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# -*-Perl-*- Test Harness script for Bioperl
# $Id: GenBank.t 16089 2009-09-15 21:34:07Z cjfields $
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 44,
-requires_modules => [qw(IO::String
LWP::UserAgent
HTTP::Request::Common)],
-requires_networking => 1);
use_ok('Bio::DB::GenBank');
}
my %expected_lengths = (
'MUSIGHBA1' => 408,
'AF303112' => 1611,
'AF303112.1' => 1611,
'AF041456' => 1156,
'CELRABGDI' => 1743,
'CH402638' => 5041
);
my ($gb, $seq, $seqio, $seqin);
#
# Bio::DB::GenBank
#
ok $gb = Bio::DB::GenBank->new('-delay'=>0), 'Bio::DB::GenBank';
# get a single seq
SKIP: {
eval {$seq = $gb->get_Seq_by_id('MUSIGHBA1');};
skip "Couldn't connect to Genbank with Bio::DB::GenBank.pm. Do you have network access? Skipping GenBank tests", 4 if $@;
is $seq->length, $expected_lengths{$seq->display_id}, $seq->display_id;
eval {$seq = $gb->get_Seq_by_acc('AF303112');};
skip "Couldn't connect to Genbank with Bio::DB::GenBank.pm. Transient network problems? Skipping GenBank tests", 3 if $@;
is $seq->length, $expected_lengths{$seq->display_id}, $seq->display_id;
eval {$seq = $gb->get_Seq_by_version('AF303112.1');};
skip "Couldn't connect to Genbank with Bio::DB::GenBank.pm. Transient network problems? Skipping GenBank tests", 2 if $@;
is $seq->length, $expected_lengths{$seq->display_id}, $seq->display_id;
eval {$seq = $gb->get_Seq_by_gi('405830');};
skip "Couldn't connect to Genbank with Bio::DB::GenBank.pm. Transient network problems? Skipping GenBank tests", 1 if $@;
is $seq->length, $expected_lengths{$seq->display_id}, $seq->display_id;
}
$seq = $seqio = undef;
# batch mode
SKIP: {
eval {$seqio = $gb->get_Stream_by_id([qw(J00522 AF303112 2981014)]);};
skip "Batch access test failed for Genbank. Skipping those tests", 4 if $@;
my $done = 0;
while (my $s = $seqio->next_seq) {
is $s->length, $expected_lengths{$s->display_id}, $s->display_id;
$done++;
}
skip('No seqs returned', 4) if !$done;
is $done, 3;
}
$seq = $seqio = undef;
# test the temporary file creation and fasta
ok $gb = Bio::DB::GenBank->new('-format' => 'fasta', '-retrievaltype' => 'tempfile', '-delay' => 0);
SKIP: {
eval {$seq = $gb->get_Seq_by_id('MUSIGHBA1');};
skip "Couldn't connect to complete GenBank tests with a tempfile with Bio::DB::GenBank.pm. Skipping those tests", 6 if $@;
# last part of id holds the key
is $seq->length, $expected_lengths{(split(/\|/,$seq->display_id))[-1]}, $seq->display_id;
eval {$seq = $gb->get_Seq_by_acc('AF303112');};
skip "Couldn't connect to complete GenBank tests with a tempfile with Bio::DB::GenBank.pm. Skipping those tests", 5 if $@;
# last part of id holds the key
is $seq->length, $expected_lengths{(split(/\|/,$seq->display_id))[-1]}, $seq->display_id;
# batch mode requires genbank format
$gb->request_format("gb");
eval {$seqio = $gb->get_Stream_by_id([qw(J00522 AF303112 2981014)]);};
skip "Couldn't connect to complete GenBank batch tests with a tempfile with Bio::DB::GenBank.pm. Skipping those tests", 4 if $@;
my $done = 0;
while (my $s = $seqio->next_seq) {
is $s->length, $expected_lengths{$s->display_id};
