def build_allplots_def(pconfig, page_num):
"""Write the configuration file for Allplots that it's expecting on stdin
Allplots used to check for 'Allplots.def' in the dcurrent
directory but we modified it to be able to read this configuration
on stdin, this writes in that format.
"""
parsing.first_page_title(pconfig)
parsing.following_page_title(pconfig)
lines = []
wl = lines.append
# NB: the "Plot Title" is disregarded, but that line
# should also contain the total number of bases
wl("%s %d" % ("FOOBAR", pconfig['length']))
# Nucleotide(s)_plotted (e.g.: `% CG`)
wl(''.join(pconfig['nucleotides']))
# First-Page title
wl(pconfig['first_page_title'].format(page_num))
# Title of following pages
wl(pconfig['following_page_title'].format(page_num))
# write the rest of the filenames that allplots might read from
for k in FILE_KEYS:
# allplots doesn't like blank lines so make sure there is at
# least a dummy value on every line.
wl(pconfig.get(k, "None"))
return '\n'.join(lines) + '\n'
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