'  => '0.072',
  57                      'other' => '0.479',
  58                      'loc'   => '_',
  59                      'RC'    => '5',
  60                      'tplen' => undef,
  61                     },
  62              '5' => {
  63                      'id' => 'BC1G_00005.1',
  64                      'len' => '244',
  65                      'mTP' => '0.526',
  66                      'SP'  => '0.035',
  67                      'other' => '0.548',
  68                      'loc'   => '_',
  69                      'RC'    => '5',
  70                      'tplen' => undef,
  71                     },
  72              '6' => {
  73                      'id' => 'BC1G_00006.1',
  74                      'len' => '35',
  75                      'mTP' => '0.234',
  76                      'SP'  => '0.036',
  77                      'other' => '0.819',
  78                      'loc'   => '_',
  79                      'RC'    => '3',
  80                      'tplen' => undef,
  81                     },
  82              '7' => {
  83                      'id' => 'BC1G_00007.1',
  84                      'len' => '73',
  85                      'mTP' => '0.292',
  86                      'SP'  => '0.127',
  87                      'other' => '0.431',
  88                      'loc'   => '_',
  89                      'RC'    => '5',
  90                      'tplen' => undef,
  91                     },
  92              '8' => {
  93                      'id' => 'BC1G_00008.1',
  94                      'len' => '349',
  95                      'mTP' => '0.088',
  96                      'SP'  => '0.958',
  97                      'other' => '0.078',
  98                      'loc'   => 'S',
  99                      'RC'    => '1',
 100                      'tplen' => '82',
 101                     },
 102              '9' => {
 103                      'id' => 'BC1G_00009.1',
 104                      'len' => '514',
 105                      'mTP' => '0.183',
 106                      'SP'  => '0.102',
 107                      'other' => '0.735',
 108                      'loc'   => '_',
 109                      'RC'    => '3',
 110                      'tplen' => undef,
 111                     },
 112              '10' => {
 113                      'id' => 'BC1G_00010.1',
 114                      'len' => '440',
 115                      'mTP' => '0.114',
 116                      'SP'  => '0.088',
 117                      'other' => '0.865',
 118                      'loc'   => '_',
 119                      'RC'    => '2',
 120                      'tplen' => undef,
 121                     },
 122              '11' => {
 123                      'id' => 'BC1G_04501.1',
 124                      'len' => '215',
 125                      'mTP' => '0.185',
 126                      'SP'  => '0.038',
 127                      'other' => '0.843',
 128                      'loc'   => '_',
 129                      'RC'    => '2',
 130                      'tplen' => undef,
 131                     },
 132              '12' => {
 133                      'id' => 'BC1G_04502.1',
 134                      'len' => '395',
 135                      'mTP' => '0.118',
 136                      'SP'  => '0.164',
 137                      'other' => '0.825',
 138                      'loc'   => '_',
 139                      'RC'    => '2',
 140                      'tplen' => undef,
 141                     },
 142              '13' => {
 143                      'id' => 'BC1G_04503.1',
 144                      'len' => '199',
 145                      'mTP' => '0.515',
 146                      'SP'  => '0.062',
 147                      'other' => '0.436',
 148                      'loc'   => 'M',
 149                      'RC'    => '5',
 150                      'tplen' => '20',
 151                     },
 152              '14' => {
 153                      'id' => 'BC1G_04504.1',
 154                      'len' => '220',
 155                      'mTP' => '0.440',
 156                      'SP'  => '0.030',
 157                      'other' => '0.707',
 158                      'loc'   => '_',
 159                      'RC'    => '4',
 160                      'tplen' => undef,
 161                     },
 162              '15' => {
 163                      'id' => 'BC1G_04505.1',
 164                      'len' => '67',
 165                      'mTP' => '0.382',
 166                      'SP'  => '0.049',
 167                      'other' => '0.610',
 168                      'loc'   => '_',
 169                      'RC'    => '4',
 170                      'tplen' => undef,
 171                     },
 172             };
 173
 174 my $i = 1;
 175 $targetp->_parse_results();
 176
 177 is($targetp->network(), 'NON-PLANT');
 178 is($targetp->analysis_method_version(), "v1.1");
 179
 180 while(my $feat = $targetp->next_prediction()){
 181
 182     is($feat->seq_id(), $items->{$i}->{id}, "good SeqID");
 183     is($feat->length(), $items->{$i}->{len}, "good Seqlength");
 184     is(($feat->get_tag_values('mitochondrionCutOff'))[0], $items->{$i}->{mTP}, "correct Mitochondrion cutoff");
 185     is(($feat->get_tag_values('signalPeptideCutOff'))[0], $items->{$i}->{SP}, "correct signalpPeptide cutoff");
 186     is(($feat->get_tag_values('otherCutOff'))[0], $items->{$i}->{other}, "correct other cutoff");
 187     is(($feat->get_tag_values('location'))[0], $targetp->_toString_location($items->{$i}->{loc}), "correct location");
 188     is(($feat->get_tag_values('reliabilityClass'))[0], $items->{$i}->{RC}, "correct Reliability class score");
 189
 190         if ($feat->has_tag('signalPeptideLength')) {
 191                 is(($feat->get_tag_values('signalPeptideLength'))[0], $items->{$i}->{tplen}, "correct peptide signal length")
 192         } else {
 193                 is($feat->has_tag('signalPeptideLength'), '', "No peptide signal length reported")
 194         }
 195     $i++;
 196 }