def test_fna(fnaconfig, executor):
nprofile.plan(fnaconfig, executor)
filename = fnaconfig[nprofile.OUTPUTKEY]
assert filename
p = py.path.local(filename)
assert p.exists()
# based on the default step:51, period:3 and the genome length of testgbk
assert 59 == len(p.readlines())
def test_gbk(gbkconfig, executor):
"Test that the enqueue runs and returns"
nprofile.plan(gbkconfig, executor)
filename = gbkconfig[nprofile.OUTPUTKEY]
assert filename
p = py.path.local(filename)
assert p.exists()
# based on the default step:51, period:3 and the genome length of testgbk
assert 59 == len(p.readlines())
def allplots(config, executor):
after = []
try:
after.extend(extract.plan(config, executor))
except:
pass
after.extend(nprofile.plan(config, executor))
after.extend(acgt_gamma.plan(config, executor))
parsing.length(config)
parsing.first_page_title(config)
parsing.following_page_title(config)
parsing.endBase(config)
h = Hasher()
# Strip down to the config for this task only
rconfig = reducedict(config, KEYS + FILE_KEYS)
basesPerGraph = rconfig['basesPerGraph']
graphsPerPage = rconfig['graphsPerPage']
startBase = rconfig.pop('startBase')
endBase = rconfig.pop('endBase')
bp_per_page = rconfig['bp_per_page'] = basesPerGraph * graphsPerPage
page_count = math.ceil(float(endBase - startBase) / bp_per_page)
log.info("Generating %d pages of allplots", page_count)
page_num = 1 # page number offset
filenames = []
waiton = []
# per-page loop
while startBase < endBase:
pconfig = dict(rconfig.items())
pconfig['page_num'] = page_num
pconfig['startBase'] = startBase
if startBase + bp_per_page < endBase:
pconfig['endBase'] = startBase + bp_per_page
else:
pconfig['endBase'] = endBase
h = Hasher().hashdict(pconfig).hashfiletime(BIN).hashfiletime(__file__)
psname = parsing.derive_filename(config, h.hexdigest(), 'ps')
filenames.append(psname)
waiton.extend(enqueue(_ap, executor, pconfig, psname, after=after))
page_num += 1
startBase += bp_per_page
# Finally set the output filenames into the master config dict
config['psnames'] = filenames
return waiton