def test_build1(self):
geneidmap = GeneIDMapHGNCGPL()
# GPL96.txt
gpl_path = os.path.abspath(os.path.join(self.test_data_root, 'gpl96_sample.txt'))
gpl_comment = '#'
gpl_delimiter = '\t'
gpl_fh = DSV.getHandle(gpl_path)
gpl_dsv = DSV(self.dbm, self.testdb, gpl_fh, dtname=self.annoTable, delimiter=gpl_delimiter, comment=gpl_comment)
gpl_dsv.create()
gpl_dsv.loadAll()
gpl_dsv.close()
# HGNC.tsv
hgnc_path = os.path.abspath(os.path.join(self.test_data_root, 'hgnc_sample.txt'))
hgnc_comment = '#'
hgnc_delimiter = '\t'
hgnc_fh = DSV.getHandle(hgnc_path)
hgnc_dsv = DSV(self.dbm, self.testdb, hgnc_fh, dtname=self.hgncTable, delimiter=hgnc_delimiter, comment=hgnc_comment)
hgnc_dsv.create()
hgnc_dsv.loadAll()
hgnc_dsv.close()
# build test map
geneidmap.build(gpl_dsv, hgnc_dsv, self.testdb)
self.assertTrue(geneidmap.built)
self.assertIsInstance(geneidmap.dbt, DBTable)
fwdmap = dict(geneidmap.gene2emid.getFwdMap())
self.assertEqual(self.ref_fwd1, fwdmap)
bwdmap = dict(geneidmap.gene2emid.getBwdMap())
self.assertEqual(self.ref_bwd1, bwdmap)
def setUp(self):
self.test_write_root = TEST_INVARIANTS['test_write_root']
self.test_data_root = TEST_INVARIANTS['test_data_root']
self.sample_data_root = self.test_write_root
self.testdb = 'DB1'
self.dbm = DBManager(self.sample_data_root)
#
self.test_dtname1 = 'LABELS1'
self.lab1_dsv_path = os.path.abspath(os.path.join(self.test_data_root, 'labels1.dsv'))
self.lab1_fh = DSV.getHandle(self.lab1_dsv_path, 'rb')
self.lab1_dsv = DSV(self.dbm, self.testdb, self.lab1_fh, dtname=self.test_dtname1)
self.lab1_dsv.create()
self.lab1_dsv.loadAll()
self.lab1_dsv.close()
self.lab1_cnt = {'A1': '1', 'A2': '1', 'A3': '1', 'A4': '1', 'B1': '-1', 'B2': '-1', 'B3': '-1', 'B4': '-1', }
self.lab1_samples1 = ['A1', 'A2', 'A3', 'A4', 'B1', 'B2', 'B3', 'B4']
self.lab1_resp1 = ['1', '1', '1', '1', '-1', '-1', '-1', '-1']
self.lab1_samples_resp1 = ['A1', 'A2', 'A3', 'A4', 'B1', 'B2', 'B3', 'B4']
self.lab1_samples2 = ['B4', 'B3', 'B2', 'B1', 'A4', 'A3', 'A2', 'A1']
self.lab1_resp2 = ['-1', '-1', '-1', '-1', '1', '1', '1', '1']
self.lab1_samples_resp2 = ['B4', 'B3', 'B2', 'B1', 'A4', 'A3', 'A2', 'A1']
self.lab1_samples3 = ['A1', 'B1', 'A2', 'B2', 'A3', 'B3', 'A4', 'B4']
self.lab1_resp3 = ['1', '-1', '1', '-1', '1', '-1', '1', '-1']
self.lab1_samples_resp3 = ['A1', 'B1', 'A2', 'B2', 'A3', 'B3', 'A4', 'B4']
self.lab1_samples4 = ['A1', 'B1', 'B4', 'A3']
self.lab1_resp4 = ['1', '-1', '-1', '1']
self.lab1_samples_resp4 = ['A1', 'B1', 'B4', 'A3']
self.lab1_samples5 = ['A1', 'B1', None, 'A3']
self.lab1_resp5 = ['1', '-1', '1']
self.lab1_samples_resp5 = ['A1', 'B1', 'A3']
self.lab1_samples6 = ['A1', 'XXX1', 'B4' 'QQQ7546dsfsdfs453']
self.lab1_resp6 = ['1']
self.lab1_samples_resp6 = ['A1']
#
self.test_dtname2 = 'LABELS2'
self.lab2_dsv_path = os.path.abspath(os.path.join(self.test_data_root, 'labels2.dsv'))
self.lab2_fh = DSV.getHandle(self.lab2_dsv_path, 'rb')
self.lab2_dsv = DSV(self.dbm, self.testdb, self.lab2_fh, dtname=self.test_dtname2)
self.lab2_dsv.create()
self.lab2_dsv.loadAll()
self.lab2_dsv.close()
self.lab2_cntN = {'A1': '1', 'A2': '1', 'A3': '1', 'A4': '1',
'B1': '-1', 'B2': '-1', 'B3': '-1', 'B4': '-1',
'PP': '0', 'QQ': '0', 'RR': '0', 'SS': '0'}
self.lab2_cntY = {'A1': '1', 'A2': '1', 'A3': '1', 'A4': '1',
