def testTaxTTests(self):
tax = testfile('multiple_tax.tab')
int = testfile('int_ttest.tab')
expanded = testfile('expand_taxttest.tab')
tax_df = expand.expand('t',
sinfo=TTEST_SINFO,
int_file=int,
pep_colname_int='peptide',
pep_colname_func='peptide',
pep_colname_tax='peptide',
data_dir=TEST_DIR,
outfile=expanded,
tax_file=tax,
tax_colname='lca')
tax_tst = stat.stat(expanded,
sinfo=TTEST_SINFO,
paired=False,
parametric=False,
ontology=None,
mode=None,
outfile=None)
# make sure false is > 0.05 and trues are less than 0.05
self.assertTrue(tax_tst['p'][210] > 0.05)
self.assertTrue(tax_tst['p'][[1496, 1870884]].le(0.05).all())
# also, make sure firmicutes phylum is sum of c difficile and clostridiaceae
self.assertEqual(tax_tst['int1'][1239], np.log2(1020))
def testDA(self):
func = testfile('multiple_func.tab')
int = testfile('int_ttest.tab')
expanded = testfile('go_expanded_ttest.tab')
test_write = testfile('go_tested.tab')
df_expd = expand.expand('f',
sinfo=TTEST_SINFO,
int_file=int,
pep_colname_int='peptide',
pep_colname_func='peptide',
pep_colname_tax='peptide',
data_dir=TEST_DIR,
outfile=expanded,
func_file=func,
func_colname='go',
ontology='go')
df_tst = stat.stat(expanded,
sinfo=TTEST_SINFO,
paired=False,
parametric=True,
ontology='go',
mode='f',
outfile=test_write)
# make sure false is > 0.05 and trues are less than 0.05
self.assertTrue(df_tst['p']['GO:0008152'] > 0.05)
self.assertTrue(df_tst['p'][['GO:0022610', 'GO:0000003',
'GO:0032505']].le(0.05).all())
def testDiffAbundEc(self):
func = testfile('multiple_func.tab')
int = testfile('int_ttest.tab')
expandfile = testfile('ec_ttest.tab')
tested_file = testfile('ec_ttest_tested.tab')
expand.expand('f',
sinfo=TTEST_SINFO,
int_file=int,
pep_colname_int='peptide',
pep_colname_func='peptide',
pep_colname_tax='peptide',
data_dir=TEST_DIR,
outfile=expandfile,
func_file=func,
func_colname='ec',
ontology='ec')
ec_tst = stat.stat(expandfile,
sinfo=TTEST_SINFO,
paired=False,
parametric=True,
ontology='ec',
mode='f',
outfile=tested_file)
# make sure false is > 0.05 and trues are less than 0.05
self.assertTrue(ec_tst['p']['3.4.11.-'] > 0.05)
self.assertTrue(ec_tst['p'][['3.4.21.70', '1.2.-.-']].le(0.05).all())
def testCogTTest(self):
func = testfile('multiple_func.tab')
int = testfile('int_ttest.tab')
expandfile = testfile('cog_ttest.tab')
cog_df = expand.expand('f', sinfo=TTEST_SINFO, int_file=int, pep_colname_int='peptide', pep_colname_func='peptide',
pep_colname_tax='peptide', outfile=expandfile, func_file=func, func_colname='cog',
ontology='cog')
cog_tst = stat.stat(expandfile, sinfo=TTEST_SINFO, paired=False, parametric=True, ontology='cog', mode='f', control_group='s2',
outfile=None)
# make sure false is > 0.05 and trues are less than 0.05
cog_tst.set_index('id', inplace=True)
self.assertTrue(cog_tst['p_s1_over_s2']['C'] > 0.05)
self.assertTrue(cog_tst['p_s1_over_s2'][['N', 'D']].le(0.05).all())
def cli():
"""
Command line interface; main entry point to metaQuantome
:return: exit code
"""
# initialize logger
logging.basicConfig(level=logging.INFO,
format='%(message)s',
stream=sys.stderr)
args = parse_args_cli()
if args.command == "db":
db_download_handler(args.dbs, args.dir, args.update)
elif args.command == "expand":
expand(mode=args.mode,
sinfo=args.samps,
int_file=args.int_file,
pep_colname_int=args.pep_colname_int,
pep_colname_func=args.pep_colname_func,
pep_colname_tax=args.pep_colname_tax,
data_dir=args.data_dir,
outfile=args.outfile,
func_file=args.func_file,
func_colname=args.func_colname,
ontology=args.ontology,
slim_down=args.slim_down,
tax_file=args.tax_file,
tax_colname=args.tax_colname,
nopep=args.nopep,
nopep_file=args.nopep_file,
ft_tar_rank=args.ft_tar_rank)
elif args.command == "filter":
run_filter(expanded_file=args.expand_file,
sinfo=args.samps,
ontology=args.ontology,
mode=args.mode,
qthreshold=args.qthreshold,
min_child_non_leaf=args.min_children_non_leaf,
min_child_nsamp=args.min_child_nsamp,
min_peptides=args.min_peptides,
min_pep_nsamp=args.min_pep_nsamp,
outfile=args.outfile)
elif args.command == "stat":
stat(infile=args.file,
sinfo=args.samps,
paired=args.paired,
parametric=args.parametric,
ontology=args.ontology,
mode=args.mode,
outfile=args.outfile)
elif args.command == "viz":
run_viz(plottype=args.plottype,
img=args.img,
infile=args.infile,
mode=args.mode,
meancol=args.meancol,
nterms=args.nterms,
strip=args.strip,
target_rank=args.target_rank,
barcol=args.barcol,
textannot=args.textannot,
calculate_sep=args.calculate_sep,
fc_name=args.fc_name,
flip_fc=args.flip_fc,
gosplit=args.gosplit,
sinfo=args.samps,
filter_to_sig=args.filter_to_sig,
alpha=args.alpha,
whichway=args.whichway,
name=args.name,
id=args.id,
target_onto=args.target_onto,
width=args.width,
height=args.height,
tabfile=args.tabfile)
else:
ValueError(
'incorrect mode. please provide one of "db", "expand", "filter", "stat", or "viz".'
)
sys.exit(0)