t/Vista.t

   1 # -*-Perl-*-
   2 ## Bioperl Test Harness Script for Modules
   3
   4 use strict;
   5 BEGIN {
   6     use Bio::Root::Test;
   7     test_begin(-tests => 7);
   8
   9     use_ok('Bio::Tools::Run::Vista');
  10     use_ok('Bio::AlignIO');
  11 }
  12
  13 SKIP: {
  14     #Java and java version check
  15     my $v;
  16     if (-d "java") {
  17         skip("Skipping because no java present to run vista", 5);
  18     }
  19
  20     open(PIPE,"java -version 2>&1 |");
  21     while (<PIPE>) {
  22         if (/Java\sVersion\:\s(\d+\.\d+)/) {
  23             $v = $1;
  24             last;
  25         }
  26         elsif (/java version\s.(\d+\.\d+)/) {
  27             $v = $1;
  28             last;
  29         }
  30         elsif (/java version\s\"(\d\.\d)"/) {
  31             $v = $1;
  32             last;
  33         }
  34     }
  35     if ($v < 1.2) {
  36         skip("Skipping due to old java version", 5);
  37     }
  38
  39     open (PIPE ,'java Vista 2>&1 |');
  40     while(<PIPE>){
  41         if (   /NoClassDefFoundError/
  42             # For JRE 1.7.0_25 - Win7 - Spanish, the message is:
  43             # "Error: no se ha encontrado o cargado la clase principal Vista"
  44             or /^Error\:/
  45             ){
  46             diag('Vista.jar is not in your class path: '.$_);
  47             skip("Vista.jar is not in your class path",5);
  48         }
  49     }
  50     my $inputfilename= test_input_file("vista.cls");
  51     my $gff_file = test_input_file("vista.gff");
  52     my $aio = Bio::AlignIO->new(-file   => $inputfilename,
  53                                 -format => 'clustalw');
  54     my $aln = $aio->next_aln;
  55
  56     my $out= test_output_file();
  57     my $vis = Bio::Tools::Run::Vista->new('outfile'           => $out,
  58                                           'title'             => "My Vista Plot",
  59                                           'annotation'        => $gff_file,
  60                                           'annotation_format' => 'GFF',
  61                                           'min_perc_id'       => 75,
  62                                           'min_length'        => 100,
  63                                           'plotmin'           => 50,
  64                                           'tickdist'          => 2000,
  65                                           'window'            => 40,
  66                                           'numwindows'        => 4,
  67                                           'start'             => 50,
  68                                           'end'               => 1500,
  69                                           'tickdist'          => 100,
  70                                           'bases'             => 1000,
  71                                           'color'             => {'EXON'=>'45 25 54','CNS'=>'0 0 100'},
  72                                           'quiet'             =>1);
  73     isa_ok $vis,'Bio::Tools::Run::Vista';
  74     is $vis->plotmin, 50;
  75     is $vis->annotation, $gff_file;
  76
  77     $vis->run($aln,1);
  78     ok -e $out;
  79     $vis->run($aln,'mouse');
  80     ok -e $out;
  81 }