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# -*-Perl-*- Test Harness script for Bioperl
# $Id$
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 14);
$ENV{OBDA_SEARCH_PATH} = 't/data/registry/flat;t/data/registry/bdb';
use_ok('Bio::DB::Registry');
use_ok('Bio::DB::Flat');
}
# we need a temp directory t/tmp since t/tmp is specified in the registry files
my $tmpdir = File::Spec->catfile(qw(t tmp));
mkdir($tmpdir,0777);
SKIP: {
skip "unable to create temp dir '$tmpdir', skipping tests", 12 unless -d $tmpdir;
my $flat = Bio::DB::Flat->new(-directory => $tmpdir,
-dbname => 'testflat',
-format => 'fasta',
-index => 'binarysearch',
-write_flag => 1 );
my $entries = $flat->build_index(test_input_file('cysprot.fa'));
is $entries, 7;
SKIP: {
test_skip(-tests => 2, -requires_modules => [qw(DB_File)]);
my $bdb = Bio::DB::Flat->new(-directory => $tmpdir,
-dbname => 'testbdb',
-format => 'fasta',
-index => 'bdb',
-write_flag => 1 );
ok defined($bdb);
$entries = $bdb->build_index(test_input_file('cysprot.fa'));
is $entries, 7;
}
SKIP: {
test_skip(-tests => 9,
-requires_modules => [qw(LWP::UserAgent HTTP::Request::Common)],
-requires_networking => 1);
my $registry = Bio::DB::Registry->new();
ok defined($registry);
my @available_services = $registry->services;
ok grep /testflat/,@available_services;
my $db = $registry->get_database('testflat');
ok defined($db);
my $seq = $db->get_Seq_by_id("ALEU_HORVU");
ok defined($seq);
my $sequence = $seq->seq;
is $sequence, "MAHARVLLLALAVLATAAVAVASSSSFADSNPIRPVTDRAASTLESAVLGALGRTRHALRFARFAVRYGKSYESAAEVRRRFRIFSESLEEVRSTNRKGLPYRLGINRFSDMSWEEFQATRLGAAQTCSATLAGNHLMRDAAALPETKDWREDGIVSPVKNQAHCGSCWTFSTTGALEAAYTQATGKNISLSEQQLVDCAGGFNNFGCNGGLPSQAFEYIKYNGGIDTEESYPYKGVNGVCHYKAENAAVQVLDSVNITLNAEDELKNAVGLVRPVSVAFQVIDGFRQYKSGVYTSDHCGTTPDDVNHAVLAVGYGVENGVPYWLIKNSWGADWGDNGYFKMEMGKNMCAIATCASYPVVAA";
SKIP: {
test_skip(-tests => 4, -requires_modules => [qw(DB_File)]);
ok grep /testbdb/,@available_services;
$db = $registry->get_database('testbdb');
ok defined($db);
$seq = $db->get_Seq_by_id("ALEU_HORVU");
ok defined($seq);
$sequence = $seq->seq;
is $sequence, "MAHARVLLLALAVLATAAVAVASSSSFADSNPIRPVTDRAASTLESAVLGALGRTRHALRFARFAVRYGKSYESAAEVRRRFRIFSESLEEVRSTNRKGLPYRLGINRFSDMSWEEFQATRLGAAQTCSATLAGNHLMRDAAALPETKDWREDGIVSPVKNQAHCGSCWTFSTTGALEAAYTQATGKNISLSEQQLVDCAGGFNNFGCNGGLPSQAFEYIKYNGGIDTEESYPYKGVNGVCHYKAENAAVQVLDSVNITLNAEDELKNAVGLVRPVSVAFQVIDGFRQYKSGVYTSDHCGTTPDDVNHAVLAVGYGVENGVPYWLIKNSWGADWGDNGYFKMEMGKNMCAIATCASYPVVAA";
}
}
}
END {
File::Path::rmtree($tmpdir) if ($tmpdir && (-d $tmpdir));
}
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