'B1': '-1', 'B2': '-1', 'B3': '-1', 'B4': '-1'}
self.lab2_samples_order1 = ['A1', 'A2', 'A3', 'A4', 'B1', 'B2', 'B3', 'B4']
self.lab2_samples_resp1 = ['A1', 'A2', 'A3', 'A4', 'B1', 'B2', 'B3', 'B4']
self.lab2_samples_order2 = ['A1', 'A2', 'QQ', 'A3', 'A4', 'SS', 'B1', 'B2', 'B3', 'RR', 'B4', 'PP']
self.lab2_samples_resp2 = ['A1', 'A2', 'A3', 'A4', 'B1', 'B2', 'B3', 'B4']
def test_init6(self):
dsv1_fh = DSV.getHandle(self.num_dsv_path)
# delimiter sniffed, comment resolved successfully
dsv1 = DSV(self.dbm, self.testdb, dsv1_fh, dtname=self.test_dtname, comment='#')
self.assertFalse(dsv1.isCreated())
self.assertEqual('#', dsv1.comment)
dsv1.close()
def test_init3(self):
dsv_fh = DSV.getHandle(self.num_dsv_path)
dsv = DSV(self.dbm, self.testdb, dsv_fh, dtname=self.test_dtname)
dsv.create()
dsv.close()
with self.assertRaises(Error):
DataSet(dbtable=dsv, cols='BBB')
def test_recache2(self):
dsv_fh = DSV.getHandle(self.num_dsv_path)
# default DSV, dialect and delimiter sniffed
dsv = DSV(self.dbm, self.testdb, dsv_fh, dtname=self.test_dtname)
dsv.create()
dsv.loadAll()
# data set by default spanning all rows and all columns
ds = DataSet(dbtable=dsv)
dsv.close()
numpy.testing.assert_array_almost_equal(self.array1, ds.array)
# wipe out underlying table
wipe_cs = dsv.db.cursor()
wipe_cs.execute('delete from "%s";' % self.test_dtname)
dsv.db.commit()
wipe_cs.execute('vacuum;')
dsv.db.commit()
# NOTE: before numpy 1.6.0, empty file in loadtxt() generates IOError,
# with 1.6.0+ only warning
if check_min_numpy_version(1, 6, 0):
# perform recache (we shall see empty array)
# suppress numpy warning of empty source file
with warnings.catch_warnings():
warnings.simplefilter("ignore")
ds.recache()
numpy.testing.assert_array_almost_equal(self.empty_array, ds.array)
else:
with self.assertRaises(Error):
ds.recache()
def test_init1(self):
dsv1_fh = DSV.getHandle(self.num_dsv_path)
# default DSV, dialect and delimiter sniffed
dsv1 = DSV(self.dbm, self.testdb, dsv1_fh, dtname=self.test_dtname)
self.assertFalse(dsv1.isCreated())
self.assertEqual(',', dsv1.dialect.delimiter)
dsv1.close()
def test_close1(self):
dsv2_fh = DSV.getHandle(self.anno_dsv_path)
dsv2 = DSV(self.dbm, self.testdb, dsv2_fh, dtname=self.test_dtname, comment=self.anno_comment)
dsv2.create()
dsv2.loadAll()
dsv2.close()
with self.assertRaises(Error):
dsv2.loadAll()
def test_init4(self):
dsv_fh = DSV.getHandle(self.num_dsv_path)
dsv = DSV(self.dbm, self.testdb, dsv_fh, dtname=self.test_dtname)
dsv.create()
dsv.close()
with self.assertRaises(Error):
DataSet(dbtable=dsv,
rows=self.sample_rows_none,
cols=self.sample_cols_none)
def test_init9(self):
dsv1_fh = DSV.getHandle(self.num_dsv_path)
# delimiter sniffed, header extracted (default), ID resolved
dsv1 = DSV(self.dbm, self.testdb, dsv1_fh, dtname=self.test_dtname)
self.assertSequenceEqual(self.num_dsv_desired_header, dsv1.header)
dsv1.create()
self.assertTrue(dsv1.isCreated())
self.assertTrue(dsv1.isEmpty())
dsv1.close()
def test_init10(self):
dsv1_fh = DSV.getHandle(self.num_dsv_path)
# delimiter sniffed, header extracted (default), ID not resolved
dsv1 = DSV(self.dbm, self.testdb, dsv1_fh, dtname=self.test_dtname, make_missing_ID_column=False)
self.assertSequenceEqual(self.num_dsv_actual_header, dsv1.header)
