def run(self):
self.logToMaster("RepSize\n")
stime = time.time()
name2sample = {}
for sam in os.listdir(self.sampledir):
filepath = os.path.join(self.sampledir, sam, sam)
sample = pickle.load(gzip.open(filepath, 'rb'))
name2sample[sam] = sample
logger.info("RepSize, done loading %d samples in %.4f s." %
(len(name2sample), (time.time() - stime)))
stime = time.time()
# Get summary of samples' sizes:
group2samples = self.options.group2samples
group2avr = libcommon.get_group_avr(name2sample, group2samples)
logger.info("RepSize, done computing group_avr in %.4f s." %
(time.time() - stime))
txtfile = os.path.join(self.options.outdir, "clonesize.txt")
repsize.repsize_table(name2sample, txtfile, group2avr, group2samples)
texfile = os.path.join(self.options.outdir, "clonesize.tex")
repsize.repsize_table(name2sample, texfile, group2avr, group2samples,
True)
self.addChildTarget(diversity.DiversityRarefaction(self.sampledir,
self.options))
def run(self):
self.load_indir()
name2sampling = self.name2obj
# Print out summary table
g2s = self.group2samples
g2avr = {}
if g2s:
g2avr = libcommon.get_group_avr(name2sampling, g2s)
txtfile = os.path.join(self.outdir, "diversity.txt")
tabcommon.table(name2sampling, txtfile, self.indices, g2avr, g2s)
texfile = os.path.join(self.outdir, "diversity.tex")
tabcommon.table(name2sampling, texfile, self.indices, g2avr, g2s, True)
# For each diversity index, each pair of groups, perform ttest
# and draw plot
if g2s and len(g2s) >= 2:
outdir = os.path.join(self.outdir, "group_comparisons")
system("mkdir -p %s" % outdir)
global_dir = os.path.join(self.getGlobalTempDir(), "ttests")
system("mkdir -p %s" % global_dir)
for index in self.indices:
self.addChildTarget(DiversityTtest(global_dir, index, g2s,
name2sampling, self.matched, self.plotfmt, outdir))
self.setFollowOnTarget(DiversityTtestSummary(global_dir, outdir,
self.pval))
def run(self):
system("rm -Rf %s" % self.workdir)
opts = self.options
indices = opts.diversity
name2size2sampling = {}
size2name2sampling = {}
for name in os.listdir(self.indir):
sampledir = os.path.join(self.indir, name)
name2size2sampling[name] = {}
for file in os.listdir(sampledir):
size = long(file.split(".")[0])
filepath = os.path.join(sampledir, file)
sampling = pickle.load(gzip.open(filepath, "rb"))
name2size2sampling[name][size] = sampling
if size not in size2name2sampling:
size2name2sampling[size] = {name: sampling}
else:
size2name2sampling[size][name] = sampling
outdir = os.path.join(opts.outdir, "diversity")
txtdir = os.path.join(outdir, "txt")
system("mkdir -p %s" % txtdir)
texdir = os.path.join(outdir, "tex")
system("mkdir -p %s" % texdir)
pdfdir = os.path.join(outdir, "pdf")
if opts.makeplots:
system("mkdir -p %s" % pdfdir)
# Summary table for each index:
groups = None
g2s = opts.group2samples
if g2s:
groups = opts.group2samples.keys()
for index in indices:
rftabfile = os.path.join(txtdir, "rf_%s.txt" % index)
rf_diversity_table(name2size2sampling, rftabfile, index)
if opts.makeplots:
rfplotfile = os.path.join(pdfdir, "rf_%s" % index)
rfplot.draw_rarefaction(name2size2sampling, groups, index,
