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# -*-Perl-*- Test Harness script for Bioperl
# $Id: GenPept.t 16089 2009-09-15 21:34:07Z cjfields $
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 21,
-requires_modules => [qw(IO::String
LWP::UserAgent
HTTP::Request::Common)],
-requires_networking => 1);
use_ok('Bio::DB::GenPept');
}
my %expected_lengths = (
'AAC06201' => 353,
'AAD15290' => 136,
'P31383' => 635,
);
my ($gb, $seq, $seqio);
#
# Bio::DB::GenPept
#
ok $gb = Bio::DB::GenPept->new();
SKIP: {
eval {$seqio = $gb->get_seq_stream(-uids => [2981015, 1621261, 195055], -mode => 'batch');};
skip "Couldn't connect to complete GenPept tests. Skipping those tests", 8 if $@;
my %result = ('AAC06201' => 353, 'CAB02640' => 193, 'AAD15290' => 136);
my $ct = 0;
while ($seq = $seqio->next_seq) {
$ct++;
my $acc = $seq->accession;
ok exists $result{ $acc };
is $seq->length, $result{ $acc };
delete $result{$acc};
}
skip('No seqs returned', 8) if !$ct;
is $ct, 3;
is %result, 0;
}
$seq = $seqio = undef;
ok $gb = Bio::DB::GenPept->new('-delay' => 0);
SKIP: {
eval {$seq = $gb->get_Seq_by_id('195055');};
skip "Couldn't connect to Genbank with Bio::DB::GenPept.pm. Skipping those tests", 10 if $@;
is $seq->length, $expected_lengths{$seq->display_id}, $seq->display_id;
eval {$seq = $gb->get_Seq_by_acc('AAC06201');};
skip "Couldn't connect to Genbank with Bio::DB::GenPept.pm. Skipping those tests", 9 if $@;
is $seq->length, $expected_lengths{$seq->display_id}, $seq->display_id;
eval {$seqio = $gb->get_Stream_by_id([qw(AAC06201 195055)]);};
skip "Couldn't connect to Genbank with Bio::DB::GenPept.pm. Skipping those tests", 8 if $@;
my $done = 0;
while( my $s = $seqio->next_seq ) {
is $s->length, $expected_lengths{$s->display_id}, $s->display_id;
$done++;
}
skip('No seqs returned', 8) if !$done;
is $done, 2;
# swissprot genpept parsing
eval {$seq = $gb->get_Seq_by_acc('2AAA_YEAST');};
skip "Couldn't connect to Genbank with Bio::DB::GenPept.pm. Skipping those tests", 5 if $@;
is $seq->length, $expected_lengths{$seq->display_id}, $seq->display_id;
# test dbsource stuff
# small chance this might change but hopefully not
my @annot = $seq->annotation->get_Annotations('dblink');
cmp_ok(scalar(@annot), '>', 31);
is $annot[0]->database, 'UniProtKB';
is $annot[0]->primary_id, '2AAA_YEAST';
is (($seq->annotation->get_Annotations('swissprot_dates'))[0]->value, 'Jul 1, 1993');
}
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