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t/fromfasta.t  view on Meta::CPAN

use JSON ();

use App::RecordStream::Operation::fromfasta;

my $input;
my $output;

my $tester = App::RecordStream::Test::Tester->new('fromfasta');

diag "basic input";
$input = <<'INPUT';
>foo baz bar
TCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGG
GGAAACTACGTGTGTTATCTCCCAACGATGACATAATATATTACT
TCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGG
GGAAACTACGTGTGTTATCTCCCAACGATGACATAATATATTACT
> baz 
SLYNTVAVLYYVHQR
>empty
>bogus
TCATTATATAATACAGTAGC>>CCCTCTATTGTGTGCATCAAAGG
>empty2
INPUT
$output = <<'OUTPUT';
{"id":"foo","description":"baz bar","name":"foo baz bar","sequence":"TCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGG\nGGAAACTACGTGTGTTATCTCCCAACGATGACATAATATATTACT\nTCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGG\nGGAAACTACGTGTGTTATCTCCCAACGATGACATAATATA...
{"id":"baz","description":null,"name":"baz", "sequence":"SLYNTVAVLYYVHQR"}
{"id":"empty","description":null,"name":"empty","sequence":null}
{"id":"bogus","description":null,"name":"bogus","sequence":"TCATTATATAATACAGTAGC>>CCCTCTATTGTGTGCATCAAAGG"}
{"id":"empty2","description":null,"name":"empty2","sequence":null}
OUTPUT
$tester->test_input([], $input, $output);

diag "--oneline";
$output = <<'OUTPUT';
{"id":"foo","description":"baz bar","name":"foo baz bar","sequence":"TCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGGGAAACTACGTGTGTTATCTCCCAACGATGACATAATATATTACTTCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGGGAAACTACGTGTGTTATCTCCCAACGATGACATAATATATTACT"...
{"id":"baz","description":null,"name":"baz", "sequence":"SLYNTVAVLYYVHQR"}
{"id":"empty","description":null,"name":"empty","sequence":null}
{"id":"bogus","description":null,"name":"bogus","sequence":"TCATTATATAATACAGTAGC>>CCCTCTATTGTGTGCATCAAAGG"}
{"id":"empty2","description":null,"name":"empty2","sequence":null}
OUTPUT
$tester->test_input(['--oneline'], $input, $output);

diag "Test multiple input files with --filename-key";
$output = "";
my $output_template = <<'OUTPUT';
{"id":"foo","description":"baz bar","file":__TMPFILE__,"name":"foo baz bar","sequence":"TCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGG\nGGAAACTACGTGTGTTATCTCCCAACGATGACATAATATATTACT\nTCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGG\nGGAAACTACGTGTGTTATCTC...
{"id":"baz","description":null,"file":__TMPFILE__,"name":"baz", "sequence":"SLYNTVAVLYYVHQR"}
{"id":"empty","description":null,"file":__TMPFILE__,"name":"empty","sequence":null}
{"id":"bogus","description":null,"file":__TMPFILE__,"name":"bogus","sequence":"TCATTATATAATACAGTAGC>>CCCTCTATTGTGTGCATCAAAGG"}
{"id":"empty2","description":null,"file":__TMPFILE__,"name":"empty2","sequence":null}
OUTPUT

my $JSON = JSON->new->utf8->allow_nonref;

my @files;
for (1..3) {
    my $fh = File::Temp->new;
    push @files, $fh;

    print { $fh } $input;
    $fh->flush;

t/tofasta.t  view on Meta::CPAN

use Test::More 'no_plan';

use App::RecordStream::Test::OperationHelper;

use App::RecordStream::Operation::tofasta;

my $input;
my $output;

diag "--passthru";
$input = <<'INPUT';
{"id":"foo","description":"baz bar","name":"foo baz bar","sequence":"TCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGGGAAACTACGTGTGTTATCTCCCAACGATGACATA\nATATATTACTTCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGGGAAACTACGTGTGTTATCTCCCAA\nCGATGACATAATATATT...
{"id":"baz","description":null,"name":"baz", "sequence":"SLYNTVA\nVLYYVHQR","lower_seq":"slyntvavlyyvhqr","num":2}
{"id":"empty","description":null,"name":"empty","sequence":null,"lower_seq":null,"num":3}
{"id":"bogus","description":null,"name":"bogus","sequence":"TCATTATATAATACAGTAGC>>CCCTCTATTGTGTGCATCAAAGG","lower_seq":"tcattatataatacagtagc>>ccctctattgtgtgcatcaaagg","num":4}
{"id":"empty2","description":null,"name":"empty2","sequence":null,"lower_seq":null,"num":5}
INPUT
$output = <<'OUTPUT';
>foo baz bar
TCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGGGAAACTACGTGTGTTATCTCCCAACGATGACATA
ATATATTACTTCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGGGAAACTACGTGTGTTATCTCCCAA
CGATGACATAATATATTACT
>baz
SLYNTVA
VLYYVHQR
>empty
>bogus
TCATTATATAATACAGTAGC>>CCCTCTATTGTGTGCATCAAAGG
>empty2
OUTPUT
App::RecordStream::Test::OperationHelper->test_output('tofasta' => ['--passthru'], $input, $output);

