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LOCUS IDs no longer work, bad for swissprot-like IDs; need to come up…

… with an alternative
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1 parent 0c90a0d commit 2e3eb594a7948c104ef58ba18539ae55e2f4179c Chris Fields committed Feb 19, 2013
Showing with 7 additions and 8 deletions.
  1. +7 −8 t/RemoteDB/GenPept.t
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15 t/RemoteDB/GenPept.t
@@ -6,13 +6,13 @@ 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');
}
@@ -49,7 +49,7 @@ SKIP: {
$seq = $seqio = undef;
ok $gb = Bio::DB::GenPept->new('-delay' => 0);
-SKIP: {
+SKIP: {
eval {$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}, $seq->display_id;
@@ -65,17 +65,16 @@ SKIP: {
}
skip('No seqs returned', 8) if !$done;
is $done, 2;
- # swissprot genpept parsing
- eval {$seq = $gb->get_Seq_by_acc('2AAA_YEAST');};
+ # swissprot genpept parsing
+ eval {$seq = $gb->get_Seq_by_acc('P31383');};
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);
+ 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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