From d4f568bdc04f99bc7b7b502d76be571df677a046 Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Wed, 18 Sep 2013 14:28:12 +0000
Subject: [PATCH] fixing for the new output format line
---
modules/t/seqDumper.t | 10 ++++------
1 file changed, 4 insertions(+), 6 deletions(-)
diff --git a/modules/t/seqDumper.t b/modules/t/seqDumper.t
index b37ee32879..a656f90b78 100644
--- a/modules/t/seqDumper.t
+++ b/modules/t/seqDumper.t
@@ -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');
}
}
--
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