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from io import StringIO
import numpy as np
import pandas as pd
import pytest
from bioframe.core.checks import (
is_bedframe,
is_cataloged,
is_contained,
is_covering,
is_overlapping,
is_sorted,
is_tiling,
is_viewframe,
)
from bioframe.ops import sort_bedframe
def test_is_cataloged():
# chr2q is not in view
view_df = pd.DataFrame(
[
["chr1", 0, 12, "chr1p"],
["chr1", 13, 26, "chr1q"],
["chrX", 1, 8, "chrX_0"],
],
columns=["chrom", "start", "end", "name"],
)
df = pd.DataFrame(
[
["chr1", 0, 12, "chr1p"],
["chr1", 5, 15, "chr1p"],
["chr2", 13, 26, "chr2q"],
["chrX", 1, 8, "chrX_0"],
],
columns=["chrom", "start", "end", "view_region"],
)
assert not is_cataloged(df, view_df)
# chr1q is in view, df_view_col and view_name_col have funny labels.
view_df = pd.DataFrame(
[
["chr1", 0, 12, "chr1p"],
["chr1", 13, 26, "chr1q"],
["chrX", 1, 8, "chrX_0"],
],
columns=["chrom", "start", "end", "funny_name"],
)
df = pd.DataFrame(
[
["chr1", 0, 12, "chr1p"],
["chr2", 13, 26, "chr1q"],
["chrX", 1, 8, "chrX_0"],
],
columns=["chrom", "start", "end", "funny_view_region"],
)
assert is_cataloged(
df, view_df, df_view_col="funny_view_region", view_name_col="funny_name"
)
def test_is_contained():
view_df = pd.DataFrame(
[
["chr1", 0, 20, "chr1p"],
["chr1", 21, 30, "chr1q"],
["chrX", 1, 10, "chrX_0"],
],
columns=["chrom", "start", "end", "name"],
)
# not contained because chr2q is not cataloged
df = pd.DataFrame(
[
["chr1", 0, 12, "chr1p"],
["chr2", 13, 26, "chr2q"],
["chrX", 1, 8, "chrX_0"],
],
columns=["chrom", "start", "end", "view_region"],
)
assert not is_contained(df, view_df, df_view_col="view_region")
# not contained because second interval falls outside the view regions
df = pd.DataFrame(
[
["chr1", 14, 15, "chr1p"],
["chr1", -1, 1, "chr1q"],
["chrX", 1, 8, "chrX_0"],
],
columns=["chrom", "start", "end", "view_region"],
)
assert not is_contained(df, view_df)
df = pd.DataFrame(
[
["chr1", 12, 12, "chr1p"],
["chr1", 13, 14, "chr1q"],
["chrX", 1, 8, "chrX_0"],
],
columns=["chrom", "start", "end", "view_region"],
)
# is contained, because assignments are inferred
assert is_contained(df, view_df)
# using previous assignments with non-standard column names
# in dataframes without argument
view_df = pd.DataFrame(
[
["chr1", 0, 12, "chr1p"],
["chr1", 13, 26, "chr1q"],
["chrX", 1, 8, "chrX_0"],
],
columns=["CHROM", "START", "END", "NAME"],
)
df = pd.DataFrame(
[
["chr1", 12, 12, "chr1p"],
["chr1", 13, 14, "chr1q"],
["chrX", 1, 8, "chrX_0"],
],
columns=["chrom1", "start1", "end1", "VIEW_REGION"],
)
assert is_contained(
df,
view_df,
cols=["chrom1", "start1", "end1"],
cols_view=["CHROM", "START", "END"],
df_view_col="VIEW_REGION",
view_name_col="NAME",
)
with pytest.raises(TypeError):
# cols and view_cols are not passed as an arguments
is_contained(df, view_df, raise_errors=True)
# is not contained, because assignments are not inferred
view_df = pd.DataFrame(
[
["chr1", 0, 12, "chr1p"],
["chr1", 13, 26, "chr1q"],
["chrX", 1, 8, "chrX_0"],
],
columns=["chrom", "start", "end", "name"],
)
assert not is_contained(df, view_df, df_view_col="view_region")
# second interval falls completely out of the view
df = pd.DataFrame(
[
["chr1", 12, 12, "chr1p"],
["chr1", 100, 101, "chr1q"],
],
columns=["chrom", "start", "end", "view_region"],
)
# fails due to NAs after overlap to infer the regions
with pytest.raises(AssertionError):
is_contained(df, view_df, raise_errors=True)
# fails due to some of the intervals being trimmed
with pytest.raises(ValueError):
is_contained(df, view_df, df_view_col="view_region", raise_errors=True)
