Sha256: 32665a1ce8e58db469560efeb0ab725d5e3f4b72208dbfc38f5620ce97de3c3e
Contents?: true
Size: 1.2 KB
Versions: 139
Compression:
Stored size: 1.2 KB
Contents
require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_helper.rb')
require 'rbbt/util/misc/bgzf'
class TestBgzf < Test::Unit::TestCase
def _test_Bgzf
content = "1234567890" * 1000000
TmpFile.with_file(content) do |file|
compressed = file + '.gz'
`bgzip #{file} -c > #{compressed}`
stream = Bgzf.setup File.open(compressed)
assert_equal "1234", stream.read(4)
assert_equal "56", stream.read(2)
stream.seek 500003
assert_equal "4567", stream.read(4)
assert_equal "89", stream.read(2)
end
end
def test_tsv
require 'rbbt/tsv'
TmpFile.with_file(datafile_test(:identifiers).read) do |file|
Misc.benchmark do
tsv = TSV.open(Open.open(file))
end
`gzip #{file}`
stream = Open.open(file + '.gz')
Misc.benchmark do
tsv = TSV.open(stream)
end
`gunzip #{file}.gz`
compressed = file + '.bgz'
`bgzip #{file} -c > #{compressed}`
stream = Bgzf.setup File.open(compressed)
Misc.benchmark do
tsv = TSV.open(stream)
end
end
end
def _test_bgzip
assert File.exist?(Bgzf.bgzip_cmd)
assert 'bgzip', File.basename(Bgzf.bgzip_cmd)
end
end
Version data entries
139 entries across 139 versions & 1 rubygems