diff --git a/tests/test_core_checks.py b/tests/test_core_checks.py index 7f7ace4..8c534bc 100644 --- a/tests/test_core_checks.py +++ b/tests/test_core_checks.py @@ -56,10 +56,7 @@ def test_is_cataloged(): columns=["chrom", "start", "end", "funny_view_region"], ) assert is_cataloged( - df, - view_df, - df_view_col="funny_view_region", - view_name_col="funny_name" + df, view_df, df_view_col="funny_view_region", view_name_col="funny_name" ) @@ -131,8 +128,8 @@ def test_is_contained(): cols=["chrom1", "start1", "end1"], cols_view=["CHROM", "START", "END"], df_view_col="VIEW_REGION", - view_name_col="NAME" - ) + view_name_col="NAME", + ) with pytest.raises(TypeError): # cols and view_cols are not passed as an arguments @@ -219,19 +216,16 @@ def test_is_covering(): columns=["chrom1", "start1", "end1"], ) chromsizes = pd.DataFrame( - [ - ["chr1", 0, 9, "chr1p"], - ["chr1", 11, 20, "chr1q"] - ], + [["chr1", 0, 9, "chr1p"], ["chr1", 11, 20, "chr1q"]], columns=["CHROM", "START", "END", "NAME"], - ) + ) assert is_covering( - df1, - chromsizes, - cols=["chrom1", "start1", "end1"], - cols_view=["CHROM", "START", "END"], - view_name_col="NAME" - ) + df1, + chromsizes, + cols=["chrom1", "start1", "end1"], + cols_view=["CHROM", "START", "END"], + view_name_col="NAME", + ) with pytest.raises(ValueError): # cols and view_cols are not passed as an arguments @@ -274,19 +268,16 @@ def test_is_tiling(): columns=["chrom1", "start1", "end1", "view_region"], ) chromsizes = pd.DataFrame( - [ - ["chr1", 0, 9, "chr1p"], - ["chr1", 11, 20, "chr1q"] - ], + [["chr1", 0, 9, "chr1p"], ["chr1", 11, 20, "chr1q"]], columns=["CHROM", "START", "END", "NAME"], - ) + ) assert is_tiling( - df1, - chromsizes, - cols=["chrom1", "start1", "end1"], - cols_view=["CHROM", "START", "END"], - view_name_col="NAME" - ) + df1, + chromsizes, + cols=["chrom1", "start1", "end1"], + cols_view=["CHROM", "START", "END"], + view_name_col="NAME", + ) with pytest.raises(KeyError): # cols and view_cols are not passed as an arguments @@ -477,7 +468,7 @@ def test_is_sorted(): view_name_col="FRUIT", df_view_col="FRUIT", cols=["CHROM", "START", "END"], - cols_view=["CHROM", "START", "END"] + cols_view=["CHROM", "START", "END"], ) with pytest.raises(ValueError): diff --git a/tests/test_core_specs.py b/tests/test_core_specs.py index 18f156e..8de7f65 100644 --- a/tests/test_core_specs.py +++ b/tests/test_core_specs.py @@ -1,4 +1,3 @@ - import numpy as np import pandas as pd import pytest diff --git a/tests/test_extras.py b/tests/test_extras.py index afb2cbb..73db88b 100644 --- a/tests/test_extras.py +++ b/tests/test_extras.py @@ -34,8 +34,7 @@ def test_make_chromarms(): cols_mids=["chromosome", "loc"], ) pd.testing.assert_frame_equal( - result, - arms.rename(columns={"chrom": "chromosome", "start": "lo", "end": "hi"}) + result, arms.rename(columns={"chrom": "chromosome", "start": "lo", "end": "hi"}) ) # test passing 2 columns @@ -52,9 +51,7 @@ def test_make_chromarms(): # test for passing Series or dict result = bioframe.make_chromarms( - pd.Series({"chrX": 8}), - mids, - cols_mids=["chromosome", "loc"] + pd.Series({"chrX": 8}), mids, cols_mids=["chromosome", "loc"] ) pd.testing.assert_frame_equal(arms, result) @@ -196,11 +193,11 @@ def test_frac_gc(): def test_seq_gc(): - assert (0 == bioframe.seq_gc("AT")) - assert (np.isnan( bioframe.seq_gc("NNN"))) - assert (1 == bioframe.seq_gc("NGnC")) - assert (0.5 == bioframe.seq_gc("GTCA")) - assert (0.25 == bioframe.seq_gc("nnnNgTCa", mapped_only=False)) + assert 0 == bioframe.seq_gc("AT") + assert np.isnan(bioframe.seq_gc("NNN")) + assert 1 == bioframe.seq_gc("NGnC") + assert 0.5 == bioframe.seq_gc("GTCA") + assert 0.25 == bioframe.seq_gc("nnnNgTCa", mapped_only=False) with pytest.raises(ValueError): bioframe.seq_gc(["A", "T"]) with pytest.raises(ValueError): diff --git a/tests/test_ops_select.py b/tests/test_ops_select.py index 019a787..57f332f 100644 --- a/tests/test_ops_select.py +++ b/tests/test_ops_select.py @@ -6,33 +6,24 @@ def test_select(): df = pd.DataFrame( - [["chrX", 3, 8], - ["chr1", 4, 5], - ["chrX", 1, 5]], + [["chrX", 3, 8], ["chr1", 4, 5], ["chrX", 1, 5]], columns=["chrom", "start", "end"], ) - result = pd.DataFrame( - [["chr1", 4, 5]], - columns=["chrom", "start", "end"] - ) + result = pd.DataFrame([["chr1", 4, 5]], columns=["chrom", "start", "end"]) pd.testing.assert_frame_equal( result, bioframe.select(df, "chr1:4-10").reset_index(drop=True) ) result = pd.DataFrame( - [["chrX", 3, 8], - ["chrX", 1, 5]], - columns=["chrom", "start", "end"] + [["chrX", 3, 8], ["chrX", 1, 5]], columns=["chrom", "start", "end"] ) pd.testing.assert_frame_equal( result, bioframe.select(df, "chrX").reset_index(drop=True) ) result = pd.DataFrame( - [["chrX", 3, 8], - ["chrX", 1, 5]], - columns=["chrom", "start", "end"] + [["chrX", 3, 8], ["chrX", 1, 5]], columns=["chrom", "start", "end"] ) pd.testing.assert_frame_equal( result, bioframe.select(df, "chrX:4-6").reset_index(drop=True) @@ -52,14 +43,11 @@ def test_select__with_colnames(): ### select with non-standard column names new_names = ["chr", "chrstart", "chrend"] df = pd.DataFrame( - [["chrX", 3, 8], - ["chr1", 4, 5], - ["chrX", 1, 5]], + [["chrX", 3, 8], ["chr1", 4, 5], ["chrX", 1, 5]], columns=new_names, ) result = pd.DataFrame( - [["chrX", 3, 8], - ["chrX", 1, 5]], + [["chrX", 3, 8], ["chrX", 1, 5]], columns=new_names, ) pd.testing.assert_frame_equal( @@ -94,47 +82,32 @@ def test_select__with_nulls(): def test_select__mask_indices_labels(): df = pd.DataFrame( - [["chrX", 3, 8], - ["chr1", 4, 5], - ["chrX", 1, 5]], + [["chrX", 3, 8], ["chr1", 4, 5], ["chrX", 1, 5]], columns=["chrom", "start", "end"], ) region = "chr1:4-10" - answer = pd.DataFrame( - [["chr1", 4, 5]], - columns=["chrom", "start", "end"] - ) + answer = pd.DataFrame([["chr1", 4, 5]], columns=["chrom", "start", "end"]) result = bioframe.select(df, region) - pd.testing.assert_frame_equal( - answer, result.reset_index(drop=True) - ) + pd.testing.assert_frame_equal(answer, result.reset_index(drop=True)) mask = bioframe.select_mask(df, region) - pd.testing.assert_frame_equal( - answer, df.loc[mask].reset_index(drop=True) - ) + pd.testing.assert_frame_equal(answer, df.loc[mask].reset_index(drop=True)) labels = bioframe.select_labels(df, region) - pd.testing.assert_frame_equal( - answer, df.loc[labels].reset_index(drop=True) - ) + pd.testing.assert_frame_equal(answer, df.loc[labels].reset_index(drop=True)) idx = bioframe.select_indices(df, region) - pd.testing.assert_frame_equal( - answer, df.iloc[idx].reset_index(drop=True) - ) + pd.testing.assert_frame_equal(answer, df.iloc[idx].reset_index(drop=True)) def test_select__query_intervals_are_half_open(): - df = pd.DataFrame({ - "chrom": ["chr1", "chr1", - "chr2", "chr2", "chr2", "chr2", "chr2", "chr2"], - "start": [0, 10, - 10, 20, 30, 40, 50, 60], - "end": [10, 20, - 20, 30, 40, 50, 60, 70], - "name": ["a", "b", - "A", "B", "C", "D", "E", "F"], - }) + df = pd.DataFrame( + { + "chrom": ["chr1", "chr1", "chr2", "chr2", "chr2", "chr2", "chr2", "chr2"], + "start": [0, 10, 10, 20, 30, 40, 50, 60], + "end": [10, 20, 20, 30, 40, 50, 60, 70], + "name": ["a", "b", "A", "B", "C", "D", "E", "F"], + } + ) result = bioframe.select(df, "chr1") assert (result["name"] == ["a", "b"]).all() @@ -172,16 +145,14 @@ def test_select__query_intervals_are_half_open(): def test_select__with_point_intervals(): # Dataframe containing "point intervals" - df = pd.DataFrame({ - "chrom": ["chr1", "chr1", - "chr2", "chr2", "chr2", "chr2", "chr2", "chr2"], - "start": [0, 10, - 10, 20, 30, 40, 50, 60], - "end": [10, 10, - 20, 30, 40, 50, 50, 70], - "name": ["a", "b", - "A", "B", "C", "D", "E", "F"], - }) + df = pd.DataFrame( + { + "chrom": ["chr1", "chr1", "chr2", "chr2", "chr2", "chr2", "chr2", "chr2"], + "start": [0, 10, 10, 20, 30, 40, 50, 60], + "end": [10, 10, 20, 30, 40, 50, 50, 70], + "name": ["a", "b", "A", "B", "C", "D", "E", "F"], + } + ) result = bioframe.select(df, "chr1") assert (result["name"] == ["a", "b"]).all() @@ -213,9 +184,7 @@ def test_select__with_point_intervals(): def test_select__with_points(): # Dataframe of points df = pd.DataFrame( - [["chrX", 3, "A"], - ["chr1", 4, "C"], - ["chrX", 1, "B"]], + [["chrX", 3, "A"], ["chr1", 4, "C"], ["chrX", 1, "B"]], columns=["chrom", "pos", "name"], ) diff --git a/tests/test_resources.py b/tests/test_resources.py index 5218f71..b2c7a0d 100644 --- a/tests/test_resources.py +++ b/tests/test_resources.py @@ -11,9 +11,7 @@ def test_fetch_chromsizes(): assert chromsizes.name == "length" assert len(chromsizes) == 25 - chromsizes_df = bioframe.fetch_chromsizes( - db, provider=provider, as_bed=True - ) + chromsizes_df = bioframe.fetch_chromsizes(db, provider=provider, as_bed=True) assert isinstance(chromsizes_df, pd.DataFrame) assert list(chromsizes_df.columns) == ["chrom", "start", "end"] assert len(chromsizes_df) == 25 diff --git a/tests/test_vis.py b/tests/test_vis.py index 6223423..644c659 100644 --- a/tests/test_vis.py +++ b/tests/test_vis.py @@ -28,11 +28,13 @@ def test_to_ucsc_colorstring(): with pytest.raises(ValueError): bioframe.to_ucsc_colorstring("notacolor") - df = bioframe.from_any([ - ["chr1", 0, 10, "red"], - ["chr1", 10, 20, "blue"], - ["chr2", 0, 10, "green"], - ["chr2", 10, 20, None], - ]) + df = bioframe.from_any( + [ + ["chr1", 0, 10, "red"], + ["chr1", 10, 20, "blue"], + ["chr2", 0, 10, "green"], + ["chr2", 10, 20, None], + ] + ) df["itemRgb"] = df["name"].apply(bioframe.to_ucsc_colorstring) assert df["itemRgb"].tolist() == ["255,0,0", "0,0,255", "0,128,0", "0"]