def mq2_run(session_id, plugin, folder, lod_threshold, session):
""" Run the scripts to extract the QTLs.
:arg session_id: the session identifier uniquely identifying the
MapQTL zip file and the JoinMap map file. The session identifier
also uniquely identifies the folder in which are the files
uploaded.
:arg lod_threshold: the LOD threshold to use to consider a value
significant for a QTL.
:arg mapqtl_session: the MapQTL session/run from which to retrieve
the QTLs.
"""
upload_folder = os.path.join(UPLOAD_FOLDER, session_id)
already_done = experiment_done(session_id, lod_threshold, session)
if already_done is not False:
return already_done
exp_id = '%s_s%s_t%s' % (generate_exp_id(), session,
lod_threshold)
exp_folder = os.path.join(upload_folder, exp_id)
if not os.path.exists(exp_folder):
os.mkdir(exp_folder)
try:
run_mq2(plugin, folder, lod_threshold=lod_threshold,
session=session, outputfolder=exp_folder)
(nline, ncol) = get_matrix_dimensions(os.path.join(
exp_folder, 'qtls_matrix.csv'))
except MQ2Exception, err:
shutil.rmtree(exp_folder)
raise MQ2Exception(err)
def test_run_mq2_from_file(self):
""" Test the run_mq2 function from a file.
"""
plugin, folder = mq2.get_plugin_and_folder(
inputfile=TEST_INPUT_FILE)
mq2.run_mq2(plugin,
folder=TEST_INPUT_FILE,
lod_threshold=3)
self.assertEqual(read_file('qtls.csv'),
read_file(os.path.join(
TEST_FOLDER, 'csv', 'qtls.exp')))
self.assertEqual(read_file('map.csv'),
read_file(os.path.join(
TEST_FOLDER, 'csv', 'map.exp')))
self.assertEqual(read_file('map_with_qtls.csv'),
read_file(os.path.join(
TEST_FOLDER, 'csv', 'map_with_qtls.exp')))
self.assertEqual(read_file('qtls_matrix.csv'),
read_file(os.path.join(
TEST_FOLDER, 'csv', 'qtls_matrix.exp')))
self.assertEqual(read_file('qtls_with_mk.csv'),
read_file(os.path.join(
TEST_FOLDER, 'csv', 'qtls_with_mk.exp')))
self.assertEqual(read_file('MapChart.map'),
read_file(os.path.join(
TEST_FOLDER, 'csv', 'MapChart.exp')))
def mq2_run(session_id, plugin, folder, lod_threshold, session):
""" Run the scripts to extract the QTLs.
:arg session_id: the session identifier uniquely identifying the
MapQTL zip file and the JoinMap map file. The session identifier
also uniquely identifies the folder in which are the files
uploaded.
:arg lod_threshold: the LOD threshold to use to consider a value
significant for a QTL.
:arg mapqtl_session: the MapQTL session/run from which to retrieve
the QTLs.
"""
upload_folder = os.path.join(UPLOAD_FOLDER, session_id)
already_done = experiment_done(session_id, lod_threshold, session)
if already_done is not False:
return already_done
exp_id = '%s_s%s_t%s' % (generate_exp_id(), session, lod_threshold)
exp_folder = os.path.join(upload_folder, exp_id)
if not os.path.exists(exp_folder):
os.mkdir(exp_folder)
try:
run_mq2(plugin,
folder,
lod_threshold=lod_threshold,
session=session,
outputfolder=exp_folder)
(nline, ncol) = get_matrix_dimensions(
os.path.join(exp_folder, 'qtls_matrix.csv'))
except MQ2Exception, err:
shutil.rmtree(exp_folder)
raise MQ2Exception(err)
def test_run_mq2(self):
""" Test the run_mq2 function from a zip archive.
"""
plugin, folder = mq2.get_plugin_and_folder(inputzip=TEST_INPUT_PASSED)
mq2.run_mq2(plugin, folder, lod_threshold=3, session='Sheet1')
self.assertEqual(
read_file('qtls.csv'),
read_file(os.path.join(TEST_FOLDER, 'xls', 'qtls.exp')))
self.assertEqual(
read_file('map.csv'),
read_file(os.path.join(TEST_FOLDER, 'xls', 'map.exp')))
self.assertEqual(
read_file('map_with_qtls.csv'),
read_file(os.path.join(TEST_FOLDER, 'xls', 'map_with_qtls.exp')))
self.assertEqual(
read_file('qtls_with_mk.csv'),
read_file(os.path.join(TEST_FOLDER, 'xls', 'qtls_with_mk.exp')))
def test_run_mq2(self):
""" Test the run_mq2 function from a zip archive.
