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# -*-Perl-*- Test Harness script for Bioperl
# $Id$
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 24,
-requires_modules => [qw(XML::Parser::PerlSAX XML::Writer)]);
use_ok('Bio::SeqIO::game');
}
my $verbose = test_debug() || -1;
my $str = Bio::SeqIO->new('-file'=> test_input_file('test.game'),
'-format' => 'game',
'-verbose' => $verbose);
isa_ok ($str, 'Bio::SeqIO');
my $seq = $str->next_seq();
isa_ok($seq, 'Bio::Seq::RichSeq');
# exercise game parsing
$str = Bio::SeqIO->new(
-format =>'game',
-file => test_input_file('test.game')
);
$seq = $str->next_seq;
ok(defined $seq);
ok(defined $seq->seq);
is($seq->alphabet, 'dna');
is($seq->display_id, 'L16622');
is($seq->length, 28735);
is($seq->species->binomial, 'Caenorhabditis elegans');
my @feats = $seq->get_SeqFeatures;
is(scalar(@feats), 7);
my $source = grep { $_->primary_tag eq 'source' } @feats;
ok($source);
my @genes = grep { $_->primary_tag eq 'gene' } @feats;
is(scalar(@genes), 3);
ok($genes[0]->has_tag('gene'));
my $gname;
if ( $genes[0]->has_tag('gene') ) {
($gname) = $genes[0]->get_tag_values('gene');
}
is($gname, 'C02D5.3');
is($genes[0]->strand, 1);
my $cds = grep { $_->primary_tag eq 'CDS' } @feats;
is($cds, 3);
# make sure we can read what we write
# test XML-writing
my $testfile = test_output_file();
# map argument is require to write a <map_position> element
my $out = Bio::SeqIO->new(-format => 'game', -file => ">$testfile", -map => 1);
$out->write_seq($seq);
$out->close();
$str = Bio::SeqIO->new(-format =>'game', -file => $testfile);
$seq = $str->next_seq;
ok(defined $seq);
ok(defined $seq->seq);
is($seq->alphabet, 'dna');
is($seq->display_id, 'L16622');
is($seq->length, 28735);
is($seq->species->binomial, 'Caenorhabditis elegans');
my $genes = grep { $_->primary_tag eq 'gene' } @feats;
$cds = grep { $_->primary_tag eq 'CDS' } @feats;
is($genes, 3);
is($cds, 3);
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