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):
with open('testfiles/oct24.json') as f:
controls, sample_groups = json.load(f)
qadata = qa_from_csv(qafile)
qd = add_ion_ratios(qadata, controls)
for d in qd.values():
self.assertTrue('ion_ratio_avg_calc' in d)
def test01(self):
with open('testfiles/oct24.json') as f:
controls, sample_groups = json.load(f)
qadata = qa_from_csv(qafile)
qd = add_ion_ratios(qadata, controls)
for d in qd.values():
self.assertTrue('ion_ratio_avg_calc' in d)
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 = 'results', ext = 'csv')
if args.calculate_ion_ratios:
qadata = add_ion_ratios(qadata, controls)
samples = get_samples(controls, sample_groups, qadata, matrix)
display_results(samples, outfile, style = style, grouped = args.grouped)
if args.outfile is None:
outfile.close()
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 action(args):
matrix = read_matrix(matrix_file)
qadata = qa_from_csv(qafile)
compound_ids, compound_codes = map(list, zip(*COMPOUND_CODES))
writer = csv.DictWriter(
args.outfile if hasattr(args.outfile, 'write') else open(args.outfile, 'w'),
fieldnames = ['infile','label'] + compound_ids,
extrasaction = 'ignore')
# create headers for the first row
d = dict(label = 'label', infile = 'infile')
d.update(dict(COMPOUND_CODES))
writer.writerow(d)
counter = count(1)
seen = defaultdict(list) # keep only the first instance of each accession
for infile in args.infiles:
d = dict(infile = infile)
controls, sample_groups = get_input(infile, split_description = args.split_desc)
if args.calculate_ion_ratios:
qadata = add_ion_ratios(qadata.copy(), controls)
patient_samples = get_samples(controls, sample_groups, qadata, matrix, quantitative = True)
for samples in patient_samples:
samples = list(samples)
# exclude any malformed samples
if any(any(c.malformed for c in sample.compounds.values()) for sample in samples):
log.warning('malformed samples in %s' % infile)
continue
# keep only the first instance of each sample
if samples[0].row_label() not in seen:
d['label'] = samples[0].row_label() if args.keep_phi else counter.next()
d.update(dict((s.COMPOUND_id, s.result) for s in samples))
writer.writerow(sanitize(d))
seen[samples[0].row_label()].append(infile)
def test01(self):
_qadata = add_ion_ratios(qadata, controls)
rows = get_samples(controls, sample_groups, _qadata, matrix)
rows.next()
def test01(self):
_qadata = add_ion_ratios(qadata, controls)
rows = get_samples(controls, sample_groups, _qadata, matrix)
rows.next()
