App-Dazz

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t/03-dazzname.t  view on Meta::CPAN

use App::Cmd::Tester;

use App::Dazz;

my $result = test_app( 'App::Dazz' => [qw(help dazzname)] );
like( $result->stdout, qr{dazzname}, 'descriptions' );

$result = test_app( 'App::Dazz' => [qw(dazzname)] );
like( $result->error, qr{need .+input file}, 'need infile' );

$result = test_app( 'App::Dazz' => [qw(dazzname t/not_exists)] );
like( $result->error, qr{doesn't exist}, 'infile not exists' );

$result = test_app( 'App::Dazz' => [qw(dazzname t/1_4.anchor.fasta --prefix B-A:D -o stdout)] );
like( $result->error, qr{Can't accept}, 'bad names' );

$result = test_app( 'App::Dazz' => [qw(dazzname t/1_4.anchor.fasta -o B-A:D)] );
like( $result->error, qr{Can't accept}, 'bad names' );

$result = test_app( 'App::Dazz' => [qw(dazzname t/1_4.anchor.fasta -o stdout)] );
is( ( scalar grep {/\S/} split( /\n/, $result->stdout ) ), 8, 'line count' );

t/04-show2ovlp.t  view on Meta::CPAN

use App::Cmd::Tester;

use App::Dazz;

my $result = test_app( 'App::Dazz' => [qw(help show2ovlp)] );
like( $result->stdout, qr{show2ovlp}, 'descriptions' );

$result = test_app( 'App::Dazz' => [qw(show2ovlp)] );
like( $result->error, qr{need .+input file}, 'need infile' );

$result = test_app( 'App::Dazz' => [qw(show2ovlp t/not_exists t/not_exists)] );
like( $result->error, qr{doesn't exist}, 'infile not exists' );

$result = test_app( 'App::Dazz' => [qw(show2ovlp t/1_4.renamed.fasta t/1_4.show.txt -o stdout)] );
is( ( scalar grep {/\S/} split( /\n/, $result->stdout ) ), 50, 'line count' );
like( $result->stdout, qr{overlap}s, 'overlaps' );

$result = test_app(
    'App::Dazz' => [qw(show2ovlp t/1_4.renamed.fasta t/1_4.show.txt -r t/not_exists -o stdout)] );
like( $result->error, qr{doesn't exist}, 'infile not exists' );

$result = test_app( 'App::Dazz' =>
        [qw(show2ovlp t/1_4.renamed.fasta t/1_4.show.txt -r t/1_4.replace.tsv -o stdout)] );
is( ( scalar grep {/\S/} split( /\n/, $result->stdout ) ), 50, 'line count' );
like( $result->stdout, qr{pac7556_20928}s, 'original name' );

done_testing();

t/07-overlap.t  view on Meta::CPAN

use App::Cmd::Tester::CaptureExternal; # `dazz overlap` calls `dazz show2ovlp` to write outputs

use App::Dazz;

my $result = test_app( 'App::Dazz' => [qw(help overlap)] );
like( $result->stdout, qr{overlap}, 'descriptions' );

$result = test_app( 'App::Dazz' => [qw(overlap)] );
like( $result->error, qr{need .+input file}, 'need infile' );

$result = test_app( 'App::Dazz' => [qw(overlap t/1_4.pac.fasta t/not_exists)] );
like( $result->error, qr{doesn't exist}, 'infile not exists' );

SKIP: {
    skip "dazz and its deps not installed", 7
        unless IPC::Cmd::can_run('dazz')
            or IPC::Cmd::can_run('faops')
            or IPC::Cmd::can_run('fasta2DB')
            or IPC::Cmd::can_run('LAshow')
            or IPC::Cmd::can_run('ovlpr');

t/08-overlap2.t  view on Meta::CPAN

use App::Cmd::Tester::CaptureExternal;   # `dazz overlap2` calls `dazz show2ovlp` to write outputs

use App::Dazz;

my $result = test_app( 'App::Dazz' => [qw(help overlap2)] );
like( $result->stdout, qr{overlap2}, 'descriptions' );

$result = test_app( 'App::Dazz' => [qw(overlap2)] );
like( $result->error, qr{need .+input file}, 'need infile' );

$result = test_app( 'App::Dazz' => [qw(overlap2 t/1_4.anchor.fasta t/not_exists)] );
like( $result->error, qr{doesn't exist}, 'infile not exists' );

SKIP: {
    skip "dazz and its deps not installed", 2
        unless IPC::Cmd::can_run('dazz')
            or IPC::Cmd::can_run('faops')
            or IPC::Cmd::can_run('fasta2DB')
            or IPC::Cmd::can_run('LAshow')
            or IPC::Cmd::can_run('ovlpr');

t/09-orient.t  view on Meta::CPAN

use App::Cmd::Tester::CaptureExternal;    # `dazz orient` calls `dazz show2ovlp` to write outputs

use App::Dazz;

my $result = test_app( 'App::Dazz' => [qw(help orient)] );
like( $result->stdout, qr{orient}, 'descriptions' );

$result = test_app( 'App::Dazz' => [qw(orient)] );
like( $result->error, qr{need .+input file}, 'need infile' );

$result = test_app( 'App::Dazz' => [qw(orient t/1_4.pac.fasta t/not_exists)] );
like( $result->error, qr{doesn't exist}, 'infile not exists' );