def test_is_overlapping():
# interval on chr1 overlaps
d = """chrom start end
0 chr1 3 6
1 chr1 5 10
2 chr2 5 10"""
df = pd.read_csv(StringIO(d), sep=r"\s+")
assert is_overlapping(df)
# adjacent intervals do not overlap
d = """chrom start end
0 chr1 3 6
1 chr1 6 10
2 chr2 5 10"""
df = pd.read_csv(StringIO(d), sep=r"\s+")
assert not is_overlapping(df)
def test_is_covering():
# test is_covering where an interval from df completely overlaps
# two different regions from view
df1 = pd.DataFrame(
[
["chr1", -5, 25],
],
columns=["chrom", "start", "end"],
)
chromsizes = [("chr1", 0, 9, "chr1p"), ("chr1", 11, 20, "chr1q")]
assert is_covering(df1, chromsizes)
# test is_covering where two intervals from df overlap
# two different regions from view
df1 = pd.DataFrame(
[
["chr1", -5, 10],
["chr1", 11, 12],
["chr1", 12, 20],
],
columns=["chrom", "start", "end"],
)
chromsizes = [("chr1", 0, 9, "chr1p"), ("chr1", 11, 20, "chr1q")]
assert is_covering(df1, chromsizes)
# test is_covering with non-standard columns names
df1 = pd.DataFrame(
[
["chr1", -5, 10],
["chr1", 11, 12],
["chr1", 12, 20],
],
columns=["chrom1", "start1", "end1"],
)
chromsizes = pd.DataFrame(
[["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",
)
with pytest.raises(ValueError):
# cols and view_cols are not passed as an arguments
is_covering(df1, chromsizes)
# test is_covering where two intervals from df overlap
# two different regions from view
df1 = pd.DataFrame(
[
["chr1", -5, 10, "chr1q"],
["chr1", 11, 12, "chr1q"],
["chr1", 12, 20, "chr1q"],
],
columns=["chrom", "start", "end", "view_region"],
)
chromsizes = [("chr1", 0, 9, "chr1p"), ("chr1", 11, 20, "chr1q")]
assert is_covering(df1, chromsizes)
def test_is_tiling():
# view region chr1p is tiled by one interval, chr1q is tiled by two
df1 = pd.DataFrame(
[
["chr1", 0, 9, "chr1p"],
["chr1", 11, 12, "chr1q"],
["chr1", 12, 20, "chr1q"],
],
columns=["chrom", "start", "end", "view_region"],
)
chromsizes = [("chr1", 0, 9, "chr1p"), ("chr1", 11, 20, "chr1q")]
assert is_tiling(df1, chromsizes)
# testing for non-standard column names
df1 = pd.DataFrame(
[
["chr1", 0, 9, "chr1p"],
["chr1", 11, 12, "chr1q"],
["chr1", 12, 20, "chr1q"],
],
columns=["chrom1", "start1", "end1", "view_region"],
)
chromsizes = pd.DataFrame(
[["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",
)
with pytest.raises(KeyError):
# cols and view_cols are not passed as an arguments
is_tiling(df1, chromsizes)
# not tiling, since (chr1,0,9) is associated with chr1q
df1 = pd.DataFrame(
[
["chr1", 0, 9, "chr1q"],
["chr1", 11, 12, "chr1q"],
["chr1", 12, 20, "chr1q"],
],
columns=["chrom", "start", "end", "view_region"],
)
chromsizes = [("chr1", 0, 9, "chr1p"), ("chr1", 11, 20, "chr1q")]
assert not is_tiling(df1, chromsizes)
# not tiling, contains overlaps
df1 = pd.DataFrame(
[
["chr1", 0, 9, "chr1p"],
["chr1", 11, 13, "chr1q"],
["chr1", 12, 20, "chr1q"],
],
columns=["chrom", "start", "end", "view_region"],
)
chromsizes = [("chr1", 0, 9, "chr1p"), ("chr1", 11, 20, "chr1q")]
assert not is_tiling(df1, chromsizes)
# not tiling, since it doesn't cover
df1 = pd.DataFrame(
[
["chr1", 11, 12, "chr1q"],
["chr1", 12, 20, "chr1q"],
],
columns=["chrom", "start", "end", "view_region"],
)
chromsizes = [("chr1", 0, 9, "chr1p"), ("chr1", 11, 20, "chr1q")]
assert not is_tiling(df1, chromsizes)
def test_is_bedframe():
# missing a column
df1 = pd.DataFrame(
[
["chr1", 11],
["chr1", 12],
],
columns=["chrom", "start"],
)
assert not is_bedframe(df1)
# end column has invalid dtype
df1 = pd.DataFrame(
[
["chr1", 10, "20"],
["chr1", 10, "12"],
],
columns=["chrom", "start", "end"],
)
assert not is_bedframe(df1)
