use warnings;
use Test::More;
use Carp;
use Data::Dumper;
BEGIN { use_ok('Bio::Gonzales::Seq::Validate::fasta'); }
my $d;
sub TEST { $d = $_[0]; }
#TESTS
TEST 'validate';
{
open my $fh, '<', "t/data/rprot-domains_ebakker.fasta" or croak "Can't open filehandle: $!";
my $z = Bio::Gonzales::Seq::Validate::fasta->new( fh => $fh );
my $errors = $z->validate;
is_deeply(
$errors,
{
'274' => ['No sequence after header.'],
'238' => ['Wrong header format, seems to be sequence in the header: >>AGCGKTTLA ... PPFVEQMSQ<<'],
'128' => ['Found unknown characters: >>|7110565||36987.1|234174_1<<'],
'131' => ['Found unknown characters: >>|7110565||36987.1|234174_1<<'],
'134' => ['Found unknown characters: >>|7110565||36987.1|234174_1<<'],
'122' => ['Found unknown characters: >>|7110565||36987.1|234174_1 <<'],
'361' => ['Wrong header format, seems to be sequence in the header: >>MAYAAVTSL ... GGRELEVVS<<'],
'336' => ['Wrong header format, seems to be sequence in the header: >>MAEVVLAGL ... DGDDIFNQL<<'],
'258' => ['Wrong header format, \'>\' not in the beginning.'],
'243' => ['Wrong header format, seems to be sequence in the header: >>GIWGMPGIG ... TFKRAQGSE<<'],
'254' => ['Wrong header format, \'>\' not in the beginning.'],
'0' => ['File seems to be in DOS format'],
'256' => ['Wrong header format, \'>\' not in the beginning.'],
'125' => ['Found unknown characters: >>|7110565||36987.1|234174_1<<'],
'275' => [ 'Wrong header format, \'>\' not in the beginning.', 'No sequence after header.' ],
'270' => ['ID is ambiguous. M-domain1']
},
$d
);
}
done_testing();