# Remove validation errors for BioPerl
$input =~ s/>//g;

diag "basic output";
$output = <<'OUTPUT';
>foo baz bar
TCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGGGAAACTACGTGTGT
TATCTCCCAACGATGACATAATATATTACTTCATTATATAATACAGTAGCAACCCTCTAT
TGTGTGCATCAAAGGGGAAACTACGTGTGTTATCTCCCAACGATGACATAATATATTACT
>baz
SLYNTVAVLYYVHQR
>empty
>bogus
TCATTATATAATACAGTAGCCCCTCTATTGTGTGCATCAAAGG
>empty2
OUTPUT
App::RecordStream::Test::OperationHelper->test_output('tofasta' => [], $input, $output);

diag "--oneline";
$output = <<'OUTPUT';
>foo baz bar
TCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGGGAAACTACGTGTGTTATCTCCCAACGATGACATAATATATTACTTCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGGGAAACTACGTGTGTTATCTCCCAACGATGACATAATATATTACT
>baz
SLYNTVAVLYYVHQR
>empty
>bogus
TCATTATATAATACAGTAGCCCCTCTATTGTGTGCATCAAAGG
>empty2
OUTPUT
App::RecordStream::Test::OperationHelper->test_output('tofasta' => ['--oneline'], $input, $output);

diag "--width";
$output = <<'OUTPUT';
>foo baz bar
TCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATC
AAAGGGGAAACTACGTGTGTTATCTCCCAACGATGACATA
ATATATTACTTCATTATATAATACAGTAGCAACCCTCTAT
TGTGTGCATCAAAGGGGAAACTACGTGTGTTATCTCCCAA
CGATGACATAATATATTACT
>baz
SLYNTVAVLYYVHQR
>empty
>bogus
TCATTATATAATACAGTAGCCCCTCTATTGTGTGCATCAA
AGG
>empty2
OUTPUT
App::RecordStream::Test::OperationHelper->test_output('tofasta' => ['--width=40'], $input, $output);

diag "--id";
$output = <<'OUTPUT';
>1 baz bar
TCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGGGAAACTACGTGTGT
TATCTCCCAACGATGACATAATATATTACTTCATTATATAATACAGTAGCAACCCTCTAT
TGTGTGCATCAAAGGGGAAACTACGTGTGTTATCTCCCAACGATGACATAATATATTACT
>2
SLYNTVAVLYYVHQR
>3
>4
TCATTATATAATACAGTAGCCCCTCTATTGTGTGCATCAAAGG
>5
OUTPUT
App::RecordStream::Test::OperationHelper->test_output('tofasta' => ['--id=num'], $input, $output);

diag "--description";
$output = <<'OUTPUT';
>1
TCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGGGAAACTACGTGTGT
TATCTCCCAACGATGACATAATATATTACTTCATTATATAATACAGTAGCAACCCTCTAT
TGTGTGCATCAAAGGGGAAACTACGTGTGTTATCTCCCAACGATGACATAATATATTACT
>2
SLYNTVAVLYYVHQR
>3
>4
TCATTATATAATACAGTAGCCCCTCTATTGTGTGCATCAAAGG
>5
OUTPUT
App::RecordStream::Test::OperationHelper->test_output('tofasta' => ['--id=num', '--desc=NONE'], $input, $output);

diag "--sequence";
$output = <<'OUTPUT';
>1
tcattatataatacagtagcaaccctctattgtgtgcatcaaaggggaaactacgtgtgt
tatctcccaacgatgacataatatattacttcattatataatacagtagcaaccctctat
tgtgtgcatcaaaggggaaactacgtgtgttatctcccaacgatgacataatatattact
>2
slyntvavlyyvhqr
>3
>4
tcattatataatacagtagcccctctattgtgtgcatcaaagg
>5
OUTPUT
App::RecordStream::Test::OperationHelper->test_output('tofasta' => ['--id=num', '--desc=NONE', '--seq=lower_seq'], $input, $output);

diag "--id=NONE";
$output = <<'OUTPUT';
> baz bar
TCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGGGAAACTACGTGTGT
TATCTCCCAACGATGACATAATATATTACTTCATTATATAATACAGTAGCAACCCTCTAT
TGTGTGCATCAAAGGGGAAACTACGTGTGTTATCTCCCAACGATGACATAATATATTACT
>
SLYNTVAVLYYVHQR
>
>
TCATTATATAATACAGTAGCCCCTCTATTGTGTGCATCAAAGG
>
OUTPUT
App::RecordStream::Test::OperationHelper->test_output('tofasta' => ['--id=NONE'], $input, $output);

diag "--id=NONE --passthru";
$output = <<'OUTPUT';
>baz bar
TCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGGGAAACTACGTGTGTTATCTCCCAACGATGACATA
ATATATTACTTCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGGGAAACTACGTGTGTTATCTCCCAA
CGATGACATAATATATTACT
>
SLYNTVA
VLYYVHQR
>
>
TCATTATATAATACAGTAGCCCCTCTATTGTGTGCATCAAAGG
>
OUTPUT
App::RecordStream::Test::OperationHelper->test_output('tofasta' => ['--id=NONE', '--passthru'], $input, $output);

diag "--sequence=NONE";
$output = <<'OUTPUT';
>1 baz bar
>2
>3
>4
>5
OUTPUT
App::RecordStream::Test::OperationHelper->test_output('tofasta' => ['--id=num', '--sequence=NONE'], $input, $output);