dsv1.create()
self.assertTrue(dsv1.isCreated())
self.assertTrue(dsv1.isEmpty())
dsv1.close()
def test_init2(self):
dsv1_fh = DSV.getHandle(self.num_dsv_path)
# predefined delimiter, resolved successfully
# NOTE: class does not check if delimiter is valid at this point
dsv1 = DSV(self.dbm, self.testdb, dsv1_fh, dtname=self.test_dtname, delimiter='\t')
self.assertFalse(dsv1.isCreated())
self.assertEqual(csv.get_dialect('excel-tab'), dsv1.dialect)
self.assertEqual('\t', dsv1.dialect.delimiter)
dsv1.close()
def test_init7(self):
dsv_fh = DSV.getHandle(self.num_dsv_path)
# default DSV, dialect and delimiter sniffed
dsv = DSV(self.dbm, self.testdb, dsv_fh, dtname=self.test_dtname)
dsv.create()
dsv.loadAll()
dsv.close()
# get only first row
ds = DataSet(dbtable=dsv, rows=self.sample_rows_1)
numpy.testing.assert_array_almost_equal(self.array_v1, ds.array)
def test_init6(self):
dsv_fh = DSV.getHandle(self.num_dsv_path)
# default DSV, dialect and delimiter sniffed
dsv = DSV(self.dbm, self.testdb, dsv_fh, dtname=self.test_dtname)
dsv.create()
dsv.loadAll()
dsv.close()
# data set by default spanning all rows and all columns
ds = DataSet(dbtable=dsv)
numpy.testing.assert_array_almost_equal(self.array1, ds.array)
def test_init12(self):
dsv1_fh = DSV.getHandle(self.num_dsv_path)
# delimiter sniffed, header supplied (proper length)
our_header = tuple(['C%d' % n for n in range(1, len(self.num_dsv_actual_header) + 1)])
dsv1 = DSV(self.dbm, self.testdb, dsv1_fh, dtname=self.test_dtname, header=our_header)
self.assertSequenceEqual(our_header, dsv1.header)
dsv1.create()
self.assertTrue(dsv1.isCreated())
self.assertTrue(dsv1.isEmpty())
dsv1.close()
def test_init11(self):
dsv1_fh = DSV.getHandle(self.num_dsv_path)
# delimiter sniffed, header auto-generated
dsv1 = DSV(self.dbm, self.testdb, dsv1_fh, dtname=self.test_dtname, header=())
ref_header = tuple(['%d' % n for n in range(1, len(self.num_dsv_actual_header) + 1)])
self.assertSequenceEqual(ref_header, dsv1.header)
dsv1.create()
self.assertTrue(dsv1.isCreated())
self.assertTrue(dsv1.isEmpty())
dsv1.close()
def setUp(self):
self.test_data_root = TEST_INVARIANTS['test_data_root']
self.test_write_root = TEST_INVARIANTS['test_write_root']
self.testdb = 'DB1'
self.test_dtname = 'Test1'
self.dbm = DBManager(self.test_write_root)
# ssdata.dsv
self.ssdata_dsv_path = os.path.abspath(
os.path.join(self.test_data_root, 'ssdata.dsv'))
self.ssdata_comment = '#'
ssdata_dsv_fh = DSV.getHandle(self.ssdata_dsv_path)
self.ssdata_dsv1 = DSV(self.dbm,
self.testdb,
ssdata_dsv_fh,
dtname=self.test_dtname,
comment=self.ssdata_comment)
self.ssdata_dsv1.create()
self.ssdata_dsv1.loadAll()
self.ssdata_dsv1.close()
self.ssdata_samples = ('S1', 'S2', 'S3', 'S4', 'S5')
# hierarchy tests
self.pkc2id = {'PKC1': ('R1', 'R2', 'R3', 'R4'), 'PKC2': ('R5', )}
self.pkc = ('PKC1', 'PKC2')
self.size_thr1 = 2
self.cat1 = SubsetSizeCategorizer(self.size_thr1, ID='Cat1')
self.cat1_uniq_le = self.cat1.uniquifyCategory(
self.cat1.ROW_SIZE_LESSER)
self.cat1_uniq_gt = self.cat1.uniquifyCategory(
self.cat1.ROW_SIZE_GREATER)
self.size_thr2 = 3
self.cat2 = SubsetSizeCategorizer(self.size_thr2, ID='Cat2')
self.cat2_uniq_le = self.cat2.uniquifyCategory(
self.cat2.ROW_SIZE_LESSER)