rfplotfile, opts.plotformat, opts.dpi)
# Summary table for each sampling size:
for size, name2sampling in size2name2sampling.iteritems():
g2avr = {}
if g2s:
g2avr = libcommon.get_group_avr(name2sampling, g2s)
txtfile = os.path.join(txtdir, "diversity_%d.txt" % size)
tabcommon.table(name2sampling, txtfile, indices, g2avr, g2s)
texfile = os.path.join(texdir, "diversity_%d.tex" % size)
tabcommon.table(name2sampling, texfile, indices, g2avr, g2s, True)
self.setFollowOnTarget(libcommon.CleanupDir(self.indir))
def test_get_group_avr(self):
group2avr = lcommon.get_group_avr(self.name2obj, self.group2names)
self.assertEqual(len(group2avr), 2)
self.assertEqual(sorted(group2avr.keys()), ['g1', 'g2'])
(name1, avr1) = group2avr['g1']
self.assertEqual(name1, 'g1_Avr')
self.assertEqual(avr1.size, (10 + 5) / 2)
self.assertEqual(avr1.numclone, (2 + 4) / 2)
self.assertEqual(avr1.clones, [(5 + 3) / 2, (0 + 2) / 2])
(name2, avr2) = group2avr['g2']
self.assertEqual(name2, 'g2_Avr')
self.assertEqual(avr2.size, 15)
self.assertEqual(avr2.numclone, 1)
self.assertEqual(avr2.clones, None)
def test_sort_objs_by_group(self):
group2avr = lcommon.get_group_avr(self.name2obj, self.group2names)
sorted_objs = lcommon.sort_objs_by_group(self.name2obj,
self.group2names, True, group2avr)
self.assertEqual(len(sorted_objs), 5)
names = ['sam1', 'sam2', 'g1_Avr', 'sam3', 'g2_Avr']
self.assertEqual(names, [o[0] for o in sorted_objs])
n2o = self.name2obj
objs = [n2o['sam1'], n2o['sam2'], group2avr['g1'][1], n2o['sam3'],
group2avr['g2'][1]]
self.assertEqual(objs, [o[1] for o in sorted_objs])
#Without adding average group
sorted_objs = lcommon.sort_objs_by_group(self.name2obj,
self.group2names, False, group2avr)
self.assertEqual(len(sorted_objs), 3)
names = ['sam1', 'sam2', 'sam3']
self.assertEqual(names, [o[0] for o in sorted_objs])
n2o = self.name2obj
objs = [n2o['sam1'], n2o['sam2'], n2o['sam3']]
self.assertEqual(objs, [o[1] for o in sorted_objs])
def run(self):
self.load_indir()
name2obj = self.name2obj
opts = self.opts
assert len(name2obj) > 0
obj0 = name2obj.values()[0]
numsam = len(name2obj)
g2s = opts.group2samples
g2name_avr = None
g2avr = None
if g2s:
g2name_avr = libcommon.get_group_avr(name2obj, g2s)
if opts.makeplots:
g2avr = {}
for g, na in g2name_avr.iteritems():
groupname = na[0]
groupavr = na[1]
g2avr[groupname] = groupavr
attrs = ['numclones', 'counts', 'topfreqs', 'numclones_cumul',
'counts_cumul', 'topfreqs_cumul']
txtdir = os.path.join(self.outdir, "txt_tables")
system("mkdir -p %s" % txtdir)
plotdir = None
if opts.makeplots:
plotdir = os.path.join(self.outdir, "figures")
system("mkdir -p %s" % plotdir)
for attr in attrs:
txtfile = os.path.join(txtdir, "%s.txt" % attr)
colfields = get_attr_colfields(attr, obj0)
tabcommon.table(name2obj, txtfile, colfields, g2name_avr,
g2s, keyattr=attr, islist=True)
if opts.makeplots:
plotfile = os.path.join(plotdir, attr)
if numsam < 100 or opts.cs_force_all:
csplot.draw_clonesize_dist(name2obj, attr, plotfile,
opts.plotformat, opts.dpi)
elif g2avr:
csplot.draw_clonesize_dist_avr(name2obj, attr, plotfile,
opts.plotformat, opts.dpi)