# second interval start > ends.
df1 = pd.DataFrame(
[
["chr1", 10, 20],
["chr1", 15, 10],
],
columns=["chrom", "start", "end"],
)
assert not is_bedframe(df1)
# third interval has a null in one column
df1 = pd.DataFrame(
[
["chr1", 10, 20, "first"],
["chr1", 10, 15, "second"],
["chr1", pd.NA, 15, "third"],
],
columns=["chrom", "start", "end", "name"],
)
# should raise a TypeError if the second column is an object
with pytest.raises(TypeError):
is_bedframe(df1, raise_errors=True)
# should raise a ValueError after recasting to pd.Int64Dtype
df1 = df1.astype({"start": pd.Int64Dtype(), "end": pd.Int64Dtype()})
with pytest.raises(ValueError):
is_bedframe(df1, raise_errors=True)
# first interval is completely NA
df1 = pd.DataFrame(
[
[pd.NA, pd.NA, pd.NA, "first"],
["chr1", 10, 15, "second"],
["chr1", 10, 15, "third"],
],
columns=["chrom", "start", "end", "name"],
)
df1 = df1.astype({"start": pd.Int64Dtype(), "end": pd.Int64Dtype()})
assert is_bedframe(df1)
def test_is_viewframe():
# not a bedframe
df1 = pd.DataFrame(
[
["chr1", 10, 20, "chr1p"],
["chr1", 15, 10, "chr1q"],
],
columns=["chrom", "start", "end", "name"],
)
assert not is_viewframe(df1)
# no column for region name
df1 = pd.DataFrame(
[
["chr1", 10, 20],
["chr1", 30, 40],
],
columns=["chrom", "start", "end"],
)
assert not is_viewframe(df1)
# contains null values
df1 = pd.DataFrame(
[
["chr1", 10, 20, "chr1p"],
["chr1", pd.NA, np.nan, "chr1q"],
],
columns=["chrom", "start", "end", "name"],
)
assert not is_viewframe(df1)
# overlapping intervals
df1 = pd.DataFrame(
[
["chr1", 10, 20, "chr1p"],
["chr1", 15, 25, "chr1q"],
],
columns=["chrom", "start", "end", "name"],
)
assert not is_viewframe(df1)
# valid view
df1 = pd.DataFrame(
[
["chr1", 10, 20, "chr1p"],
["chr1", 20, 25, "chr1q"],
["chr2", 20, 25, "chrTEST_2p"],
],
columns=["chrom", "start", "end", "name"],
)
assert is_viewframe(df1)
def test_is_sorted():
view_df = pd.DataFrame(
[
["chrX", 1, 8, "oranges"],
["chrX", 8, 20, "grapefruit"],
["chr1", 0, 10, "apples"],
],
columns=["chrom", "start", "end", "fruit"],
)
df_view_cat = pd.CategoricalDtype(
categories=["oranges", "grapefruit", "apples"], ordered=True
)
view_df = view_df.astype({"fruit": df_view_cat})
assert is_sorted(
view_df, view_df=view_df, view_name_col="fruit", df_view_col="fruit"
)
# testing for non-standard column names
view_df = pd.DataFrame(
[
["chrX", 1, 8, "oranges"],
["chrX", 8, 20, "grapefruit"],
["chr1", 0, 10, "apples"],
],
columns=["CHROM", "START", "END", "FRUIT"],
)
assert is_sorted(
view_df,
view_df=view_df,
view_name_col="FRUIT",
df_view_col="FRUIT",
cols=["CHROM", "START", "END"],
cols_view=["CHROM", "START", "END"],
)
with pytest.raises(ValueError):
# cols and view_cols are not passed as an arguments
is_sorted(view_df, view_df=view_df)
df = pd.DataFrame(
[
["chr1", 0, 10, "+"],
["chrX", 5, 10, "+"],
["chrX", 0, 5, "+"],
["chr2", 5, 10, "+"],
],
columns=["chrom", "start", "end", "strand"],
)
assert not is_sorted(df)
view_df = pd.DataFrame(
[
["chrX", 1, 8, "oranges"],
["chrX", 8, 20, "grapefruit"],
["chr1", 0, 10, "apples"],
],
columns=["chrom", "start", "end", "fruit"],
)
bfs = sort_bedframe(df, view_df=view_df, view_name_col="fruit")
assert is_sorted(bfs, view_df=view_df, view_name_col="fruit")
# view_df specifies a different ordering, so should not be sorted
assert not is_sorted(bfs)
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