Sha256: 3b465478f3c90774c2b63cd3ad540c58a2e3f7591eca75f32292aaf18837de1d
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Size: 1.82 KB
Versions: 18
Compression:
Stored size: 1.82 KB
Contents
require File.expand_path(File.dirname(__FILE__) + '/../../test_helper')
require 'rbbt/persist'
require 'rbbt/annotations'
require 'rbbt/util/tmpfile'
require 'test/unit'
class TestPersistTSV < Test::Unit::TestCase
MAX = 100_002
def tsv_path
Random.new
require 'rbbt/workflow'
Workflow.require_workflow "Genomes1000"
require 'rbbt/sources/genomes1000'
CMD.cmd("grep -v '^\\.\t' | head -n #{MAX}", :in => Genomes1000.mutations.open, :pipe => true)
end
def run_bechmark(file, engine)
Log.info "Testing #{ Term::ANSIColor.red(engine) }"
TmpFile.with_file nil, false do |tmp_file|
db= nil
Misc.benchmark(1, "Build database with #{MAX - 2} entries") do
db = TSV.open(file, :fields => [1], :persist => true, :persist_engine => engine, :persist_dir => tmp_file, :type => :single, :unnamed => true)
end
_test = db.keys.sort{rand}[1..100000]
Misc.benchmark(5, "Access #{test.length} random entries") do
_test.each do |k| db[k] end
end
Log.info "Profiling access to #{test.length} random entries"
Misc.profile :min_percent => 0.1 do
_test.each do |k| db[k] end
end
assert_equal "1:10611:G", db["rs189107123"]
end
end
def _test_benchmark_tch
engine = "HDB"
run_bechmark(tsv_path, engine)
end
def _test_benchmark_tcb
engine = "BDB"
run_bechmark(tsv_path, engine)
end
def _test_benchmark_kch
engine = "kch"
run_bechmark(tsv_path, engine)
end
def _test_benchmark_kcb
engine = "kct"
run_bechmark(tsv_path, engine)
end
def _test_benchmark_cdb
engine = "CDB"
run_bechmark(tsv_path, engine)
end
def _test_benchmark_leveldb
engine = "LevelDB"
run_bechmark(tsv_path, engine)
end
def __test_benchmark_lmdb
engine = "LMDB"
run_bechmark(tsv_path, engine)
end
end
Version data entries
18 entries across 18 versions & 1 rubygems