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# -*-Perl-*- Test Harness script for Bioperl
# $Id$
use strict;
BEGIN {
use Test::RequiresInternet;
use Test::Most tests => 44;
use_ok('Bio::DB::GenBank');
}
my %expected_lengths = (
'MUSIGHBA1' => 408,
'J00522.1' => 408,
'AF303112' => 1611,
'AF303112.1' => 1611,
'AF041456' => 1156,
'CELRABGDI' => 1743,
'JH374761' => 38055,
);
my ($gb, $seq, $seqio, $seqin);
my %params;
if (defined $ENV{BIOPERLEMAIL}) {
$params{'-email'} = $ENV{BIOPERLEMAIL};
$params{'-delay'} = 2;
}
$params{'-verbose'} = $ENV{BIOPERLDEBUG};
#
# Bio::DB::GenBank
#
ok $gb = Bio::DB::GenBank->new(%params), 'Bio::DB::GenBank';
# get a single seq
SKIP: {
eval {$seq = $gb->get_Seq_by_id('J00522');1};
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 $gb = Bio::DB::GenBank->new('-format' => 'fasta', '-retrievaltype' => 'tempfile', %params),
"Tempfile tests";
SKIP: {
eval {$seq = $gb->get_Seq_by_id('J00522');};
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]}, "Check tmpfile: get_Seq_by_id:".$seq->display_id;
eval {$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]}, "Check tmpfile: get_Seq_by_acc:".$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}, "Check tmpfile: get_Stream_by_id:".$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 $gb = Bio::DB::GenBank->new('-retrievaltype' => 'pipeline', %params), "Pipeline tests";
SKIP: {
eval {$seq = $gb->get_Seq_by_id('J00522');};
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}, "Check pipeline: get_Seq_by_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}, "Check pipeline: get_Seq_by_acc:".$seq->display_id;
eval {$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}, "Check pipeline: get_Stream_by_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 $gb = Bio::DB::GenBank->new('-format' => 'gbwithparts', %params);
SKIP: {
eval {$seq = $gb->get_Seq_by_id('JH374761');};
skip "Couldn't connect to GenBank with Bio::DB::GenBank.pm. Skipping those tests: $@", 3 if $@;
is $seq->length, $expected_lengths{$seq->display_id}, "Check contig: get_Seq_by_id:".$seq->display_id;
# now to check that postprocess_data in NCBIHelper catches CONTIG...
ok $gb = Bio::DB::GenBank->new('-format' => 'gb',%params);
eval {$seq = $gb->get_Seq_by_id('JH374761');};
skip "Couldn't connect to GenBank with Bio::DB::GenBank.pm. Skipping those tests: $@", 1 if $@;
is $seq->length, $expected_lengths{$seq->display_id}, "Check contig: get_Seq_by_acc".$seq->display_id;
}
$seq = $seqio = undef;
# bug 1405
my @result;
ok $gb = Bio::DB::GenBank->new(-format => 'Fasta', -seq_start => 2, -seq_stop => 7, %params);
SKIP: {
eval {$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 $gb = Bio::DB::GenBank->new(-format => 'fasta', -complexity => 0, %params);
eval {$seqin = $gb->get_Stream_by_acc("21614549");};
skip "Couldn't connect to complete GenBank tests. Skipping those tests: $@", 13 if $@;
my @result = (4366, 'dna', 620, 'protein');
# Test number is labile (dependent on remote results)
while ($seq = $seqin->next_seq) {
is $seq->length, shift(@result);
is $seq->alphabet, shift(@result);
}
is(@result, 0, @result ? "Missing results:".join(",", @result) : "All results checked");
# 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
$gb = Bio::DB::GenBank->new(%params);
eval {$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 $ct = 0;
# Test number is labile (dependent on remote results)
while ($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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