self.cat2_uniq_gt = self.cat2.uniquifyCategory(
self.cat2.ROW_SIZE_GREATER)
self.size_thr3 = 0
self.cat3 = SubsetSizeCategorizer(self.size_thr3, ID='Cat3')
self.cat3_uniq_le = self.cat3.uniquifyCategory(
self.cat3.ROW_SIZE_LESSER)
self.cat3_uniq_gt = self.cat3.uniquifyCategory(
self.cat3.ROW_SIZE_GREATER)
self.cinst = {
'Cat1': self.cat1,
'Cat2': self.cat2,
'Cat3': self.cat3,
}
self.cmap1 = ['Cat1', 'Cat2', 'Cat3']
self.cmap2 = ['Cat3', 'Cat1', 'Cat2']
self.symbols = list(self.pkc)
def test_em2annotation1(self):
geneidmap = GeneIDMapHGNCGPL()
# GPL96.txt
gpl_path = os.path.abspath(os.path.join(self.test_data_root, 'gpl96_sample.txt'))
gpl_comment = '#'
gpl_delimiter = '\t'
gpl_fh = DSV.getHandle(gpl_path)
gpl_dsv = DSV(self.dbm, self.testdb, gpl_fh, dtname=self.annoTable, delimiter=gpl_delimiter, comment=gpl_comment)
gpl_dsv.create()
gpl_dsv.loadAll()
gpl_dsv.close()
# HGNC.tsv
hgnc_path = os.path.abspath(os.path.join(self.test_data_root, 'hgnc_sample.txt'))
hgnc_comment = '#'
hgnc_delimiter = '\t'
hgnc_fh = DSV.getHandle(hgnc_path)
hgnc_dsv = DSV(self.dbm, self.testdb, hgnc_fh, dtname=self.hgncTable, delimiter=hgnc_delimiter, comment=hgnc_comment)
hgnc_dsv.create()
hgnc_dsv.loadAll()
hgnc_dsv.close()
# build test map
geneidmap.build(gpl_dsv, hgnc_dsv, self.testdb)
em2a = get_em2annotation(geneidmap.dbt)
self.assertEqual(self.ref_em2a, em2a)
def test_loadall3(self):
dsv2_fh = DSV.getHandle(self.anno_dsv_path)
dsv2 = DSV(self.dbm, self.testdb, dsv2_fh, dtname=self.test_dtname, comment=self.anno_comment)
dsv2.create()
st = dsv2.loadAll(debug=True)
dsv2.close()
ref_st = ['insert into "Test1" values ("1007_s_at","U48705","","H**o sapiens","Mar 11, 2009",'
'"Exemplar sequence","Affymetrix Proprietary Database",'
'"U48705 /FEATURE=mRNA /DEFINITION=HSU48705 Human receptor tyrosine kinase DDR gene, complete cds",'
'"U48705","discoidin domain receptor tyrosine kinase 1",'
'"DDR1","780","NM_001954 /// NM_013993 /// NM_013994",'
'"0006468 // protein amino acid phosphorylation // inferred from electronic annotation ///'
' 0007155 // cell adhesion // traceable author statement ///'
' 0007155 // cell adhesion // inferred from electronic annotation ///'
' 0007169 // transmembrane receptor protein tyrosine kinase signaling pathway // inferred from electronic annotation",'
'"0005887 // integral to plasma membrane // traceable author statement ///'
' 0016020 // membrane // inferred from electronic annotation ///'
' 0016021 // integral to membrane // inferred from electronic annotation",'
'"0000166 // nucleotide binding // inferred from electronic annotation ///'
' 0004672 // protein kinase activity // inferred from electronic annotation ///'
' 0004713 // protein tyrosine kinase activity // inferred from electronic annotation ///'
' 0004714 // transmembrane receptor protein tyrosine kinase activity // traceable author statement ///'
' 0004714 // transmembrane receptor protein tyrosine kinase activity // inferred from electronic annotation ///'
' 0004872 // receptor activity // inferred from electronic annotation ///'
' 0005515 // protein binding // inferred from physical interaction ///'
' 0005524 // ATP binding // inferred from electronic annotation ///'
' 0016301 // kinase activity // inferred from electronic annotation ///'
