t/ESEfinder.t

   1 # -*-Perl-*- Test Harness script for Bioperl
   2 # $Id$
   3
   4 use strict;
   5
   6 BEGIN {
   7         use lib 't/lib';
   8         use BioperlTest;
   9
  10         test_begin(-tests => 13,
  11                            -requires_modules => [qw(IO::String
  12                                                                                 LWP::UserAgent
  13                                                                                 Bio::WebAgent
  14                                                                                 HTML::HeadParser
  15                                                                                 HTTP::Request::Common)],
  16                            -requires_networking => 1);
  17
  18         use_ok('Bio::Tools::Analysis::DNA::ESEfinder');
  19         use_ok('Data::Dumper');
  20         use_ok('Bio::PrimarySeq');
  21 }
  22
  23 #######all these tests work with 1ary seq########
  24 my $seq = Bio::PrimarySeq->new(-id=>'bioperl',
  25                                -seq=>'atcgatgctatgcatgctatgggtgtgattcgatgcgactgttcatcgtagccccccccccccccctttt');
  26 ok my $tool = Bio::Tools::Analysis::DNA::ESEfinder->new(-seq => $seq);
  27
  28 SKIP: {
  29         eval {$tool->run;};
  30         skip "Could not connect to ESEfinder server, skipping those tests", 9 if $@;
  31     ok my @res = $tool->result('Bio::SeqFeatureI');
  32         ok @res > 0;
  33     ok my $raw = $tool->result('');
  34     ok my $parsed = $tool->result('parsed');
  35     ok my $meta = $tool->result('all');
  36     is $parsed->[0][1], 41;
  37
  38         SKIP: {
  39                 test_skip(-tests => 3, -requires_module => 'Bio::Seq::Meta::Array');
  40                 is $meta->{'seq'}, "atcgatgctatgcatgctatgggtgtgattcgatgcgactgttcatcgtagccccccccccccccctttt";
  41                 is $meta->named_submeta_text('ESEfinder_SRp55', 1,2), "-3.221149 -1.602223";
  42                 is $meta->seq, "atcgatgctatgcatgctatgggtgtgattcgatgcgactgttcatcgtagccccccccccccccctttt";
  43         }
  44 }