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# This is -*-Perl-*- code
## Bioperl Test Harness Script for Modules
##
# $Id: flat.t,v 1.11 2003/07/09 01:12:11 jason Exp $
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl test.t'
use strict;
use vars qw($NUMTESTS);
my $error;
BEGIN {
# to handle systems with no installed Test module
# we include the t dir (where a copy of Test.pm is located)
# as a fallback
eval { require Test; };
$error = 0;
if( $@ ) {
use lib 't';
}
use Test;
$NUMTESTS = 16;
plan tests => $NUMTESTS;
eval {
require DB_File;
require Bio::DB::Flat;
require Bio::Root::IO;
1;
};
if( $@ ) {
print STDERR "DB_File not loaded. This means flat.t test cannot be executed. Skipping\n";
foreach ( $Test::ntest..$NUMTESTS ) {
skip('DB_File not installed',1);
}
$error = 1;
}
}
if( $error == 1 ) {
exit(0);
}
my $testnum;
my $verbose = 0;
## End of black magic.
##
## Insert additional test code below but remember to change
## the print "1..x\n" in the BEGIN block to reflect the
## total number of tests that will be run.
#First of all we need to create an flat db
use Bio::Root::IO;
use Cwd;
my $cd = cwd();
my $tmpdir = Bio::Root::IO->catfile($cd,qw(t tmp));
&maketmpdir();
my $db = Bio::DB::Flat->new(-directory => $tmpdir,
-index => 'bdb',
-dbname => 'mydb',
-format => 'fasta',
-verbose => $verbose,
-write_flag => 1
);
ok($db);
my $dir = Bio::Root::IO->catfile($cd,qw(t data 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);
ok($seq->length,504);
undef $db;
&cleanup();
&maketmpdir();
$db = Bio::DB::Flat->new(-directory => $tmpdir,
-index => 'bdb',
-format => 'embl',
-dbname => 'myembl',
-verbose => $verbose,
-write_flag => 1
);
$dir= Bio::Root::IO->catfile($cd,qw(t data factor7.embl));
$result = $db->build_index(glob($dir));
ok($result);
$seq = $db->get_Seq_by_id('HSCFVII');
ok($seq);
ok($seq->length,12850);
# deal with wantarray conditions
$seq = $db->get_Seq_by_acc('J02933');
ok($seq && ref($seq));
ok($seq->length,12850);
undef $db;
&cleanup();
&maketmpdir();
$db = Bio::DB::Flat->new(-directory => $tmpdir,
-index => 'binarysearch',
-format => 'fasta',
-dbname => 'mybinfa',
-verbose => $verbose,
-write_flag => 1
);
$dir= Bio::Root::IO->catfile($cd,qw(t data dbfa 1.fa));
$result = $db->build_index($dir);
ok($result);
$seq = $db->get_Seq_by_id('AW057119');
ok($seq);
ok($seq->length,808);
undef $db;
&cleanup();
&maketmpdir();
$db = Bio::DB::Flat->new(-directory => $tmpdir,
-index => 'binarysearch',
-format => 'swiss',
-dbname => 'mybinswiss',
-verbose => $verbose,
-write_flag => 1
);
$dir= Bio::Root::IO->catfile($cd,qw(t data swiss.dat));
$result = $db->build_index($dir);
ok($result);
$seq = $db->get_Seq_by_id('ACON_CAEEL');
ok($seq);
ok($seq->length,788);
$seq = $db->get_Seq_by_id('ACON_CAEEL');
ok($seq && ref($seq));
undef $db;
&cleanup();
sub maketmpdir {
mkdir ($tmpdir,0777);
}
sub cleanup {
eval {
Bio::Root::IO->rmtree($tmpdir) if( defined $tmpdir && -d $tmpdir);
};
}
END {
&cleanup();
}
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