' 0016740 // transferase activity // inferred from electronic annotation")',
'insert into "Test1" values ("1053_at","M87338","","H**o sapiens","Mar 11, 2009",'
'"Exemplar sequence","GenBank",'
'"M87338 /FEATURE= /DEFINITION=HUMA1SBU Human replication factor C, 40-kDa subunit (A1) mRNA, complete cds",'
'"M87338","replication factor C (activator 1) 2, 40kDa",'
'"RFC2","5982","NM_002914 /// NM_181471",'
'"0006260 // DNA replication // not recorded ///'
' 0006260 // DNA replication // inferred from electronic annotation ///'
' 0006297 // nucleotide-excision repair, DNA gap filling // not recorded",'
'"0005634 // nucleus // inferred from electronic annotation ///'
' 0005654 // nucleoplasm // not recorded ///'
' 0005663 // DNA replication factor C complex // inferred from direct assay ///'
' 0005663 // DNA replication factor C complex // inferred from electronic annotation",'
'"0000166 // nucleotide binding // inferred from electronic annotation ///'
' 0003677 // DNA binding // inferred from electronic annotation ///'
' 0003689 // DNA clamp loader activity // inferred from electronic annotation ///'
' 0005515 // protein binding // inferred from physical interaction ///'
' 0005524 // ATP binding // traceable author statement ///'
' 0005524 // ATP binding // inferred from electronic annotation ///'
' 0017111 // nucleoside-triphosphatase activity // inferred from electronic annotation")']
self.assertSequenceEqual(ref_st, st)
def setUp(self):
self.test_data_root = TEST_INVARIANTS['test_data_root']
self.test_write_root = TEST_INVARIANTS['test_write_root']
self.testdb = 'DB1'
self.hgncTable = 'HGNC'
self.dbm = DBManager(self.test_write_root)
#
hgnc_path = os.path.abspath(
os.path.join(self.test_data_root, 'hgnc_sample_2.txt'))
hgnc_comment = '#'
hgnc_delimiter = '\t'
hgnc_fh = DSV.getHandle(hgnc_path)
self.hgnc_dsv = DSV(self.dbm,
self.testdb,
hgnc_fh,
dtname=self.hgncTable,
delimiter=hgnc_delimiter,
comment=hgnc_comment)
self.hgnc_dsv.create()
self.hgnc_dsv.loadAll()
self.hgnc_dsv.close()
#
self.withdrawn_pattern = '%~withdrawn'
self.symbol_col = 'Approved Symbol'
#
# NOTE: we use unicode since we do not reparse immediately after querying
self.ref_previous1 = {
u'NTRK4': [u'DDR1'],
u'PTK3A': [u'DDR1'],
u'NEP': [u'DDR1'],
u'CAK': [u'DDR1'],
u'EDDR1': [u'DDR1'],
u'C19orf72': [u'DCAF15'],
}
self.ref_synonyms1 = {
u'A1': [u'RFC2'],
u'BEHAB': [u'BCAN'],
u'CD167': [u'DDR1'],
u'CSPG7': [u'BCAN'],
u'DRC3': [u'EPS8L1'],
u'FLJ20258': [u'EPS8L1'],
u'MGC13038': [u'BCAN'],
u'MGC23164': [u'EPS8L1'],
u'MGC4642': [u'EPS8L1'],
u'MGC99481': [u'DCAF15'],
u'RFC40': [u'RFC2'],
u'RTK6': [u'DDR1']
}
def test_loadall2(self):
dsv1_fh = DSV.getHandle(self.num_dsv_path)
# default DSV
dsv1 = DSV(self.dbm, self.testdb, dsv1_fh, dtname=self.test_dtname)
self.assertSequenceEqual(self.num_dsv_desired_header, dsv1.header)
dsv1.create()
dsv1.loadAll()
dsv1.close()
# low level checks
cs = dsv1.db.cursor()
cs.execute('select %s from %s' % (self.num_dsv_desired_header[0], dsv1.name))
rres = cs.fetchall()
res = [str(r[0]) for r in rres]
self.assertSequenceEqual(self.num_rows, res)
cs.execute('select %s from %s' % (self.num_dsv_desired_header[3], dsv1.name))
rres = cs.fetchall()
res = [str(r[0]) for r in rres]
self.assertSequenceEqual(self.num_column_3, res)
