Skip to content
Snippets Groups Projects
Commit d4f568bd authored by Andy Yates's avatar Andy Yates
Browse files

fixing for the new output format line

parent 95af1803
No related branches found
No related tags found
No related merge requests found
......@@ -79,25 +79,23 @@ my $index_count_fh = sub {
};
{
my $frag_size = 1e7;
my $seq = 'A'x$frag_size.'C'x$frag_size.'T'x$frag_size.'G'x$frag_size;
my $sd = Bio::EnsEMBL::Utils::SeqDumper->new();
$sd->{feature_types}->{$_} = 0 for keys %{$sd->{feature_types}};
{
my $fh = IO::String->new();
$sd->dump_embl($slice, $fh, $seq);
$sd->dump_embl($slice, $fh);
my $lines = $index_fh->($fh, 'SQ ');
is(scalar(@{$lines}), 1, 'Expect only 1 EMBL SQ line describing a sequence');
is($lines->[0], 'SQ Sequence 40000000 BP; 10000000 A; 10000000 C; 10000000 G; 10000000 T; 0 other;', 'Formatting of SQ as expected');
is($lines->[0], 'SQ Sequence 100001 BP; 24986 A; 24316 C; 24224 G; 26475 T; 0 other;', 'Formatting of SQ as expected');
}
{
my $fh = IO::String->new();
$sd->dump_genbank($slice, $fh, $seq);
$sd->dump_genbank($slice, $fh);
my $lines = $index_fh->($fh, 'BASE COUNT');
is(@{$lines}, 1, 'Expect only 1 Genbank BASE COUNT line describing a sequence');
is($lines->[0], 'BASE COUNT 10000000 a 10000000 c 10000000 g 10000000 t', 'Formatting of BASE COUNT as expected');
is($lines->[0], 'BASE COUNT 24986 a 24316 c 24224 g 26475 t 0 n', 'Formatting of BASE COUNT as expected');
}
}
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment