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lib/BioX/Seq/Stream.pm  view on Meta::CPAN

    }
    else {
        $self->{fh} = \*STDIN;
    }

    # handle files coming from different platforms
    #my @layers = PerlIO::get_layers($self->{fh});
    #binmode($self->{fh},':unix:stdio:crlf');

    $self->_guess_format;

    $self->_init;

    return $self;

}

sub fast {

    my ($self, $bool) = @_;
    $self->{fast} = $bool // 1;

}

sub _guess_format {

    my ($self) = @_;

    # Filetype guessing must be based on first two bytes (or less)
    # which are stored in an object buffer
    my $r = (read $self->{fh}, $self->{buffer}, 2);
    die "failed to read initial bytes" if ($r != 2);

    my $search_path = abs_path(__FILE__);
    $search_path =~ s/\.pm$//i;
    my @matched;
    for my $module ( glob "$search_path/*.pm" ) {
        my ($name,$path,$suff) = fileparse($module, qr/\.pm/i);
        my $classname = blessed($self) . "::$name";
        eval "require $classname";
        if ($classname->_check_type($self)) {
            push @matched, $classname;
        }
    }

    die "Failed to guess filetype\n"   if (scalar(@matched) < 1);
    # uncoverable branch true
    die "Multiple filetypes matched\n" if (scalar(@matched) > 1);

    eval "require $matched[0]";
    bless $self => $matched[0];

}


1;

t/test.t  view on Meta::CPAN

    300,
);

ok( scalar(@orfs) == 5, "check ORF count 2" );

throws_ok { all_orfs($seq) } qr/Missing mode/, "missing mode";
throws_ok { all_orfs($seq, 0) } qr/Missing min/, "missing minimum length";

throws_ok { BioX::Seq::Stream->new($test_onebyte) } qr/initial bytes/, "truncated input";

throws_ok { BioX::Seq::Stream->new($test_foobar) } qr/Failed to guess/, "non-sequence input";

# simulate missing zstd
my $zstd_bin_tmp = $BioX::Seq::Stream::ZSTD_BIN;
$BioX::Seq::Stream::ZSTD_BIN = undef;
throws_ok { BioX::Seq::Stream->new($test_zst) } qr/no zstd/, "missing zstd";
$BioX::Seq::Stream::ZSTD_BIN = 'nonexistent';
throws_ok { BioX::Seq::Stream->new($test_zst) } qr/[Error opening|not recognized]/, "bad zstd binary";
$BioX::Seq::Stream::ZSTD_BIN = $zstd_bin_tmp;

# simulate missing dsrc