# outstats.write(line[0])
# os.remove(tempfile)
# outstats.close()
if __name__ == "__main__":
import ipyrad as ip
## get path to test dir/
ROOT = os.path.realpath(
os.path.dirname(
os.path.dirname(
os.path.dirname(__file__)
)
)
)
## run test on RAD data1
TEST = ip.load_assembly(os.path.join(ROOT, "tests", "test_rad", "data1"))
TEST.step4(force=True)
print(TEST.stats)
## run test on messy data set
#TEST = ip.load_assembly(os.path.join(ROOT, "tests", "radmess", "data1"))
## check if results are correct
## cleanup
## if sample is already done skip
if not force:
if sample.stats.state >= 2:
print("skipping {}. Already edited. Use force=True to overwrite"\
.format(sample.name))
else:
submitted, results = run_full(data, sample, ipyclient, nreplace)
cleanup(data, sample, submitted, results)
else:
submitted, results = run_full(data, sample, ipyclient, nreplace)
cleanup(data, sample, submitted, results)
return ipyclient
if __name__ == "__main__":
## run test
import ipyrad as ip
## test rad
TEST = ip.load_assembly("testrad")
TEST.step2(force=True)
## test gbs
TEST = ip.load_assembly("testgbs")
TEST.step2(force=True)
## test pairgbs
TEST = ip.load_assembly("testpairgbs")
TEST.step2(force=True)
# ## remove stats temp files
# for handle in funcfiles:
# end = handle.split("/")[-1].replace(".clustS.gz", "")
# tempfile = params["work"]+"stats/."+end+".temp"
# line = open(tempfile).readlines()
# outstats.write(line[0])
# os.remove(tempfile)
# outstats.close()
if __name__ == "__main__":
import ipyrad as ip
## get path to test dir/
ROOT = os.path.realpath(
os.path.dirname(os.path.dirname(os.path.dirname(__file__))))
## run test on RAD data1
TEST = ip.load_assembly(os.path.join(ROOT, "tests", "test_rad", "data1"))
TEST.step4(force=True)
print(TEST.stats)
## run test on messy data set
#TEST = ip.load_assembly(os.path.join(ROOT, "tests", "radmess", "data1"))
## check if results are correct
## cleanup
if sample.stats.state >= 2:
print("skipping {}. Already edited. Use force=True to overwrite"\
.format(sample.name))
else:
submitted, results = run_full(data, sample, ipyclient, nreplace)
cleanup(data, sample, submitted, results)
else:
submitted, results = run_full(data, sample, ipyclient, nreplace)
cleanup(data, sample, submitted, results)
return ipyclient
if __name__ == "__main__":
## run test
import ipyrad as ip
## test rad
TEST = ip.load_assembly("testrad")
TEST.step2(force=True)
## test gbs
TEST = ip.load_assembly("testgbs")
TEST.step2(force=True)
## test pairgbs
TEST = ip.load_assembly("testpairgbs")
TEST.step2(force=True)
