def setUpClass(cls):
cls.filename = "tests/fake_genome.txt"
cls.genome = arv.load(cls.filename)
cls.keys = sorted([
"i3001754",
"i3001755",
"i3001759",
"i3001761",
"i3001773",
"i4000755",
"i4000759",
"rs10488822",
"rs10810289",
"rs11980927",
"rs12913832",
"rs1426654",
"rs1540613",
"rs28504042",
"rs3135027",
"rs4477212",
"rs4536786",
"rs4672279",
"rs6015286",
"rs6026400",
"rs6123756",
"rs671",
"rs742927",
"rs7715122",
"rs913897",
])
def _main():
opts = _parse_args()
genomes = []
for filename in opts.files:
log("%s ... " % os.path.basename(filename))
genome = arv.load(filename, ethnicity=opts.ethnicity)
log("%s\n" % summary(genome))
genomes.append(genome)
if opts.example:
for filename, genome in zip(opts.files, genomes):
log("%s ... %s\n" % (os.path.basename(filename), example(genome)))
if opts.repl:
env = dict(globals())
if len(genomes) == 1:
env.update({"genome": genomes[0]})
message = "Type `genome` to see the parsed 23andMe raw genome file"
else:
env.update({"genomes": genomes})
message = "Type `genomes` to see the parsed 23andMe raw genome files"
import code
code.interact(message, local=env)
def all_benchmarks(filename, times):
log("Benchmarking arv %s at %s\n" % (arv.__version__, arv.__file__))
log("Measuring time with %s\n\n" % mark_time)
results = {}
genome = arv.load(filename)
for name, code in sorted(benchmarks.items()):
log("Benchmarking %s x %d ... " % (repr(name), times))
try:
results[name] = benchmark(times,
code,
filename=filename,
genome=genome,
random=random)
except Exception as e:
log(str(e))
finally:
if name == "parsing":
genome = arv.load(filename)
log(" %.2g SNPs / second" % (len(genome) / results[name]))
log("\n")
return results
def test_parser_speed(self):
filename = os.getenv("ARV_BENCHMARK")
self.assertTrue(os.path.isfile(filename),
"File not found: %s" % filename)
try:
times = int(os.getenv("ARV_BENCHMARK_COUNT", "40"))
except:
times = 40
code = benchmarks["parsing"]
seconds = benchmark(times,
code,
filename=filename,
stream=sys.stderr,
prefix=" ")
genome = arv.load(filename)
sys.stderr.flush()
sys.stderr.write(" %d SNPs in ~%dms or %.1g SNPs/second ... " %
(len(genome), int(
round(seconds, 3) * 1000), len(genome) / seconds))
sys.stderr.flush()
def setUpClass(cls):
cls.genome = arv.load("tests/fake_genome.txt")
def setUpClass(cls):
cls.genome = arv.load("tests/fake_genome.txt", ethnicity="european")
from arv import load, unphased_match as match
genome = load("genome.txt")
print("You are a {gender} with {color} eyes and {complexion} skin.".format(
gender="man" if genome.y_chromosome else "woman",
complexion="light" if genome["rs1426654"] == "AA" else "dark",
color=match(genome["rs12913832"], {
"AA": "brown",
"AG": "brown or green",
"GG": "blue"
})))
def test_female_genome(self):
female = arv.load("tests/fake_genome_female.txt")
self.assertFalse(female.y_chromosome)
self.assertEqual(female.y_chromosome, False)
self.assertEqual(len(female), 24)
self.assertEqual(female["rs4477212"].chromosome, 1)
self.assertEqual(female["rs4477212"].position, 82154)
self.assertEqual(female["rs4477212"].genotype, "AT")
self.assertEqual(female["rs4477212"].genotype,
female["rs7715122"].genotype)
self.assertNotEqual(female["rs4477212"].genotype, "TA")
self.assertNotEqual(female["rs4477212"].genotype, "AA")
self.assertNotEqual(female["rs4477212"].genotype, "")
self.assertEqual(female["rs4672279"].chromosome, 2)
self.assertEqual(female["rs4672279"].position, 59444675)
self.assertEqual(female["rs4672279"].genotype, "GT")
self.assertEqual(female["rs4536786"].chromosome, 3)
