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# -*-Perl-*- Test Harness script for Bioperl
# $Id: epost.t 15112 2008-12-08 18:12:38Z sendu $
use strict;
use warnings;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 58,
-requires_module => 'XML::Simple');
use_ok('Bio::Tools::EUtilities');
use_ok('Bio::Tools::EUtilities::EUtilParameters');
}
# check -correspondence => 0 (default) - this is set up to return the
# exact same thing as correspondece = 1, tested below)
my $eutil = Bio::Tools::EUtilities->new(
-eutil => 'elink',
-file => test_input_file('eutils','elink_scores.xml'));
isa_ok($eutil, 'Bio::Tools::EUtilities::Link');
is(join(',',$eutil->get_databases), 'protein');
# for elinks, IDs are globbed together when called from the parser unless a database is specified
is(join(',',$eutil->get_ids), '15622530,15921743,70607303,68567951,145702933,'.
'146304683,6015889,13813749,15897502,15622530,74573864,15921743', 'get_ids');
my @ls = $eutil->get_LinkSets;
is(scalar(@ls), 2, 'uncorrelated LinkSets lump everything together');
is(join(',',$ls[1]->get_databases), 'protein');
isa_ok($ls[0], 'Bio::Tools::EUtilities::EUtilDataI');
isa_ok($ls[0], 'Bio::Tools::EUtilities::Link::LinkSet');
# check data in LinkSets
is(join(',',$ls[0]->get_ids), '15622530,15921743,70607303,68567951,145702933,'.
'146304683,6015889,13813749,15897502');
is(join(',',$ls[0]->get_databases), 'protein');
is(join(',',$ls[0]->get_submitted_ids), '15622530');
is($ls[0]->get_dbfrom, 'protein');
is(join(',',$ls[0]->get_link_names), 'protein_protein');
is($ls[0]->has_linkout, 0);
is($ls[0]->has_neighbor, 0);
# has relatedness scores!
is($ls[0]->has_scores, 1);
my %sd = (
15622530 => 2147483647,
15921743 => 381,
70607303 => 178,
68567951 => 178,
145702933 => 161,
146304683 => 161,
6015889 => 142,
13813749 => 142,
15897502 => 142);
my %sc = $ls[0]->get_scores;
for my $id ($ls[0]->get_ids) {
ok(exists($sc{$id}));
is($sc{$id}, $sd{$id});
delete $sd{$id};
}
is(keys %sd, 0);
# no LinkInfo
my @info = $ls[0]->get_LinkInfo;
is(scalar(@info), 0);
# no UrlLinks
my @urls = $ls[0]->get_UrlLinks;
is(scalar(@urls), 0);
is(join(',',$ls[1]->get_ids), '15622530,74573864,15921743');
is(join(',',$ls[1]->get_databases), 'protein');
is(join(',',$ls[1]->get_submitted_ids), '15622530');
is(join(',',$ls[1]->get_link_names), 'protein_protein_identical');
is($ls[1]->get_webenv, undef);
is($ls[1]->get_dbfrom, 'protein');
is($ls[1]->has_linkout, 0);
is($ls[1]->has_neighbor, 0);
# has relatedness scores!
is($ls[1]->has_scores, 1);
%sd = (
15622530 => 2147483647,
74573864 => 0,
15921743 => 0,
);
%sc = $ls[1]->get_scores;
for my $id ($ls[1]->get_ids) {
ok(exists($sc{$id}));
is($sc{$id}, $sd{$id});
delete $sd{$id};
}
is(keys %sd, 0);
# HistoryI
is($ls[1]->get_webenv, undef);
is($ls[1]->get_query_key, undef);
# no LinkInfo
@info = $ls[1]->get_LinkInfo;
is(scalar(@info), 0);
# no UrlLinks
@urls = $ls[1]->get_UrlLinks;
is(scalar(@urls), 0);
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