def test_loader():
paths = get_test_data()
out_file = 'test_loader.h5'
mzml_to_hdf(paths['basic'], out_file_name=out_file)
check_file(out_file)
def setup():
global fid
paths = get_test_data()
out_file = 'test_query.h5'
mzml_to_hdf(paths['basic'], out_file_name=out_file)
fid = tables.open_file('test_query.h5')
def test_loader():
paths = get_test_data()
out_file = 'test_loader.h5'
mzml_to_hdf(paths['basic'], out_file_name=out_file)
check_file(out_file)
def setup():
global fid
paths = get_test_data()
out_file = 'test_query.h5'
mzml_to_hdf(paths['basic'], out_file_name=out_file)
fid = tables.open_file('test_query.h5')
def test_xcms():
path = get_test_data()['basic']
xset = get_xmcs_set([path])
xset = group(xset)
df = peak_table(xset)
assert 'mz' in df.columns
assert 'rtmin' in df.columns
assert df.shape == (279, 13)
def test_invalid_file():
paths = get_test_data()
out_file = 'test_invalid.h5'
assert_raises(TypeError,
mzml_to_hdf,
paths['wrong_fmt'],
out_file_name=out_file)
def test_loader_main():
paths = get_test_data()
out_file = 'test_loader_main.h5'
sys.argv = ['dummy', '--input', paths['basic'],
'--output', out_file,
'--debug']
main()
check_file(out_file)
def test_loader_main():
paths = get_test_data()
out_file = 'test_loader_main.h5'
sys.argv = ['dummy', '--input', paths['basic'],
'--output', out_file,
'--debug']
main()
check_file(out_file)
def test_ms_ms():
paths = get_test_data()
file2 = 'ms_ms.h5'
mzml_to_hdf(paths['ms_ms'], out_file_name=file2)
fid = tables.open_file(file2)
table = fid.root.ms2_pos
assert table.nrows == 604775, table.nrows
def test_ms_ms():
paths = get_test_data()
file2 = 'ms_ms.h5'
mzml_to_hdf(paths['ms_ms'], out_file_name=file2)
fid = tables.open_file(file2)
table = fid.root.ms2_pos
assert table.nrows == 604775, table.nrows
def test_load_lcms_files():
paths = get_test_data().values()
runs = mo.load_lcms_files(paths)
for run in runs:
assert run.mzml_file
assert run.hdf5_file
assert run.creation_time
assert run.description
assert run.name
assert run.last_modified
assert run.username
assert run.unique_id
assert mo.retrieve('lcmsrun', unique_id=run.unique_id)
def test_load_lcms_files():
paths = get_test_data().values()
runs = mo.load_lcms_files(paths)
for run in runs:
assert run.mzml_file
assert run.hdf5_file
assert run.creation_time
assert run.description
assert run.name
assert run.last_modified
assert run.username
assert run.unique_id
assert mo.retrieve('lcmsrun', unique_id=run.unique_id)
def test_32_64():
paths = get_test_data()
fname = 'mix32_64.h5'
mzml_to_hdf(paths['mix32_64'], out_file_name=fname)
fid = tables.open_file(fname)
print(fid)
table = fid.root.ms1_pos
assert table.nrows == 1041183, table.nrows
table2 = fid.root.ms1_neg
assert table2.nrows == 762699, table2.nrows
def test_32_64():
paths = get_test_data()
fname = 'mix32_64.h5'
mzml_to_hdf(paths['mix32_64'], out_file_name=fname)
fid = tables.open_file(fname)
print(fid)
table = fid.root.ms1_pos
assert table.nrows == 1041183, table.nrows
table2 = fid.root.ms1_neg
assert table2.nrows == 762699, table2.nrows
def test_invalid_file():
paths = get_test_data()
out_file = 'test_invalid.h5'
assert_raises(TypeError, mzml_to_hdf, paths['wrong_fmt'],
out_file_name=out_file)
def prep():
path = get_test_data()['basic']
if os.path.exists(path.replace('.mzML', '_finfo.json')):
os.remove(path.replace('.mzML', '_finfo.json'))
return path
def prep():
path = get_test_data()['basic']
if os.path.exists(path.replace('.mzML', '_finfo.json')):
os.remove(path.replace('.mzML', '_finfo.json'))
return path