def test_cload_custom_tempdir(bins_path, pairs_path): for temp_dir in [op.join(testdir, 'data'), '-']: cload_pairs.callback( bins_path, pairs_path, testcool_path, metadata=None, assembly='toy', chunksize=10, zero_based=False, comment_char='#', input_copy_status='unique', no_symmetric_upper=False, field=(), temp_dir=temp_dir, no_delete_temp=False, storage_options=None, no_count=True, max_merge=200, chrom1=1, pos1=2, chrom2=3, pos2=4, ) pixels = cooler.Cooler(testcool_path).pixels()[:] assert 'count' in pixels.columns and types.is_integer_dtype( pixels.dtypes['count'])
def test_cload_field(bins_path, pairs_path): kwargs = dict( metadata=None, assembly='toy', chunksize=10, zero_based=False, comment_char='#', input_copy_status='unique', no_symmetric_upper=False, temp_dir=None, no_delete_temp=False, storage_options=None, no_count=True, max_merge=200, chrom1=1, pos1=2, chrom2=3, pos2=4, ) cload_pairs.callback(bins_path, pairs_path, testcool_path, field=('score=7:dtype=float', ), **kwargs) pixels = cooler.Cooler(testcool_path).pixels()[:] assert 'count' in pixels.columns and types.is_integer_dtype( pixels.dtypes['count']) assert 'score' in pixels.columns and types.is_float_dtype( pixels.dtypes['score'])
def test_cload_custom_tempdir(bins_path, pairs_path): for temp_dir in [op.join(testdir, "data"), "-"]: cload_pairs.callback( bins_path, pairs_path, testcool_path, metadata=None, assembly="toy", chunksize=10, zero_based=False, comment_char="#", input_copy_status="unique", no_symmetric_upper=False, field=(), temp_dir=temp_dir, no_delete_temp=False, storage_options=None, no_count=True, max_merge=200, chrom1=2, pos1=3, chrom2=4, pos2=5, ) pixels = cooler.Cooler(testcool_path).pixels()[:] assert "count" in pixels.columns and types.is_integer_dtype( pixels.dtypes["count"])
def test_cload_pairs(bins_path, pairs_path, ref_path): kwargs = dict( metadata=None, assembly='hg19', chunksize=int(15e6), zero_based=False, comment_char='#', input_copy_status='unique', no_symmetric_upper=False, field=(), temp_dir=None, no_delete_temp=False, storage_options=None, no_count=False, max_merge=200, chrom1=1, pos1=2, chrom2=3, pos2=4, ) cload_pairs.callback(bins_path, pairs_path, testcool_path, **kwargs) with h5py.File(testcool_path, 'r') as f1, \ h5py.File(ref_path, 'r') as f2: assert np.all(f1['pixels/bin1_id'][:] == f2['pixels/bin1_id'][:]) assert np.all(f1['pixels/bin2_id'][:] == f2['pixels/bin2_id'][:]) assert np.all(f1['pixels/count'][:] == f2['pixels/count'][:]) try: os.remove(testcool_path) except OSError: pass
def test_cload_field(bins_path, pairs_path): kwargs = dict( metadata=None, assembly="toy", chunksize=10, zero_based=False, comment_char="#", input_copy_status="unique", no_symmetric_upper=False, temp_dir=None, no_delete_temp=False, storage_options=None, no_count=True, max_merge=200, chrom1=2, pos1=3, chrom2=4, pos2=5, ) cload_pairs.callback(bins_path, pairs_path, testcool_path, field=("score=8:dtype=float", ), **kwargs) pixels = cooler.Cooler(testcool_path).pixels()[:] assert "count" in pixels.columns and types.is_integer_dtype( pixels.dtypes["count"]) assert "score" in pixels.columns and types.is_float_dtype( pixels.dtypes["score"])