def test_loadall1(self):
dsv1_fh = DSV.getHandle(self.num_dsv_path)
# default DSV
dsv1 = DSV(self.dbm, self.testdb, dsv1_fh, dtname=self.test_dtname)
self.assertSequenceEqual(self.num_dsv_desired_header, dsv1.header)
dsv1.create()
self.assertTrue(dsv1.isCreated())
self.assertTrue(dsv1.isEmpty())
# load from file
st = dsv1.loadAll(debug=True)
dsv1.close()
ref_st = ['insert into "Test1" values ("V1","7.29865639942","7.1839394018853","8.08785988003525","8.43784327460378","7.56725674896063","7.17150350961048",'
'"8.23772125375395","7.26860393651388","6.74186036580687","7.55493056104098","7.37521470969549","6.35468766815909",'
'"7.03794441889888","6.75197742759923","7.26608934160658","8.70335292880697","6.85443361759566","7.59055769774248",'
'"8.01751559655053","6.99993079846214","7.10871523619365","7.65161630470663","6.71058065426046","6.64437907655326",'
'"6.93172233805358","7.61870427987243","6.9634175191832","6.37433009206648","6.34485366708736","6.0977075555399",'
'"6.9061361459302","6.54264897912374","6.31961323363347","6.16533391728077","6.90481905323935","6.7168440158265",'
'"7.22535319774288","6.20123577217092","6.93391118518623","6.82985307889579","6.35468239627533","7.09693639659124",'
'"7.60449775270475","7.12266778930967","6.35835046528365","6.76414046791","6.17508883882112","6.52508274039929",'
'"7.11162248509395","6.89152906126555","6.49949720627377","6.69448041622817","6.37526926527225","5.80401273298264",'
'"7.12987703240072","6.05831629170905","6.81624397767137","6.66820808623227","6.64998519558867","6.42308111524492",'
'"7.58672787003923","3.84767749509431","6.71665724008276","6.35468766815909","6.54859953448512","7.23447515724748",'
'"6.70007125889196","6.28445976227631","6.75206243946758","6.7168440158265","6.55922419484843","6.93675713126568",'
'"6.80067557800434","6.50103393612957","6.91542815411986","6.19960368164491","7.6448783709798","6.2125929974423",'
'"6.35468766815909","7.32784699996015","6.14659907126786","6.7168440158265","6.8825610653412","6.72831600642366",'
'"6.46374697412319","5.79584776993902","6.0825372527799","7.1204899554919","6.39620062779895","6.35814627516342",'
'"6.35814627516342")',
'insert into "Test1" values ("V2","2.38904325749261","2.37588862645719","2.37310583895584","2.38904325749261","2.42091222425779","2.38904325749261",'
'"2.38626046999126","2.38904325749261","2.38904325749261","2.41002306956031","2.38904325749261","2.38904325749261",'
'"2.38904325749261","2.37310583895584","2.38626046999126","2.34429782913723","2.38904325749261","2.98112952430922",'
'"2.34553574786241","2.37310583895584","2.39660701797421","2.38904325749261","2.40955866820479","2.38626046999126",'
'"2.35577218230877","2.39443448171899","2.34433277775847","2.69053923836483","2.38430054425455","2.86158891209344",'
'"2.34595261411454","2.89813268468409","2.42777977950130","2.38626046999126","2.44904175049461","3.55795174775419",'
'"2.66896481156844","2.38626046999126","2.71772299956764","2.61602731442131","2.56996895766296","3.86202701130675",'
'"2.38904325749261","2.35577218230877","2.60505670342601","3.12697260562512","2.38904325749261","3.15740854425796",'
'"2.65364423092787","2.45124596034905","3.14913252263311","2.38904325749261","2.39700474393300","2.38904325749261",'
