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 test05(self):
args = Args(infile = self.infile,
outfile = None,
outdir = None)
outfile = get_outfile(args)
log.debug(outfile)
def test06(self):
args = Args(infile = self.infile,
outfile = None,
outdir = None)
outfile = get_outfile(args, include_version = False)
log.debug(outfile)
def test03(self):
args = Args(infile = self.infile,
outfile = open(path.join(self.outdir, 'outfile.csv'), 'w'),
outdir = None)
outfile = get_outfile(args, label = 'qa')
log.debug(outfile)
def test01(self):
args = Args(infile = self.infile,
outfile = None,
outdir = None)
outfile = get_outfile(args, label = 'qa')
log.debug(outfile)
def test04(self):
outdir = mkdir(path.join(self.outdir, 'subdir'), clobber = True)
args = Args(infile = self.infile,
outfile = None,
outdir = outdir)
outfile = get_outfile(args, label = 'qa')
log.debug(outfile)
def action(args):
fmt = 'json'
samples = get_input(args.infile)
if args.sanitize:
samples = remove_patient_info(samples)
outfile = get_outfile(args, ext=fmt)
json.dump(samples, outfile, indent=4)
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):
nullchar = "." if args.outfile == sys.stdout else ""
fmt = lambda s: "%.2f" % s if isinstance(s, float) else (s or nullchar)
controls, sample_groups = get_input(args.infile)
qadata = qa_from_csv(qafile)
outfile = get_outfile(args, label="ion_ratios", ext="csv")
std_ids, std_names = zip(*[(i, n) for i, n in CONTROL_NAMES if n.startswith("std")])
headers = ["qa_id", "qa_compound"] + list(std_names) + ["ion_ratio_avg_calc", "ion_ratio_avg"]
writer = csv.DictWriter(outfile, fieldnames=headers, extrasaction="ignore")
ion_ratios = mean_ion_ratios(controls, set(std_ids))
for compound_id, d in ion_ratios.items():
if compound_id == min(ion_ratios.keys()):
writer.writerow(dict(zip(headers, headers)))
d.update(qadata[compound_id])
writer.writerow(dict((k, fmt(d.get(k))) for k in headers))
def action(args):
nullchar = '.' if args.outfile == sys.stdout else ''
fmt = lambda s: '%.2f' % s if isinstance(s, float) else (s or nullchar)
controls, sample_groups = get_input(args.infile)
qadata = qa_from_csv(qafile)
outfile = get_outfile(args, label='ion_ratios', ext='csv')
std_ids, std_names = zip(*[(i, n) for i, n in CONTROL_NAMES
if n.startswith('std')])
headers = ['qa_id', 'qa_compound'] + \
list(std_names) + ['ion_ratio_avg_calc', 'ion_ratio_avg']
writer = csv.DictWriter(outfile, fieldnames=headers, extrasaction='ignore')
ion_ratios = mean_ion_ratios(controls, set(std_ids))
for compound_id, d in ion_ratios.items():
if compound_id == min(ion_ratios.keys()):
writer.writerow(dict(zip(headers, headers)))
d.update(qadata[compound_id])
writer.writerow(dict((k, fmt(d.get(k))) for k in headers))
def test06(self):
args = Args(infile=self.infile, outfile=None, outdir=None)
outfile = get_outfile(args, include_version=False)
log.debug(outfile)
def test05(self):
args = Args(infile=self.infile, outfile=None, outdir=None)
outfile = get_outfile(args)
log.debug(outfile)
def test04(self):
outdir = mkdir(path.join(self.outdir, "subdir"), clobber=True)
args = Args(infile=self.infile, outfile=None, outdir=outdir)
outfile = get_outfile(args, label="qa")
log.debug(outfile)
def test03(self):
args = Args(infile=self.infile, outfile=open(path.join(self.outdir, "outfile.csv"), "w"), outdir=None)
outfile = get_outfile(args, label="qa")
log.debug(outfile)
def test01(self):
args = Args(infile=self.infile, outfile=None, outdir=None)
outfile = get_outfile(args, label="qa")
log.debug(outfile)