def action(args):
controls, sample_groups = get_input(args.infile, split_description=args.split_desc)
qadata = qa_from_csv(qafile)
matrix = read_matrix(matrix_file)
style = "screen" if args.outfile == sys.stdout else "file"
outfile = get_outfile(args, label="qa", ext="csv")
if args.calculate_ion_ratios:
qadata = add_ion_ratios(qadata, controls)
# if a single compound is specified, define lambda cond to use as
# a filter
if args.compound_id:
cond = lambda c: c["COMPOUND_id"] == args.compound_id
else:
cond = lambda c: True
# controls
compounds = [Compound(c, matrix, **qadata[c["COMPOUND_id"]]) for c in flatten(controls.values()) if cond(c)]
display_controls(compounds, outfile=outfile, show_all=args.show_all, message=not args.outcomes_only, style=style)
compounds = [Compound(c, matrix, **qadata[c["COMPOUND_id"]]) for c in flatten(sample_groups.values()) if cond(c)]
display_specimens(compounds, outfile=outfile, show_all=args.show_all, message=not args.outcomes_only, style=style)
if args.outfile is None:
outfile.close()
def test01(self):
compounds = [Compound(c, matrix, **qadata[c['COMPOUND_id']]) for c in flatten(patient_sample)]
compounds.sort(key = lambda c: c.sort_by_patient())
for cmpnd_id, cmpnds in groupby(compounds, lambda c: c.COMPOUND_id):
sample = Sample(cmpnds)
self.assertEqual(cmpnd_id, sample.COMPOUND_id)
self.assertEqual(sample.type, 'patient')
def test02(self):
compounds = [
Compound(c, matrix, **qadata[c['COMPOUND_id']])
for c in flatten(misc_sample)
]
compounds.sort(key=lambda c: c.sort_by_patient())
for cmpnd_id, cmpnds in groupby(compounds, lambda c: c.COMPOUND_id):
self.assertRaises(TypeError, Sample, cmpnds)
def test01(self):
compounds = [
Compound(c, matrix, **qadata[c['COMPOUND_id']])
for c in flatten(patient_sample)
]
compounds.sort(key=lambda c: c.sort_by_patient())
for cmpnd_id, cmpnds in groupby(compounds, lambda c: c.COMPOUND_id):
sample = Sample(cmpnds)
self.assertEqual(cmpnd_id, sample.COMPOUND_id)
self.assertEqual(sample.type, 'patient')
def action(args):
controls, sample_groups = get_input(args.infile,
split_description=args.split_desc)
qadata = qa_from_csv(qafile)
matrix = read_matrix(matrix_file)
style = 'screen' if args.outfile == sys.stdout else 'file'
outfile = get_outfile(args, label='qa', ext='csv')
if args.calculate_ion_ratios:
qadata = add_ion_ratios(qadata, controls)
# if a single compound is specified, define lambda cond to use as
# a filter
if args.compound_id:
cond = lambda c: c['COMPOUND_id'] == args.compound_id
else:
cond = lambda c: True
# controls
compounds = [
Compound(c, matrix, **qadata[c['COMPOUND_id']])
for c in flatten(controls.values()) if cond(c)
]
display_controls(compounds,
outfile=outfile,
show_all=args.show_all,
message=not args.outcomes_only,
style=style)
compounds = [
Compound(c, matrix, **qadata[c['COMPOUND_id']])
for c in flatten(sample_groups.values()) if cond(c)
]
display_specimens(compounds,
outfile=outfile,
show_all=args.show_all,
message=not args.outcomes_only,
style=style)
if args.outfile is None:
outfile.close()
def test02(self):
compounds = [
Compound(c, matrix, **qadata[c['COMPOUND_id']])
for c in flatten(controls.values())
]
self.assertTrue(all(x.type == 'control' for x in compounds))
def test03(self):
compounds = [
Compound(c, matrix, **qadata[c['COMPOUND_id']])
for c in flatten(compound1)
]
self.assertTrue(all(x.type == 'patient' for x in compounds))
def test02(self):
compounds = [Compound(c, matrix, **qadata[c['COMPOUND_id']]) for c in flatten(sample_groups.values())]
display_specimens(compounds, sys.stdout, message = False)
def test02(self):
flat = flatten(controls.values())
self.assertTrue(all(isinstance(x, dict) for x in flat))
def test01(self):
flat = flatten(sample_groups.values())
self.assertTrue(all(isinstance(x, dict) for x in flat))
def test02(self):
flat = flatten(controls.values())
self.assertTrue(all(isinstance(x, dict) for x in flat))
def test01(self):
flat = flatten(sample_groups.values())
self.assertTrue(all(isinstance(x, dict) for x in flat))
def test02(self):
compounds = [
Compound(c, matrix, **qadata[c['COMPOUND_id']])
for c in flatten(sample_groups.values())
]
display_specimens(compounds, sys.stdout, message=False)
def test03(self):
compounds = [Compound(c, matrix, **qadata[c['COMPOUND_id']]) for c in flatten(compound1)]
self.assertTrue(all(x.type == 'patient' for x in compounds))
def test02(self):
compounds = [Compound(c, matrix, **qadata[c['COMPOUND_id']]) for c in flatten(controls.values())]
self.assertTrue(all(x.type == 'control' for x in compounds))
def test02(self):
compounds = [Compound(c, matrix, **qadata[c['COMPOUND_id']]) for c in flatten(misc_sample)]
compounds.sort(key = lambda c: c.sort_by_patient())
for cmpnd_id, cmpnds in groupby(compounds, lambda c: c.COMPOUND_id):
self.assertRaises(TypeError, Sample, cmpnds)