'"2.46188514405506","3.23873137510437","2.55373906857937","3.39601442806742","3.16936129560691","3.18777558546775",'
'"2.38904325749261","2.38904325749261","2.38626046999126","2.34553574786241","2.35577218230877","2.38624782221570",'
'"2.35577218230877","2.38904325749261","2.74265374191966","2.37188401381886","2.37588862645719","2.38904325749261",'
'"2.35577218230877","2.35121946858936","2.49946444329392","2.38904325749261","2.34553574786241","2.93960156829307",'
'"2.38904325749261","2.39182604499395","2.38904325749261","2.35315614841910","2.47149945385376","2.38626046999126",'
'"2.39596753440869","2.38904325749261","2.40223987191512","2.34715558421848","2.38210356896247","2.34719053283972",'
'"2.76820667786915")']
self.assertSequenceEqual(ref_st, st)
def test_init5(self):
dsv_fh = DSV.getHandle(self.num_dsv_path)
# default DSV, dialect and delimiter sniffed
dsv = DSV(self.dbm, self.testdb, dsv_fh, dtname=self.test_dtname)
# data set by default spanning all rows and all columns
# data not loaded, we shall see empty array
dsv.create()
dsv.close()
# NOTE: before numpy 1.6.0, empty file in loadtxt() generates IOError,
# with 1.6.0+ only warning
if check_min_numpy_version(1, 6, 0):
# suppress numpy warning of empty source file
with warnings.catch_warnings():
warnings.simplefilter("ignore")
ds = DataSet(dbtable=dsv)
numpy.testing.assert_equal(self.empty_array, ds.array)
else:
with self.assertRaises(Error):
DataSet(dbtable=dsv)
def test_build1(self):
pkcidmap = PKCIDMapGOGPL()
# GPL96.txt
# gpl_path = os.path.abspath(os.path.join(self.test_data_root, 'GPL96.txt.bz2'))
gpl_path = os.path.abspath(
os.path.join(self.test_data_root, 'gpl96_sample.txt'))
gpl_comment = '#'
gpl_delimiter = '\t'
gpl_fh = DSV.getHandle(gpl_path)
gpl_dsv = DSV(self.dbm,
self.testdb,
gpl_fh,
dtname=self.annoTable,
delimiter=gpl_delimiter,
comment=gpl_comment)
gpl_dsv.create()
gpl_dsv.loadAll()
gpl_dsv.close()
pkcidmap.build(gpl_dsv, self.testdb)
self.assertTrue(pkcidmap.built)
self.assertIsInstance(pkcidmap.dbt, DBTable)
# test bidirectional map
bwdmap = pkcidmap.pkc2emid.getBwdMap()
fwdmap = pkcidmap.pkc2emid.getFwdMap()
# check valid probes and terms for existence
for ref_probe, ref_terms in self.test_bwd.iteritems():
# backward map
self.assertIn(ref_probe, bwdmap)
terms = bwdmap[ref_probe]
self.assertEqual(ref_terms, terms)
# forward map
for term in terms:
self.assertIn(term, fwdmap)
probes = fwdmap[term]
self.assertIn(ref_probe, probes)
# check control probes for nonexistence
for test_ctrl in self.test_ctrl_probes:
# backward map
self.assertNotIn(test_ctrl, bwdmap)
for probes in fwdmap.values():
# forward map
self.assertNotIn(test_ctrl, probes)
def test_loadall4(self):
dsv2_fh = DSV.getHandle(self.anno_dsv_path)
dsv2 = DSV(self.dbm, self.testdb, dsv2_fh, dtname=self.test_dtname, comment=self.anno_comment)
self.assertSequenceEqual(self.anno_header, dsv2.header)
dsv2.create()
dsv2.loadAll()
dsv2.close()
# low level checks
cs = dsv2.db.cursor()
cs.execute('select %s from %s' % (self.anno_header[0], dsv2.name))
rres = cs.fetchall()
res = [str(r[0]) for r in rres]
self.assertSequenceEqual(self.anno_rows, res)
cols = ','.join([quote(c) for c in self.anno_columns])
cs.execute('select %s from %s' % (cols, dsv2.name))
