def test_slice_and_exclude_rids(self):
out_gct = sg.slice_gctoo(self.in_gct, rid=["a", "c", "d"], exclude_rid=["d"])
# Outputs should be dataframes even if there is only 1 index or column
pd.util.testing.assert_frame_equal(out_gct.data_df, self.in_gct.data_df.iloc[[0, 2], :])
pd.util.testing.assert_frame_equal(out_gct.row_metadata_df, self.in_gct.row_metadata_df.iloc[[0, 2], :])
pd.util.testing.assert_frame_equal(out_gct.col_metadata_df, self.in_gct.col_metadata_df)
def test_slice_bools(self):
out_gct = sg.slice_gctoo(self.in_gct, row_bool=[True, False, True, False], col_bool=[False, False, True])
# Outputs should be dataframes even if there is only 1 index or column
pd.util.testing.assert_frame_equal(out_gct.data_df, pd.DataFrame(self.in_gct.data_df.iloc[[0, 2], 2]))
pd.util.testing.assert_frame_equal(out_gct.row_metadata_df, self.in_gct.row_metadata_df.iloc[[0, 2], :])
pd.util.testing.assert_frame_equal(out_gct.col_metadata_df, pd.DataFrame(self.in_gct.col_metadata_df.iloc[2, :]).T)
def main():
# Get args
args = build_parser().parse_args(sys.argv[1:])
setup_logger.setup(verbose=args.verbose)
# Read the input gct
in_gct = parse.parse(args.in_gct_path)
# Read in each of the command line arguments
rid = _read_arg(args.rid)
cid = _read_arg(args.cid)
exclude_rid = _read_arg(args.exclude_rid)
exclude_cid = _read_arg(args.exclude_cid)
# Slice the gct
out_gct = sg.slice_gctoo(in_gct,
rid=rid,
cid=cid,
exclude_rid=exclude_rid,
exclude_cid=exclude_cid)
assert out_gct.data_df.size > 0, "Slicing yielded an empty gct!"
# Write the output gct
if args.use_gctx:
wgx.write(out_gct, args.out_name)
else:
wg.write(out_gct,
args.out_name,
data_null="NaN",
metadata_null="NA",
filler_null="NA")
def test_slice_cid_and_col_bool(self):
# cid and col_bool should not both be provided
with self.assertRaises(AssertionError) as e:
sg.slice_gctoo(self.in_gct, cid=["e", "f", "g"], col_bool=[True, True, False])
self.assertIn("cid and col_bool", str(e.exception))
def test_gctx_parsing(self):
# parse in gctx, no other arguments
mg1 = mini_gctoo_for_testing.make()
mg2 = parse.parse("functional_tests/mini_gctoo_for_testing.gctx")
pandas_testing.assert_frame_equal(mg1.data_df, mg2.data_df)
pandas_testing.assert_frame_equal(mg1.row_metadata_df,
mg2.row_metadata_df)
pandas_testing.assert_frame_equal(mg1.col_metadata_df,
mg2.col_metadata_df)
# check convert_neg_666 worked correctly
self.assertTrue(mg2.col_metadata_df["mfc_plate_id"].isnull().all())
# parse w/o convert_neg_666
mg2_alt = parse.parse("functional_tests/mini_gctoo_for_testing.gctx",
convert_neg_666=False)
self.assertFalse(
mg2_alt.col_metadata_df["mfc_plate_id"].isnull().all())
# parsing w/rids & cids specified
test_rids = [
'LJP007_MCF10A_24H:TRT_CP:BRD-K93918653:3.33',
'LJP007_MCF7_24H:CTL_VEHICLE:DMSO:-666'
]
test_cids = ['LJP007_MCF7_24H:TRT_POSCON:BRD-A61304759:10']
mg3 = slice_gctoo.slice_gctoo(mg1, rid=test_rids, cid=test_cids)
mg4 = parse.parse("functional_tests/mini_gctoo_for_testing.gctx",
rid=test_rids,
cid=test_cids)
pandas_testing.assert_frame_equal(mg3.data_df, mg4.data_df)
pandas_testing.assert_frame_equal(mg3.row_metadata_df,
mg4.row_metadata_df)
pandas_testing.assert_frame_equal(mg3.col_metadata_df,
mg4.col_metadata_df)
# parsing w/ridx & cidx specified
mg5 = slice_gctoo.slice_gctoo(
mg1,
rid=['LJP007_MCF7_24H:CTL_VEHICLE:DMSO:-666'],
cid='LJP007_MCF7_24H:CTL_VEHICLE:DMSO:-666')
mg6 = parse.parse("functional_tests/mini_gctoo_for_testing.gctx",
ridx=[4],
cidx=[4])
pandas_testing.assert_frame_equal(mg5.data_df, mg6.data_df)
pandas_testing.assert_frame_equal(mg5.row_metadata_df,
mg6.row_metadata_df)
pandas_testing.assert_frame_equal(mg5.col_metadata_df,
mg6.col_metadata_df)
# parsing row metadata only
mg7 = parse.parse("functional_tests/mini_gctoo_for_testing.gctx",
row_meta_only=True)
pandas_testing.assert_frame_equal(mg7, mg1.row_metadata_df)
# parsing col metadata only
mg8 = parse.parse("functional_tests/mini_gctoo_for_testing.gctx",
col_meta_only=True)
pandas_testing.assert_frame_equal(mg8, mg1.col_metadata_df)
# parsing w/multiindex
mg9 = parse.parse("functional_tests/mini_gctoo_for_testing.gctx",
make_multiindex=True)
