def __init__(self, gds_name, remove_unknown=None):
""" Retrieval of a specific GEO DataSet as a :obj:`Orange.data.Table`.
Constructor returns the object that can retrieve GEO DataSet (samples and gene expressions).
It first checks a local cache directory if the particular data file is loaded locally,
else it downloads it from `NCBI's GEO FTP site <ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/GDS/>`_.
:param gds_name: An NCBI's ID for the data set in the form "GDSn" where "n" is a GDS ID number.
:param remove_unknown: Remove spots with sample profiles that include unknown values. They are removed
if the proportion of samples with unknown values is above the threshold set by
``remove_unknown``. If None, nothing is removed.
"""
self.gds_name = gds_name
self.filename = serverfiles.localpath(DOMAIN,
self.gds_name + '.soft.gz')
gds_ensure_downloaded(self.gds_name)
self.spot2gene = {}
self.gene2spots = {}
self.info = None
self.gds_data = None
self.parse_file(remove_unknown=remove_unknown)
taxid = taxonomy.search(self.info["sample_organism"], exact=True)
self.info["taxid"] = taxid[0] if len(taxid) == 1 else None
self.genes = sorted(self.gene2spots.keys())
self.spots = sorted(self.spot2gene.keys())
self.info["gene_count"] = len(self.genes)
def get_data(gds_id, report_genes, transpose, sample_type, title):
gds_ensure_downloaded(gds_id, progress)
gds = GDS(gds_id)
data = gds.get_data(report_genes=report_genes,
transpose=transpose,
sample_type=sample_type)
data.name = title
return data
def test_gds_data(self):
# test url
self.assertIsNotNone(gds_download_url(self.test_sample))
# file not in cache
self.assertFalse(gds_is_cached(self.test_sample))
# download gds from serverfiles
try:
makedirs(serverfiles.localpath(DOMAIN))
except OSError:
if path.exists(serverfiles.localpath(DOMAIN)):
pass
else:
# There was an error on creation, so make sure we know about it
raise
gds_download(self.test_sample)
# file in cache
self.assertIsNone(gds_ensure_downloaded(self.test_sample))
self.assertTrue(gds_is_cached(self.test_sample))
gds = GDS(self.test_sample)
self.assertIsNotNone(gds.info)
self.assertEqual(gds.info['gene_count'], 9561)
self.assertEqual(len(gds.info['samples']), 4)
self.assertEqual(len(gds.info['subsets']), 2)
self.assertEqual(gds.info['taxid'], self.test_organism)
self.assertIsInstance(gds.get_data(), Table)
self.assertIsInstance(gds.get_data(transpose=True), Table)