# -*-Perl-*- mode (to keep my emacs happy)
# $Id: SeqIO.t,v 1.99 2005/08/28 13:56:45 bosborne Exp $
use strict;
BEGIN {
        eval { require Test; };
        if ( $@ ) {
                use lib 't';
        }
        use Test;
        plan tests => 29;
}
use Bio::SeqIO;
ok(1);
# Set to -1 for release version, so warnings aren't printed
my $verbose = $ENV{'BIOPERLDEBUG'} || 0;
# Basic read and/or write tests for SeqIO. Specific tests for
# given module should go into their own file.
my @formats = qw(gcg fasta raw pir tab ace );
# The following files or formats are failing: swiss genbank interpro embl
foreach my $format (@formats) {
        print "======== $format ========\n" if $verbose;
        read_write($format);
}
sub read_write {
        my $format = shift;
        my $seq;
        my $str = Bio::SeqIO->new(-file=> Bio::Root::IO->catfile
                                                                          ("t","data","test.$format"),
                                                                          -format => $format);
        ok $seq = $str->next_seq();
        print "Sequence 1 of 2 from $format stream:\n", $seq->seq, "\n\n"
          if  $verbose;
        unless ($format eq 'raw') {
                ok $seq->id, 'roa1_drome',"ID for format $format";
                ok $seq->length, 358;
        }
        unless ($format eq 'gcg') { # GCG file can contain only one sequence
                ok $seq = $str->next_seq();
                print "Sequence 2 of 2 from $format stream:\n", $seq->seq,
                  $seq->seq, "\n" if $verbose;
        }
        my $out = Bio::SeqIO->new(-file => ">". Bio::Root::IO->catfile
                                                                          ("t","data","$format.out"),
                                                                          -format => $format);
        ok $out->write_seq($seq);
        if ($format eq 'fasta') {
                my $id_type;
                ok($id_type = $out->preferred_id_type('accession.version'),
                        'accession.version');
        }
}
END {
        map { unlink Bio::Root::IO->catfile("t","data","$_.out") } @formats
}