undef $gb; # test the case where the db is gone,
# but a temp file should remain until seqio goes away.
$done++;
}
skip('No seqs returned', 4) if !$done;
is $done, 3;
}
$seq = $seqio = undef;
# test pipeline creation
ok $gb = Bio::DB::GenBank->new('-retrievaltype' => 'pipeline', '-delay' => 0);
SKIP: {
eval {$seq = $gb->get_Seq_by_id('MUSIGHBA1');};
skip "Couldn't connect to complete GenBank tests with a pipeline with Bio::DB::GenBank.pm. Skipping those tests", 6 if $@;
is $seq->length, $expected_lengths{$seq->display_id}, $seq->display_id;
eval {$seq = $gb->get_Seq_by_acc('AF303112');};
skip "Couldn't connect to complete GenBank tests with a pipeline with Bio::DB::GenBank.pm. Skipping those tests", 5 if $@;
is $seq->length, $expected_lengths{$seq->display_id}, $seq->display_id;
eval {$seqio = $gb->get_Stream_by_id([qw(J00522 AF303112 2981014)]);};
skip "Couldn't connect to complete GenBank tests with a pipeline with Bio::DB::GenBank.pm. Skipping those tests", 4 if $@;
my $done = 0;
while (my $s = $seqio->next_seq) {
is $s->length, $expected_lengths{$s->display_id}, $s->display_id;
undef $gb; # test the case where the db is gone,
# but the pipeline should remain until seqio goes away
$done++;
}
skip('No seqs returned', 4) if !$done;
is $done, 3;
}
$seq = $seqio = undef;
# test contig retrieval
ok $gb = Bio::DB::GenBank->new('-delay' => 0, '-format' => 'gbwithparts');
SKIP: {
eval {$seq = $gb->get_Seq_by_id('CH402638');};
skip "Couldn't connect to GenBank with Bio::DB::GenBank.pm. Skipping those tests", 3 if $@;
is $seq->length, $expected_lengths{$seq->display_id}, $seq->display_id;
# now to check that postprocess_data in NCBIHelper catches CONTIG...
ok $gb = Bio::DB::GenBank->new('-delay' => 0, '-format' => 'gb');
eval {$seq = $gb->get_Seq_by_id('CH402638');};
skip "Couldn't connect to GenBank with Bio::DB::GenBank.pm. Skipping those tests", 1 if $@;
is $seq->length, $expected_lengths{$seq->display_id}, $seq->display_id;
}
$seq = $seqio = undef;
# bug 1405
my @result;
ok $gb = Bio::DB::GenBank->new(-format => 'Fasta', -seq_start => 2, -seq_stop => 7);
SKIP: {
eval {$seq = $gb->get_Seq_by_acc("A11111");};
skip "Couldn't connect to complete GenBank tests. Skipping those tests", 15 if $@;
is $seq->length, 6;
# complexity tests
ok $gb = Bio::DB::GenBank->new(-format => 'Fasta', -complexity => 0);
eval {$seqin = $gb->get_Stream_by_acc("5");};
skip "Couldn't connect to complete GenBank tests. Skipping those tests", 13 if $@;
@result = (1136, 'dna', 342, 'protein');
while ($seq = $seqin->next_seq) {
is $seq->length, shift(@result);
is $seq->alphabet, shift(@result);
}
is @result, 0;
# Real batch retrieval using epost/efetch
# these tests may change if integrated further into Bio::DB::Gen*
# Currently only useful for retrieving GI's via get_seq_stream
$gb = Bio::DB::GenBank->new();
eval {$seqin = $gb->get_seq_stream(-uids => [4887706 ,431229, 147460], -mode => 'batch');};
skip "Couldn't connect to complete GenBank batchmode epost/efetch tests. Skipping those tests", 8 if $@;
my %result = ('M59757' => 12611 ,'X76083'=> 3140, 'J01670'=> 1593);
my $ct = 0;
while ($seq = $seqin->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;
}
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