def get_isatab(arrayexpress_id, target_dir=None):
"""
This function downloads MAGE-TAB content as ISA-Tab from the ArrayExpress FTP site.
:param ax_experiment_id: Experiment identifier for ArrayExpress study to get, as a str (e.g. E-GEOD-59671)
:param target_dir: Path to write ISA-Tab files to. If None, writes to temporary directory (generated on the fly)
:return: Path where the files were written to
Example usage:
from isatools.io import ax as AX
AX.get_isatab('E-GEOD-59671', '/tmp/ax')
"""
tmp_dir = tempfile.mkdtemp()
try:
get(arrayexpress_id=arrayexpress_id, target_dir=tmp_dir)
if target_dir is None:
target_dir = tempfile.mkdtemp()
log.info("Using directory '{}'".format(target_dir))
magetab2isatab.convert(os.path.join(
tmp_dir, "{}.idf.txt".format(arrayexpress_id)),
output_path=target_dir)
except Exception as e:
log.fatal("Something went wrong: {}".format(e))
finally:
shutil.rmtree(tmp_dir)
return target_dir
def convert(idf_file_path):
tmp = tempfile.mkdtemp()
ISA = None
try:
magetab2isatab.convert(idf_file_path, output_path=tmp)
with open(os.path.join(tmp, "i_investigation.txt")) as isa_inv_fp:
ISA = isatab.load(isa_inv_fp)
finally:
shutil.rmtree(tmp)
if ISA is not None:
return json.loads(json.dumps(ISA, cls=ISAJSONEncoder))
def test_magetab2isatab_convert_e_geod_59671(self):
magetab2isatab.convert(
os.path.join(self._magetab_data_dir, 'E-GEOD-59671.idf.txt'),
self._tmp_dir)
self.assertTrue(
os.path.isfile(os.path.join(self._tmp_dir, 'i_investigation.txt')))
self.assertTrue(
os.path.isfile(
os.path.join(self._tmp_dir, 's_E-GEOD-59671_study.txt')))
self.assertTrue(
os.path.isfile(
os.path.join(self._tmp_dir,
'a_E-GEOD-59671_assay-RNA-Seq.txt')))
with open(os.path.join(self._tmp_dir, 'i_investigation.txt')) as i_fp:
isatab.validate(i_fp)
def test_magetab2isatab_convert_e_mexp_31(self):
magetab2isatab.convert(
os.path.join(self._magetab_data_dir, 'E-MEXP-31.idf.txt'),
self._tmp_dir)
self.assertTrue(
os.path.isfile(os.path.join(self._tmp_dir, 'i_investigation.txt')))
self.assertTrue(
os.path.isfile(os.path.join(self._tmp_dir,
's_E-MEXP-31_study.txt')))
self.assertTrue(
os.path.isfile(
os.path.join(
self._tmp_dir,
'a_E-MEXP-31_assay-transcription profiling by array.txt')))
with open(os.path.join(self._tmp_dir, 'i_investigation.txt')) as i_fp:
isatab.validate(i_fp)
def test_magetab2isatab_convert_e_geod_59671(self):
with open(os.path.join(self._magetab_data_dir,
'E-GEOD-59671.idf.txt')) as idf_fp:
magetab2isatab.convert(idf_fp, self._tmp_dir)
self.assertTrue(
os.path.isfile(
os.path.join(self._tmp_dir, 'i_investigation.txt')))
self.assertTrue(
os.path.isfile(
os.path.join(self._tmp_dir, 's_E-GEOD-59671.sdrf.txt')))
self.assertTrue(
os.path.isfile(
os.path.join(self._tmp_dir, 'a_E-GEOD-59671.sdrf.txt')))
from isatools import isatab
with open(os.path.join(self._tmp_dir,
'i_investigation.txt')) as i_fp:
isatab.validate(i_fp)
def test_magetab2isatab_convert_e_mexp_31(self):
with open(os.path.join(self._magetab_data_dir,
'E-MEXP-31.idf.txt')) as idf_fp:
magetab2isatab.convert(idf_fp, self._tmp_dir, 'protein microarray',
'protein expression profiling')
self.assertTrue(
os.path.isfile(
os.path.join(self._tmp_dir, 'i_investigation.txt')))
self.assertTrue(
os.path.isfile(
os.path.join(self._tmp_dir, 's_E-MEXP-31.sdrf.txt')))
self.assertTrue(
os.path.isfile(
os.path.join(self._tmp_dir, 'a_E-MEXP-31.sdrf.txt')))
from isatools import isatab
with open(os.path.join(self._tmp_dir,
'i_investigation.txt')) as i_fp:
isatab.validate(i_fp)