t/Vista.t

   1 # -*-Perl-*-
   2 ## Bioperl Test Harness Script for Modules
   3
   4 use strict;
   5 BEGIN {
   6     eval { require Test; };
   7     if( $@ ) {
   8         use lib 't';
   9     }
  10     use Test;
  11     use vars qw($NTESTS);
  12     $NTESTS = 5;
  13     plan tests => $NTESTS;
  14 }
  15
  16 use vars qw( $reason);
  17 $reason = 'Unable to run Vista , java may not be installed';
  18
  19 END {
  20    foreach ( $Test::ntest..$NTESTS ) {
  21        skip($reason,1);
  22    }
  23    unlink "t/data/vista.pdf";
  24 }
  25
  26 use Bio::Tools::Run::Vista;
  27 use Bio::AlignIO;
  28
  29 #Java and java version check
  30 my $v;
  31 if (-d "java") {
  32     print STDERR "You must have java to run vista\n";
  33     $reason = "Skipping because no java present to run vista ";
  34     exit(0);
  35 }
  36 my $output = `java -version 2>&1`;
  37 open(PIPE,"java -version 2>&1 |");
  38
  39 while (<PIPE>) {
  40     if (/Java\sVersion\:\s(\d+\.\d+)/) {
  41         $v = $1;
  42         last;
  43     }
  44     elsif (/java version\s.(\d+\.\d+)/) {
  45         $v = $1;
  46         last;
  47     }
  48     elsif (/java version\s\"(\d\.\d)"/) {
  49          $v = $1;
  50         last;
  51     }
  52 }
  53 if ($v < 1.2) {
  54     print STDERR "You need at least version 1.2 of JDK to run vista\n";
  55     $reason = "Skipping due to old java version";
  56     exit(0);
  57 }
  58 open (PIPE ,'java Vista 2>&1 |');
  59 while(<PIPE>){
  60   if(/NoClassDefFoundError/){
  61     print STDERR "Vista.jar is not your class path \n";
  62     exit(0);
  63   }
  64 }
  65 my $inputfilename= Bio::Root::IO->catfile("t","data","vista.cls");
  66 my $gff_file = Bio::Root::IO->catfile("t","data","vista.gff");
  67 my $aio = Bio::AlignIO->new(-file=>$inputfilename,-format=>'clustalw');
  68 my $aln = $aio->next_aln;
  69
  70 my $out= Bio::Root::IO->catfile("t","data","vista.pdf");
  71 my $vis = Bio::Tools::Run::Vista->new('outfile'=>$out,
  72                                       'title' => "My Vista Plot",
  73                                         'annotation'=>$gff_file,
  74                                         'annotation_format'=>'GFF',
  75                                         'min_perc_id'=>75,
  76                                         'min_length'=>100,
  77                                         'plotmin'   => 50,
  78                                         'tickdist' => 2000,
  79                                         'window'=>40,
  80                                         'numwindows'=>4,
  81                                         'start'=>50,
  82                                         'end'=>1500,
  83                                         'tickdist'=>100,
  84                                         'bases'=>1000,
  85                                         'color'=> {'EXON'=>'45 25 54','CNS'=>'0 0 100'},
  86                                         'quiet'=>1);
  87 ok $vis->isa('Bio::Tools::Run::Vista');
  88 ok $vis->plotmin, 50,
  89 ok $vis->annotation, $gff_file;
  90
  91 $vis->run($aln,1);
  92 ok -e $out;
  93 unlink $out;
  94 $vis->run($aln,'mouse');
  95 ok -e $out;
  96
  97