def action(args):
qadata = qa_from_csv(qafile)
matrix = read_matrix(matrix_file)
# first get an ungrouped list of samples
tree = xml.etree.ElementTree.ElementTree(file=args.infile)
compound_ids = [d['qa_id'] for d in qadata.values()]
samples = [list(parse_sample(elem, compound_ids)) \
for elem in tree.getiterator('SAMPLELISTDATA')[0].findall('SAMPLE')]
compound_keys = set(['COMPOUND_id', 'COMPOUND_name',
'CONFIRMATIONIONPEAK1_area', 'ISPEAK_area', 'PEAK_analconc',
'PEAK_area', 'PEAK_foundrrt', 'PEAK_signoise', 'SAMPLE_desc',
'SAMPLE_id'])
for sample in samples:
descriptions = set(compound['SAMPLE_desc'] for compound in sample)
assert len(descriptions) == 1
desc = descriptions.pop()
# are all elements present?
for compound in sample:
if compound_keys - set(compound.keys()):
print 'sample %(SAMPLE_desc)s compound %(COMPOUND_id)s is missing' % compound,
print 'element(s)', ''.join(compound_keys - set(compound.keys()))
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):
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)
from collections import OrderedDict
from itertools import groupby
log = logging.getLogger(__name__)
from opiate.containers import Compound, Sample
from opiate.utils import flatten
from opiate.parsers import qa_from_csv, read_matrix
from opiate import qafile, matrix_file
import __init__ as config
## test data
# default qa values for this package
qadata = qa_from_csv(qafile)
matrix = read_matrix(matrix_file)
with open('testfiles/oct24.json') as f:
controls, sample_groups = json.load(f)
expt_stda = controls['stdA']
# type 'misc'
misc_sample = sample_groups['Accession01']
# type 'patient'
patient_sample = sample_groups['Accession02']
compound1 = patient_sample[0]
class TestCompound(unittest.TestCase):
def setUp(self):
def test01(self):
matrix = read_matrix(matrix_file)
from itertools import chain
log = logging.getLogger(__name__)
from opiate import qafile, matrix_file
from opiate.calculations import all_checks
from opiate.parsers import qa_from_csv, read_matrix, get_samples
from opiate.display import display_specimens, display_results
from opiate.containers import Compound
from opiate.utils import flatten
import __init__ as config
from __init__ import TestCaseSuppressOutput
qadata = qa_from_csv(qafile)
matrix = read_matrix(matrix_file)
with open('testfiles/oct24.json') as f:
controls, sample_groups = json.load(f)
class TestDisplayQA(TestCaseSuppressOutput):
def test01(self):
compounds = [Compound(c, matrix, **qadata[c['COMPOUND_id']]) for c in flatten(sample_groups.values())]
display_specimens(compounds, sys.stdout)
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)
class TestDisplayResults(TestCaseSuppressOutput):
samples = list(get_samples(controls, sample_groups, qadata, matrix))
def test01(self):
matrix = read_matrix(matrix_file)