self.assertEqual(female["rs4536786"].position, 140049121)
self.assertEqual(female["rs4536786"].genotype, "CA")
self.assertEqual(female["rs7715122"].chromosome, 5)
self.assertEqual(female["rs7715122"].position, 94197884)
self.assertEqual(female["rs7715122"].genotype, "AT")
self.assertEqual(female["rs11980927"].chromosome, 7)
self.assertEqual(female["rs11980927"].position, 20010422)
self.assertEqual(female["rs11980927"].genotype, "GG")
self.assertEqual(female["rs10810289"].chromosome, 9)
self.assertEqual(female["rs10810289"].position, 14899708)
self.assertEqual(female["rs10810289"].genotype, "AA")
self.assertEqual(female["rs10488822"].chromosome, 11)
self.assertEqual(female["rs10488822"].position, 35984271)
self.assertEqual(female["rs10488822"].genotype, "TC")
self.assertEqual(female["rs913897"].chromosome, 13)
self.assertEqual(female["rs913897"].position, 73892459)
self.assertEqual(female["rs913897"].genotype, "AC")
self.assertEqual(female["rs1540613"].chromosome, 16)
self.assertEqual(female["rs1540613"].position, 80476182)
self.assertEqual(female["rs1540613"].genotype, "AG")
self.assertEqual(female["rs6123756"].chromosome, 20)
self.assertEqual(female["rs6123756"].position, 56556146)
self.assertEqual(female["rs6123756"].genotype, "TT")
self.assertEqual(female["rs6015286"].chromosome, 20)
self.assertEqual(female["rs6015286"].position, 57048415)
self.assertEqual(female["rs6015286"].genotype, "--")
self.assertEqual(female["rs6026400"].chromosome, 20)
self.assertEqual(female["rs6026400"].position, 57183524)
self.assertEqual(female["rs6026400"].genotype, "CC")
self.assertEqual(female["i3001754"].chromosome, "MT")
self.assertEqual(female["i3001754"].position, 16256)
self.assertEqual(female["i3001754"].genotype, "A")
self.assertEqual(female["i3001755"].chromosome, "MT")
self.assertEqual(female["i3001755"].position, 16257)
self.assertEqual(female["i3001755"].genotype, "--")
self.assertEqual(female["i3001759"].chromosome, "MT")
self.assertEqual(female["i3001759"].position, 16258)
self.assertEqual(female["i3001759"].genotype, "--")
self.assertEqual(female["i3001761"].chromosome, "MT")
self.assertEqual(female["i3001761"].position, 16259)
self.assertEqual(female["i3001761"].genotype, "--")
self.assertEqual(female["i3001773"].chromosome, "MT")
self.assertEqual(female["i3001773"].position, 16265)
self.assertEqual(female["i3001773"].genotype, "T")
self.assertEqual(female["i4000755"].chromosome, "MT")
self.assertEqual(female["i4000755"].position, 16548)
self.assertEqual(female["i4000755"].genotype, "C")
self.assertEqual(female["i4000759"].chromosome, "MT")
self.assertEqual(female["i4000759"].position, 16567)
self.assertEqual(female["i4000759"].genotype, "G")
self.assertEqual(female["rs1426654"].chromosome, 15)
self.assertEqual(female["rs1426654"].position, 48426484)
self.assertEqual(female["rs1426654"].genotype, "AA")
self.assertEqual(female["rs12913832"].chromosome, 15)
self.assertEqual(female["rs12913832"].position, 28365618)
self.assertEqual(female["rs12913832"].genotype, "GG")
self.assertEqual(female["rs28504042"].chromosome, "MT")
self.assertEqual(female["rs28504042"].position, 1549)
self.assertEqual(female["rs28504042"].genotype, "--")
self.assertEqual(female["rs3135027"].chromosome, "MT")
self.assertEqual(female["rs3135027"].position, 1598)
self.assertEqual(female["rs3135027"].genotype, "G")
self.assertEqual(female["rs671"].chromosome, 12)
self.assertEqual(female["rs671"].position, 112241766)
self.assertEqual(female["rs671"].genotype, "GG")
def test_open_error(self):
with self.assertRaises(RuntimeError):
arv.load("non-existing-file")
