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 repsize_table(name2sample, outfile, group2avr={}, group2names={}, tex=False):
# Sort the samples by group and/or size
if len(group2avr) > 0:
avrnames = [gavr[0] for gavr in group2avr.values()]
sortedsamples = libcommon.sort_objs_by_group(name2sample, group2names,
True, group2avr)
else:
avrnames = []
sortedsamples = libcommon.sort_dict_by_value(name2sample,
keyfunc=lambda item: item[0].size)
#sortedsamples = sorted(name2sample.values(), key=lambda s: s.size,
# reverse=True)
# Write to output file
if tex:
repsize_latex(sortedsamples, outfile, avrnames)
else:
repsize_text(sortedsamples, outfile)
def table(name2obj, outfile, colfields, group2avr={}, group2names={},
tex=False, keyattr='numclone', caption='', label='', islist=False):
# rows=samples; cols=colfields;
if not name2obj or not colfields:
return
# Sort the samples by group and/or size
keyfunc = None
listattr = None
if islist or keyattr not in colfields:
listattr = keyattr
else:
keyfunc = lambda item: item[0][keyattr]
if group2avr:
sortedobjs = libcommon.sort_objs_by_group(name2obj, group2names,
True, group2avr, keyfunc=keyfunc)
else:
sortedobjs = libcommon.sort_dict_by_value(name2obj, keyfunc=keyfunc)
if tex:
table_latex(sortedobjs, outfile, colfields, caption, label, listattr)
else:
table_text(sortedobjs, outfile, colfields, listattr)