self.assertTrue(mg9.multi_index_df is not None)
def test_parse(self):
# parse whole thing
mg1 = mini_gctoo_for_testing.make()
mg2 = parse_gctx.parse("functional_tests/mini_gctoo_for_testing.gctx")
pandas_testing.assert_frame_equal(mg1.data_df, mg2.data_df)
pandas_testing.assert_frame_equal(mg1.row_metadata_df,
mg2.row_metadata_df)
pandas_testing.assert_frame_equal(mg1.col_metadata_df,
mg2.col_metadata_df)
# test with string rid/cid
test_rids = [
'LJP007_MCF10A_24H:TRT_CP:BRD-K93918653:3.33',
'LJP007_MCF7_24H:CTL_VEHICLE:DMSO:-666'
]
test_cids = ['LJP007_MCF7_24H:TRT_POSCON:BRD-A61304759:10']
mg3 = slice_gctoo.slice_gctoo(mg1, rid=test_rids, cid=test_cids)
mg4 = parse_gctx.parse("functional_tests/mini_gctoo_for_testing.gctx",
rid=test_rids,
cid=test_cids)
pandas_testing.assert_frame_equal(mg3.data_df, mg4.data_df)
pandas_testing.assert_frame_equal(mg3.row_metadata_df,
mg4.row_metadata_df)
pandas_testing.assert_frame_equal(mg3.col_metadata_df,
mg4.col_metadata_df)
# first, make & write out temp version of mini_gctoo with int rids/cids
new_mg = mini_gctoo_for_testing.make(convert_neg_666=False)
int_indexed_data_df = new_mg.data_df.copy()
int_indexed_data_df.index = [str(i) for i in range(0, 6)]
int_indexed_data_df.columns = [str(i) for i in range(10, 16)]
int_indexed_row_meta = new_mg.row_metadata_df.copy()
int_indexed_row_meta.index = int_indexed_data_df.index
int_indexed_col_meta = new_mg.col_metadata_df.copy()
int_indexed_col_meta.index = int_indexed_data_df.columns
int_indexed_gctoo = GCToo.GCToo(data_df=int_indexed_data_df,
row_metadata_df=int_indexed_row_meta,
col_metadata_df=int_indexed_col_meta)
write_gctx.write(int_indexed_gctoo, "int_indexed_mini_gctoo.gctx")
# test with numeric (repr as string) rid/cid
mg5 = GCToo.GCToo(data_df=int_indexed_data_df,
row_metadata_df=int_indexed_row_meta,
col_metadata_df=int_indexed_col_meta)
mg5 = slice_gctoo.slice_gctoo(
mg5,
row_bool=[True, False, True, False, True, False],
col_bool=[True, False, False, True, True, True])
mg5.data_df.index.name = "rid"
mg5.data_df.columns.name = "cid"
mg5.row_metadata_df.index.name = "rid"
mg5.row_metadata_df.columns.name = "rhd"
mg5.col_metadata_df.index.name = "cid"
mg5.col_metadata_df.columns.name = "chd"
mg6 = parse_gctx.parse("int_indexed_mini_gctoo.gctx",
rid=["0", "2", "4"],
cid=["10", "13", "14", "15"],
convert_neg_666=False)
os.remove("int_indexed_mini_gctoo.gctx")
pandas_testing.assert_frame_equal(mg5.data_df, mg6.data_df)
pandas_testing.assert_frame_equal(mg5.row_metadata_df,
mg6.row_metadata_df)
pandas_testing.assert_frame_equal(mg5.col_metadata_df,
mg6.col_metadata_df)
# test with ridx/cidx
mg7 = slice_gctoo.slice_gctoo(
mg1,
rid=['LJP007_MCF7_24H:CTL_VEHICLE:DMSO:-666'],
cid='LJP007_MCF7_24H:CTL_VEHICLE:DMSO:-666')
mg8 = parse_gctx.parse("functional_tests/mini_gctoo_for_testing.gctx",
ridx=[4],
cidx=[4])
pandas_testing.assert_frame_equal(mg7.data_df, mg8.data_df)
pandas_testing.assert_frame_equal(mg7.row_metadata_df,
mg8.row_metadata_df)
pandas_testing.assert_frame_equal(mg7.col_metadata_df,
mg8.col_metadata_df)
# test with rid/cidx
mg9 = parse_gctx.parse("functional_tests/mini_gctoo_for_testing.gctx",
rid=['LJP007_MCF7_24H:CTL_VEHICLE:DMSO:-666'],
cidx=[4])
pandas_testing.assert_frame_equal(mg7.data_df, mg9.data_df)
pandas_testing.assert_frame_equal(mg7.row_metadata_df,
mg9.row_metadata_df)
pandas_testing.assert_frame_equal(mg7.col_metadata_df,
mg9.col_metadata_df)
# test with ridx/cid
mg10 = parse_gctx.parse("functional_tests/mini_gctoo_for_testing.gctx",
ridx=[4],
cid=['LJP007_MCF7_24H:CTL_VEHICLE:DMSO:-666'])
pandas_testing.assert_frame_equal(mg7.data_df, mg10.data_df)
pandas_testing.assert_frame_equal(mg7.row_metadata_df,
mg10.row_metadata_df)
pandas_testing.assert_frame_equal(mg7.col_metadata_df,
mg10.col_metadata_df)
# test with row_meta_only
mg11 = parse_gctx.parse("functional_tests/mini_gctoo_for_testing.gctx",
row_meta_only=True)
pandas_testing.assert_frame_equal(mg11, mg1.row_metadata_df)
# test with col_meta_only
mg12 = parse_gctx.parse("functional_tests/mini_gctoo_for_testing.gctx",
col_meta_only=True)
pandas_testing.assert_frame_equal(mg12, mg1.col_metadata_df)