def test_profile_mut_bin_noerr(self):
""" Test the ability of sortseq_tools.profile_mut to compute mutation rates
"""
print '\nIn test_profile_mut_bin_noerr_...'
library_files = glob.glob(self.input_dir+'library_*.txt')
library_files += glob.glob(self.input_dir+'dataset_*.txt')
good_bin_num = 2
bad_bin_num = 5
for file_name in library_files:
print '\t%s ='%file_name,
description = file_name.split('_')[-1].split('.')[0]
executable = lambda:\
profile_mut.main(io.load_dataset(file_name),bin=good_bin_num,err=False)
print '(bin=%d)'%good_bin_num,
# If bad or library, then profile_mut.main should raise SortSeqError
if ('_bad' in file_name) or ('library' in file_name):
try:
self.assertRaises(SortSeqError,executable)
print 'badtype,',
except:
print 'good (ERROR).'
raise
# If good, then profile_mut.main should produce a valid df
elif '_good' in file_name:
try:
df = executable()
qc.validate_profile_mut(df)
out_file = self.output_dir+\
'profile_mut_bin_noerr_%s.txt'%description
io.write(df,out_file) # Test writing
io.load_profile_mut(out_file) # Test loading
print 'good,',
except:
print 'bad (ERROR).'
raise
# There are no other options
else:
raise SortSeqError('Unrecognized class of file_name.')
# Should always raise an error if bin num is too large
executable = lambda:\
profile_mut.main(io.load_dataset(file_name),bin=bad_bin_num)
print '(bin=%d)'%bad_bin_num,
try:
self.assertRaises(SortSeqError,executable)
print 'badtype.'
except:
print 'good (ERROR).'
raise
def test_profile_mut_total_err(self):
""" Test the ability of sortseq_tools.profile_mut to compute mutation rates based on total count values
"""
print '\nIn test_profile_mut_total_err...'
library_files = glob.glob(self.input_dir+'library_*.txt')
library_files += glob.glob(self.input_dir+'dataset_*.txt')
for file_name in library_files:
print '\t%s ='%file_name,
description = file_name.split('_')[-1].split('.')[0]
executable = lambda: profile_mut.main(io.load_dataset(file_name),err=True)
# If good, then profile_mut.main should produce a valid df
if '_good' in file_name:
try:
df = executable()
qc.validate_profile_mut(df)
out_file = self.output_dir+\
'profile_mut_total_err_%s.txt'%description
io.write(df,out_file)
io.load_profile_mut(out_file)
print 'good.'
except:
print 'bad (ERROR).'
raise
# If bad, then profile_mut.main should raise SortSeqError
elif '_bad' in file_name:
try:
self.assertRaises(SortSeqError,executable)
print 'badtype.'
except:
print 'good (ERROR).'
raise
# There are no other options
else:
raise SortSeqError('Unrecognized class of file_name.')
def test_profile_mut_seqslicing(self):
""" Test the ability of sortseq_tools.profile_mut to slice sequences properly, and to raise the correct errors
"""
print '\nIn test_profile_mut_seqslicing...'
library_files = glob.glob(self.input_dir+'library_*.txt')
library_files += glob.glob(self.input_dir+'dataset_*.txt')
for file_name in library_files:
print '\t%s ='%file_name,
description = file_name.split('_')[-1].split('.')[0]
executable_good1 =\
lambda: profile_mut.main(io.load_dataset(file_name),\
start=2,end=10)
executable_good2 =\
lambda: profile_mut.main(io.load_dataset(file_name),\
end=10)
executable_good3 =\
lambda: profile_mut.main(io.load_dataset(file_name),\
end=2)
executable_nopro =\
lambda: profile_mut.main(io.load_dataset(file_name),\
start=50,end=60)
executable_bad1 =\
lambda: profile_mut.main(io.load_dataset(file_name),\
start=-1)
executable_bad2 =\
lambda: profile_mut.main(io.load_dataset(file_name),\
end=100)
executable_bad3 =\
lambda: profile_mut.main(io.load_dataset(file_name),\
start=20,end=10)
# If good, then sequences will be valid
if '_good' in file_name:
try:
df = executable_good1()
io.write(df,self.output_dir+\
'profile_mut_splice2-10_%s.txt'%description)
executable_good2()
executable_good3()
self.assertRaises(SortSeqError,executable_bad1)
self.assertRaises(SortSeqError,executable_bad2)
self.assertRaises(SortSeqError,executable_bad3)
if '_pro' in file_name:
self.assertRaises(SortSeqError,executable_nopro)
else:
df = executable_nopro()
print 'ok.'
except:
print 'ok (ERROR).'
raise
# If bad, then profile_mut.main should raise SortSeqError
elif '_bad' in file_name:
try:
self.assertRaises(SortSeqError,executable_good1)
self.assertRaises(SortSeqError,executable_good2)
self.assertRaises(SortSeqError,executable_good3)
self.assertRaises(SortSeqError,executable_nopro)
self.assertRaises(SortSeqError,executable_bad1)
self.assertRaises(SortSeqError,executable_bad2)
self.assertRaises(SortSeqError,executable_bad3)
print 'ok.'
except:
print 'not ok (ERROR).'
raise
# There are no other options
else:
raise SortSeqError('Unrecognized class of file_name.')