"""
plugin, folder = mq2.get_plugin_and_folder(
inputzip=TEST_INPUT_PASSED)
mq2.run_mq2(plugin, folder, lod_threshold=3, session='Sheet1')
self.assertEqual(read_file('qtls.csv'),
read_file(os.path.join(
TEST_FOLDER, 'xls', 'qtls.exp')))
self.assertEqual(read_file('map.csv'),
read_file(os.path.join(
TEST_FOLDER, 'xls', 'map.exp')))
self.assertEqual(read_file('map_with_qtls.csv'),
read_file(os.path.join(
TEST_FOLDER, 'xls', 'map_with_qtls.exp')))
self.assertEqual(read_file('qtls_with_mk.csv'),
read_file(os.path.join(
TEST_FOLDER, 'xls', 'qtls_with_mk.exp')))
def test_run_mq2_from_file(self):
""" Test the run_mq2 function from a file.
"""
plugin, folder = mq2.get_plugin_and_folder(inputfile=TEST_INPUT_FILE)
mq2.run_mq2(plugin, folder=TEST_INPUT_FILE, lod_threshold=3)
self.assertEqual(
read_file('qtls.csv'),
read_file(os.path.join(TEST_FOLDER, 'csv', 'qtls.exp')))
self.assertEqual(
read_file('map.csv'),
read_file(os.path.join(TEST_FOLDER, 'csv', 'map.exp')))
self.assertEqual(
read_file('map_with_qtls.csv'),
read_file(os.path.join(TEST_FOLDER, 'csv', 'map_with_qtls.exp')))
self.assertEqual(
read_file('qtls_matrix.csv'),
read_file(os.path.join(TEST_FOLDER, 'csv', 'qtls_matrix.exp')))
self.assertEqual(
read_file('qtls_with_mk.csv'),
read_file(os.path.join(TEST_FOLDER, 'csv', 'qtls_with_mk.exp')))
self.assertEqual(
read_file('MapChart.map'),
read_file(os.path.join(TEST_FOLDER, 'csv', 'MapChart.exp')))
def test_run_mq2(self):
""" Test the run_mq2 function with MapQTL zip input.
"""
plugin, folder = mq2.get_plugin_and_folder(inputzip=TEST_INPUT_PASSED)
mq2.run_mq2(plugin, folder, lod_threshold=3, session=2)
self.assertEqual(
read_file('qtls.csv'),
read_file(os.path.join(TEST_FOLDER, 'csv', 'qtls.exp')))
self.assertEqual(
read_file('map.csv'),
read_file(os.path.join(TEST_FOLDER, 'csv', 'map.exp')))
self.assertEqual(
read_file('map_with_qtls.csv'),
read_file(os.path.join(TEST_FOLDER, 'csv', 'map_with_qtls.exp')))
self.assertEqual(
read_file('qtls_matrix.csv'),
read_file(os.path.join(TEST_FOLDER, 'csv', 'qtls_matrix.exp')))
self.assertEqual(
read_file('qtls_with_mk.csv'),
read_file(os.path.join(TEST_FOLDER, 'csv', 'qtls_with_mk.exp')))
self.assertEqual(
read_file('MapChart.map'),
read_file(os.path.join(TEST_FOLDER, 'csv', 'MapChart.exp')))
def test_run_mq2(self):
""" Test the run_mq2 function with MapQTL zip input.
"""
plugin, folder = mq2.get_plugin_and_folder(
inputzip=TEST_INPUT_PASSED)
mq2.run_mq2(plugin, folder, lod_threshold=3, session=2)
self.assertEqual(read_file('qtls.csv'),
read_file(os.path.join(
TEST_FOLDER, 'csv', 'qtls.exp')))
self.assertEqual(read_file('map.csv'),
read_file(os.path.join(
TEST_FOLDER, 'csv', 'map.exp')))
self.assertEqual(read_file('map_with_qtls.csv'),
read_file(os.path.join(
TEST_FOLDER, 'csv', 'map_with_qtls.exp')))
self.assertEqual(read_file('qtls_matrix.csv'),
read_file(os.path.join(
TEST_FOLDER, 'csv', 'qtls_matrix.exp')))
self.assertEqual(read_file('qtls_with_mk.csv'),
read_file(os.path.join(
TEST_FOLDER, 'csv', 'qtls_with_mk.exp')))
self.assertEqual(read_file('MapChart.map'),
read_file(os.path.join(
TEST_FOLDER, 'csv', 'MapChart.exp')))
