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# -*-Perl-*- Test Harness script for Bioperl
# $Id$
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 27,
-requires_module => 'DB_File');
use_ok('Bio::DB::Flat');
}
my $verbose = test_debug();
# First of all we need to create an flat db
my $tmpdir = test_output_dir();
my $db = Bio::DB::Flat->new(-directory => $tmpdir,
-index => 'bdb',
-dbname => 'mydb',
-format => 'fasta',
-verbose => $verbose,
-write_flag => 1 );
ok($db);
my $dir = test_input_file('AAC12660.fa');
my $result = $db->build_index(glob($dir));
ok($result);
# Now let's get the sequence out again
my $seq = $db->get_Seq_by_id('AAC12660');
ok($seq);
is($seq->length,504);
undef $db;
$db = Bio::DB::Flat->new(-directory => $tmpdir,
-index => 'bdb',
-format => 'embl',
-dbname => 'myembl',
-verbose => $verbose,
-write_flag => 1 );
$dir= test_input_file('cds_sample.embl');
$result = $db->build_index(glob($dir));
is ($db->get_all_primary_ids, 1);
#is ($db->get_all_accs, 1);
ok($result);
$seq = $db->get_Seq_by_id('EAL24309');
ok($seq);
is($seq->length,192);
# deal with wantarray conditions
$seq = $db->get_Seq_by_acc('CH236947.1');
ok($seq && ref($seq));
is($seq->length,192);
undef $db;
$db = Bio::DB::Flat->new(-directory => $tmpdir,
-index => 'binarysearch',
-format => 'fasta',
-dbname => 'mybinfa',
-verbose => $verbose,
-write_flag => 1
);
$dir = test_input_file('dbfa', '1.fa');
$result = $db->build_index($dir);
ok($result);
$seq = $db->get_Seq_by_id('AW057119');
ok($seq);
is($seq->length, 808);
$seq = $db->get_Seq_by_id('AW057118');
ok($seq);
is($seq->length, 299);
undef $db;
SKIP: {
test_skip(-tests => 4, -requires_module => 'Data::Stag');
$db = Bio::DB::Flat->new(-directory => $tmpdir,
-index => 'binarysearch',
-format => 'swiss',
-dbname => 'mybinswiss',
-verbose => $verbose,
-write_flag => 1
);
$dir= test_input_file('swiss.dat');
$result = $db->build_index($dir);
ok($result);
$seq = $db->get_Seq_by_id('ACON_CAEEL');
ok($seq);
is($seq->length,788);
$seq = $db->get_Seq_by_id('ACON_CAEEL');
ok($seq && ref($seq));
undef $db;
}
$db = Bio::DB::Flat->new(-directory => $tmpdir,
-index => 'binarysearch',
-format => 'fasta',
-dbname => 'myfasta',
-verbose => $verbose,
-write_flag => 1 );
$dir = test_input_file('tmp.fst');
$result = $db->build_index(glob($dir));
ok($result);
$seq = $db->get_Seq_by_id('TEST00004');
is($seq->length,98);
undef $db;
$db = Bio::DB::Flat->new(-directory => $tmpdir,
-index => 'bdb',
-format => 'fasta',
-dbname => 'mybfasta',
-verbose => $verbose,
-write_flag => 1 );
$dir = test_input_file('tmp.fst');
$result = $db->build_index(glob($dir));
ok($result);
for my $id ( qw(TEST00001 TEST00002 TEST00003 TEST00004) ) {
$seq = $db->get_Seq_by_id($id);
is($seq->length,98);
}
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