t/RemoteDB/SwissProt.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               => 23,
  11                -requires_modules    => [qw(IO::String
  12                                            LWP::UserAgent
  13                                            HTTP::Request::Common
  14                                            Data::Stag)],
  15                -requires_networking => 1);
  16
  17     use_ok('Bio::DB::SwissProt');
  18 }
  19
  20 ok my $gb = Bio::DB::SwissProt->new(-retrievaltype => 'pipeline',
  21                                     -delay         => 0);
  22
  23 my %expected_lengths = (
  24                         'NDP_MOUSE'   => 131,
  25                         'NDP_HUMAN'   => 133,
  26                         'BOLA_HAEIN'  => 103,
  27                         'YNB3_YEAST'  => 125,
  28                         'O39869'      => 56,
  29                         'DEGP_CHLTR'  => 497,
  30                         'DEGPL_CHLTR' => 497
  31                         );
  32
  33 my ($seq, $seqio);
  34
  35 SKIP: {
  36     eval {$seq = $gb->get_Seq_by_id('YNB3_YEAST');};
  37     skip "Couldn't connect to SwissProt with Bio::DB::SwissProt.pm. Skipping those tests", 14 if $@;
  38     is $seq->length, $expected_lengths{$seq->display_id}, $seq->display_id;
  39     is $seq->division, 'YEAST';
  40
  41     eval {$seq = $gb->get_Seq_by_acc('P43780');};
  42     skip "Couldn't connect to SwissProt with Bio::DB::SwissProt.pm. Skipping those tests", 12 if $@;
  43     is $seq->length, $expected_lengths{$seq->display_id}, $seq->display_id;
  44     eval {$seq = $gb->get_Seq_by_acc('O39869');};
  45     skip "Couldn't connect to SwissProt with Bio::DB::SwissProt.pm. Skipping those tests", 11 if $@;
  46     is $seq->length, $expected_lengths{$seq->accession_number}, $seq->accession_number;
  47     is $seq->accession_number, 'O39869';
  48     is $seq->division, '9PICO';
  49
  50     # test for bug #958
  51     eval {$seq = $gb->get_Seq_by_id('P18584');};
  52     skip "Couldn't connect to SwissProt with Bio::DB::SwissProt.pm. Skipping those tests", 8 if $@;
  53     ok exists $expected_lengths{$seq->display_id}, 'P18584';
  54     is $seq->length, $expected_lengths{$seq->display_id}, $seq->display_id;
  55     is $seq->division, 'CHLTR';
  56
  57     ok $gb = Bio::DB::SwissProt->new('-retrievaltype' => 'tempfile', '-delay' => 0);
  58     eval {$seqio = $gb->get_Stream_by_id(['NDP_MOUSE', 'NDP_HUMAN']);};
  59     skip "Couldn't connect to SwissProt with Bio::DB::SwissProt.pm. Skipping those tests", 4 if $@;
  60     undef $gb; # testing to see if we can remove gb
  61     ok $seq = $seqio->next_seq();
  62     is $seq->length, $expected_lengths{$seq->display_id}, $seq->display_id;
  63     ok $seq = $seqio->next_seq();
  64     is $seq->length, $expected_lengths{$seq->display_id}, $seq->display_id;
  65 }
  66
  67 # test idtracker() method
  68 ok $gb = Bio::DB::SwissProt->new(-retrievaltype => 'pipeline',
  69                                  -delay         => 0,
  70                                  -verbose       => 2);
  71
  72 SKIP: {
  73     my $map;
  74     # check old ID
  75     eval {$map = $gb->id_mapper(-from => 'ACC+ID',
  76                                 -to   => 'ACC',
  77                                 -ids  => [qw(MYOD1_PIG PYRC_YEAST)]
  78                                 )};
  79     skip("Problem with idtracker(), skipping these tests: $@", 6) if $@;
  80
  81     cmp_ok(@{$map->{MYOD1_PIG}}, '>=', 1);
  82     is($map->{MYOD1_PIG}[0], 'P49811');
  83     cmp_ok(@{$map->{PYRC_YEAST}}, '>=', 1);
  84     is($map->{PYRC_YEAST}[0], 'P20051');
  85
  86     eval {$map = $gb->id_mapper(-from => 'ACC+ID',
  87                                 -to   => 'EMBL',
  88                                 -ids  => [qw(PYRC_YEAST)]
  89                                 )};
  90     skip("Problem with idtracker(), skipping these tests: $@", 2) if $@;
  91
  92     cmp_ok(@{$map->{PYRC_YEAST}}, '>=', 2);
  93     like($map->{PYRC_YEAST}[0], qr/^[A-Z0-9]/);
  94 }
  95
  96 1;