$result = test_app(
    'App::Dazz' => [qw(orient t/1_4.anchor.fasta t/1_4.pac.fasta -r t/not_exists -o stdout)] );
like( $result->error, qr{doesn't exist}, 'restrict file not exists' );

SKIP: {
    skip "dazz and its deps not installed", 3
        unless IPC::Cmd::can_run('dazz')
            or IPC::Cmd::can_run('faops')
            or IPC::Cmd::can_run('fasta2DB')
            or IPC::Cmd::can_run('LAshow')
            or IPC::Cmd::can_run('ovlpr');

t/10-cover.t  view on Meta::CPAN

use App::Cmd::Tester::CaptureExternal;

use App::Dazz;

my $result = test_app( 'App::Dazz' => [qw(help cover --range 1-4)] );
like( $result->stdout, qr{cover}, 'descriptions' );

$result = test_app( 'App::Dazz' => [qw(cover --range 1-4)] );
like( $result->error, qr{need .+input file}, 'need infile' );

$result = test_app( 'App::Dazz' => [qw(cover t/not_exists --range 1-4)] );
like( $result->error, qr{doesn't exist}, 'infile not exists' );

SKIP: {
    skip "dazz and its deps not installed", 3
        unless IPC::Cmd::can_run('dazz')
            or IPC::Cmd::can_run('faops')
            or IPC::Cmd::can_run('fasta2DB')
            or IPC::Cmd::can_run('LAshow')
            or IPC::Cmd::can_run('ovlpr');

t/11-group.t  view on Meta::CPAN

use App::Cmd::Tester::CaptureExternal;

use App::Dazz;

my $result = test_app( 'App::Dazz' => [qw(help group --range 1-4)] );
like( $result->stdout, qr{group}, 'descriptions' );

$result = test_app( 'App::Dazz' => [qw(group --range 1-4)] );
like( $result->error, qr{need .+input file}, 'need infile' );

$result = test_app( 'App::Dazz' => [qw(group t/not_exists --range 1-4)] );
like( $result->error, qr{need .+input file}, 'need 2 infiles' );

$result = test_app( 'App::Dazz' => [qw(group t/not_exists t/not_exists --range 1-4)] );
like( $result->error, qr{doesn't exist}, 'infile not exists' );

SKIP: {
    skip "dazz and its deps not installed", 2
        unless IPC::Cmd::can_run('dazz')
            or IPC::Cmd::can_run('faops')
            or IPC::Cmd::can_run('fasta2DB')
            or IPC::Cmd::can_run('LAshow')
            or IPC::Cmd::can_run('ovlpr');

t/14-contained.t  view on Meta::CPAN

use App::Cmd::Tester::CaptureExternal;

use App::Dazz;

my $result = test_app( 'App::Dazz' => [qw(help contained)] );
like( $result->stdout, qr{contained}, 'descriptions' );

$result = test_app( 'App::Dazz' => [qw(contained)] );
like( $result->error, qr{need .+input file}, 'need infile' );

$result = test_app( 'App::Dazz' => [qw(contained t/1_4.pac.fasta t/not_exists)] );
like( $result->error, qr{doesn't exist}, 'infile not exists' );

SKIP: {
    skip "dazz and its deps not installed", 7
        unless IPC::Cmd::can_run('dazz')
            or IPC::Cmd::can_run('faops')
            or IPC::Cmd::can_run('fasta2DB')
            or IPC::Cmd::can_run('LAshow')
            or IPC::Cmd::can_run('ovlpr');

t/15-merge.t  view on Meta::CPAN

use App::Cmd::Tester::CaptureExternal;

use App::Dazz;

my $result = test_app( 'App::Dazz' => [qw(help merge)] );
like( $result->stdout, qr{merge}, 'descriptions' );

$result = test_app( 'App::Dazz' => [qw(merge)] );
like( $result->error, qr{need .+input file}, 'need infile' );

$result = test_app( 'App::Dazz' => [qw(merge t/not_exists)] );
like( $result->error, qr{doesn't exist}, 'infile not exists' );

SKIP: {
    skip "dazz and its deps not installed", 3
        unless IPC::Cmd::can_run('dazz')
            or IPC::Cmd::can_run('faops')
            or IPC::Cmd::can_run('fasta2DB')
            or IPC::Cmd::can_run('LAshow')
            or IPC::Cmd::can_run('ovlpr');

t/16-layout.t  view on Meta::CPAN

use App::Cmd::Tester::CaptureExternal;

use App::Dazz;

my $result = test_app( 'App::Dazz' => [qw(help layout)] );
like( $result->stdout, qr{layout}, 'descriptions' );

$result = test_app( 'App::Dazz' => [qw(layout)] );
like( $result->error, qr{need .+input file}, 'need infile' );

$result = test_app( 'App::Dazz' => [qw(layout t/not_exists)] );
like( $result->error, qr{need .+input file}, 'need 3 infiles' );

$result = test_app( 'App::Dazz' => [qw(layout t/not_exists t/not_exists t/not_exists)] );
like( $result->error, qr{doesn't exist}, 'infile not exists' );

SKIP: {
    skip "dazz and its deps not installed", 3
        unless IPC::Cmd::can_run('dazz')
            or IPC::Cmd::can_run('poa');

    my $tempdir = Path::Tiny->tempdir;
    $result = test_app(
        'App::Dazz' => [