def setUp(self):
"""
"""
self.paths = test_file_paths.paths
file_compressed_indexed = self.paths[2]
file_compressed_unindexed = self.paths[1]
file_uncompressed_indexed = self.paths[0]
file_uncompressed_unindexed = self.paths[0]
file_bad_obo_version = self.paths[10]
file_no_obo_version = self.paths[11]
self.reader_compressed_indexed = run.Reader(file_compressed_indexed)
self.reader_compressed_unindexed = run.Reader(file_compressed_unindexed)
self.reader_uncompressed_indexed = run.Reader(file_uncompressed_indexed)
self.reader_uncompressed_unindexed = run.Reader(file_uncompressed_unindexed)
self.reader_bad_obo_version = run.Reader(file_bad_obo_version)
self.reader_set_obo_version = run.Reader(
file_bad_obo_version, obo_version="3.25.0"
)
self.reader_set_year_obo_version = run.Reader(
file_uncompressed_indexed, obo_version="23:06:2017"
)
self.reader_set_bad_obo_version = run.Reader(
file_uncompressed_indexed, obo_version="bad_obo_version"
)
self.reader_set_no_obo_version = run.Reader(file_no_obo_version)
def setUp(self):
"""
"""
self.paths = test_file_paths.paths
path = self.paths[2]
self.Run = run.Reader(path)
self.spec = self.Run[6]
def setUp(self):
"""
"""
self.paths = test_file_paths.paths
file_compressed_indexed = self.paths[2]
file_compressed_unindexed = self.paths[1]
file_uncompressed_indexed = self.paths[0]
file_uncompressed_unindexed = self.paths[0]
self.reader_compressed_indexed = run.Reader(file_compressed_indexed)
self.reader_compressed_unindexed = run.Reader(
file_compressed_unindexed)
self.reader_uncompressed_indexed = run.Reader(
file_uncompressed_indexed)
self.reader_uncompressed_unindexed = run.Reader(
file_uncompressed_unindexed)
def test_getitem_index_gzip(self):
idx_gzip = self.paths[2]
run_idx_gzip = run.Reader(idx_gzip)
randInt = 6
spec = run_idx_gzip[randInt]
self.assertIsInstance(spec, Spectrum)
self.assertEqual(spec.ID, randInt)
self.assertIsInstance(run_idx_gzip['TIC'], Chromatogram)
def test_getitem_index_mzml(self):
idx_mzml = self.paths[1]
run_idx_mzml = run.Reader(idx_mzml)
randInt = 1
spec = run_idx_mzml[randInt]
self.assertIsInstance(spec, Spectrum)
self.assertEqual(spec.ID, randInt)
self.assertIsInstance(run_idx_mzml['TIC'], Chromatogram)
def test_getitem_2_times_standard_mzml(self):
mzml = self.paths[0]
RunMzml = run.Reader(mzml)
randInt = 10
spec1 = RunMzml[randInt]
self.assertIn(spec1.ID, RunMzml.info['offset_dict'])
spec2= RunMzml[randInt]
self.assertIsInstance(RunMzml[randInt], Spectrum)
self.assertEqual(spec1.ID, spec2.ID)
def setUp(self):
"""
"""
# self.paths = [
# os.path.join( DATA_FOLDER, file ) for file in DATA_FILES]
self.paths = test_file_paths.paths
path = self.paths[9]
self.Run = run.Reader(path)
self.spec = self.Run[2548]
def test_mz(self):
"""
"""
mz = self.spec.mz
self.spec.mz = [1,2,3]
self.assertCountEqual(self.spec.mz, [1,2,3])
Run64 = run.Reader(self.paths[0])
spec64 = Run64[2]
mz64 = spec64.mz
def test_read_custom_regex(self):
custom_regex_file = os.path.join(os.path.dirname(__file__), "data",
"Manuels_custom_ids.mzML")
reader = run.Reader(
custom_regex_file,
index_regex=re.compile(
b'.*idRef="ManuelsCustomID=(?P<ID>.*) diesdas">(?P<offset>[0-9]*)</offset>'
))
ids = sorted(
[k for k in reader.info['offset_dict'].keys() if k != 'TIC'])
assert ids == list(range(1, 11))
def __init__(self, path, *args, **kwargs):
"""
Imports mzML file, adds the chromatogram into a single spectrum.
:param path: .mzML file path
:param args: arguments (unused)
:param kwargs: keywords (unused)
:return: mzMLimporter object
"""
print "Reading mzML:", path
self.msrun = pymzml_run.Reader(path)
self.data = []
self.scans = []
self.times = []
for i, spectrum in enumerate(self.msrun):
if 'scan start time' in spectrum.keys():
impdat = np.transpose([spectrum.mz, spectrum.i])
impdat = impdat[impdat[:, 0] > 10]
self.data.append(impdat)
self.times.append(float(spectrum['scan start time']))
self.scans.append(i)
self.times = np.array(self.times)
self.scans = np.array(self.scans)
self.data = np.array(self.data)
def test_setting_measured_precision(self):
reader = run.Reader(self.paths[2], MS_precisions={1: 61})
spec = reader[1]
self.assertEqual(spec.measured_precision, 61)
def test_getitem_standard_gzip_tic(self):
gzip = self.paths[1]
run_gzip = run.Reader(gzip)
self.assertIsInstance(run_gzip['TIC'], Chromatogram)
def test_getitem_index_mzml_double(self):
idx_mzml = self.paths[0]
run_idx_mzml = run.Reader(idx_mzml)
self.assertIsInstance(run_idx_mzml[4], Spectrum)
self.assertIn(4, run_idx_mzml.info['offset_dict'])
self.assertIsInstance(run_idx_mzml[4], Spectrum)
def test_get_search_spec_with_string(self):
mzml = self.paths[0]
Reader = run.Reader(mzml)
string = 'scan=2'
self.assertIsInstance(Reader[string], Spectrum)
def create_parser(self):
return pymzml_run.Reader(self.filename)
def test_getitem_index_mzml_last(self):
idx_mzml = self.paths[0]
run_idx_mzml = run.Reader(idx_mzml)
spec = run_idx_mzml[11]
self.assertIsInstance(spec, Spectrum)
self.assertEqual(spec.ID, 11)
def test_getitems_end_standard_mzml(self):
mzml = self.paths[0]
RunMzml = run.Reader(mzml)
spec = RunMzml[11]
self.assertEqual(spec.ID, 11)
def reset(self):
self.source = pymzml_run.Reader(self.filename)
self.last_scan = 1
def setUp(self):
self.paths = test_file_paths.paths
path = self.paths[2]
self.Run_np = run.Reader(path)
self.chrom = self.Run_np['TIC']
def test_getitem_standard_gzip_1(self):
gzip = self.paths[1]
run_gzip = run.Reader(gzip)
self.assertIsInstance(run_gzip[1], Spectrum)
def test_chrom_count_spec_file(self):
reader = run.Reader(self.paths[0])
self.assertEqual(reader.get_chromatogram_count(), None)
def test_with_context(self):
with run.Reader(self.paths[0]) as reader:
reader[2]
def test_getitem_standard_mzml_random(self):
mzml = self.paths[0]
RunMzml = run.Reader(mzml)
randInt = 4
self.assertIsInstance(RunMzml[randInt], Spectrum)
self.assertIsInstance(RunMzml['TIC'], Chromatogram)