rres = cs.fetchall()
res = {}
for ix, ac in enumerate(self.anno_columns):
res[ac] = [str(r[ix]) for r in rres]
self.assertDictEqual(self.anno_columns_dict, res)
def test_init13(self):
dsv1_fh = DSV.getHandle(self.num_dsv_path)
# delimiter sniffed, header supplied (improper length)
our_header = tuple(['C%d' % n for n in range(1, len(self.num_dsv_actual_header) * 2 + 1)])
with self.assertRaises(Error):
DSV(self.dbm, self.testdb, dsv1_fh, dtname=self.test_dtname, header=our_header)
def setUp(self):
self.test_data_root = TEST_INVARIANTS['test_data_root']
self.test_write_root = TEST_INVARIANTS['test_write_root']
self.testdb = 'DB1'
self.test_dtname = 'Test1'
self.dbm = DBManager(self.test_write_root)
# ssdata.dsv
self.ssdata_dsv_path = os.path.abspath(
os.path.join(self.test_data_root, 'ssdata.dsv'))
self.ssdata_comment = '#'
ssdata_dsv_fh = DSV.getHandle(self.ssdata_dsv_path)
self.ssdata_dsv1 = DSV(self.dbm,
self.testdb,
ssdata_dsv_fh,
dtname=self.test_dtname,
comment=self.ssdata_comment)
self.ssdata_dsv1.create()
self.ssdata_dsv1.loadAll()
self.ssdata_dsv1.close()
self.ssdata_samples = ('S1', 'S2', 'S3', 'S4', 'S5')
# pkcidmap
self.pkc2id1 = {
'PKC1': ('R1', 'R2'),
'PKC2': ('R3', ),
'PKC3': ('R4', 'R5')
}
self.pkc1 = ('PKC1', 'PKC2', 'PKC3')
self.ss_cols1 = '*'
self.ref_ss1 = [
({
'pkcID': 'PKC1',
'dtable': self.ssdata_dsv1,
'rows': ['R1', 'R2'],
'cols': list(self.ssdata_samples)
}, None),
({
'pkcID': 'PKC2',
'dtable': self.ssdata_dsv1,
'rows': ['R3'],
'cols': list(self.ssdata_samples)
}, None),
({
'pkcID': 'PKC3',
'dtable': self.ssdata_dsv1,
'rows': ['R4', 'R5'],
'cols': list(self.ssdata_samples)
}, None),
]
self.ss_cols2 = ('S1', 'S4', 'S5')
self.ref_ss2 = [
({
'pkcID': 'PKC1',
'dtable': self.ssdata_dsv1,
'rows': ['R1', 'R2'],
'cols': list(self.ss_cols2)
}, None),
({
'pkcID': 'PKC2',
'dtable': self.ssdata_dsv1,
'rows': ['R3'],
'cols': list(self.ss_cols2)
}, None),
({
'pkcID': 'PKC3',
'dtable': self.ssdata_dsv1,
'rows': ['R4', 'R5'],
'cols': list(self.ss_cols2)
}, None),
]
self.pkc2 = ('PKC3', 'PKC1')
self.ref_ss3 = [
({
'pkcID': 'PKC3',
'dtable': self.ssdata_dsv1,
'rows': ['R4', 'R5'],
'cols': list(self.ss_cols2)
}, None),
({
'pkcID': 'PKC1',
'dtable': self.ssdata_dsv1,
'rows': ['R1', 'R2'],
'cols': list(self.ss_cols2)
}, None),
]
self.ref_ss4 = [
(None,
numpy.array([
[2.44753543273, 42.9497086717, 30.8331998765],
[42.1888598933, 39.1743921225, 15.9744094108],
])),
(None,
numpy.array([
[16.5734780715, 14.8233987496, 21.7385342744],
[60.0958378228, 98.4321570519, 71.9193619126],
])),
]
# for categorization tests
self.pkc2id2 = {'PKC1': ('R1', 'R2', 'R3', 'R4'), 'PKC2': ('R5', )}
self.pkc3 = ('PKC1', 'PKC2')
self.size_thr = 3
self.cat1 = SubsetSizeCategorizer(self.size_thr)
self.exp_categories1 = ['>', '<=']
self.cat2 = NullCategorizer()
self.exp_categories2 = [self.cat2.NULL] * len(self.pkc3)
def test_init7(self):
dsv1_fh = DSV.getHandle(self.num_dsv_path)
# delimiter sniffed, comment not resolved
with self.assertRaises(Error):
DSV(self.dbm, self.testdb, dsv1_fh, dtname=self.test_dtname, comment=('#',))
def test_init5(self):
dsv1_fh = DSV.getHandle(self.num_dsv_path)
# delimiter not resolved
with self.assertRaises(Error):
DSV(self.dbm, self.testdb, dsv1_fh, dtname=self.test_dtname, delimiter=100)
