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linter import errors fixed
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@smitkadvani
smitkadvani committed Jan 19, 2024
1 parent 87fce0d commit 3c85755
Showing 1 changed file with 54 additions and 82 deletions.
136 changes: 54 additions & 82 deletions bioframe/core/checks.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,11 +2,8 @@
import pandas as pd

from . import construction
from .specs import (
_get_default_colnames,
_verify_column_dtypes,
_verify_columns
)
from .specs import (_get_default_colnames, _verify_column_dtypes,
_verify_columns)
from .. import ops

__all__ = [
Expand Down Expand Up @@ -66,10 +63,8 @@ def is_bedframe(
raise TypeError("Invalid bedFrame: Invalid column names")
return False

if not _verify_column_dtypes(
df,
cols=[ck1, sk1, ek1],
return_as_bool=True):
if not _verify_column_dtypes(df, cols=[ck1, sk1, ek1],
return_as_bool=True):
if raise_errors:
raise TypeError("Invalid bedFrame: Invalid column dtypes")
return False
Expand All @@ -85,22 +80,18 @@ def is_bedframe(

if ((df[ek1] - df[sk1]) < 0).any():
if raise_errors:
raise ValueError(
f"Invalid bedframe: starts exceed ends for "
f"{sum((df[ek1] - df[sk1]) < 0)} intervals"
)
raise ValueError(f"Invalid bedframe: starts exceed ends for "
f"{sum((df[ek1] - df[sk1]) < 0)} intervals")
return False

return True


def is_cataloged(
df,
view_df,
raise_errors=False,
df_view_col="view_region",
view_name_col="name"
):
def is_cataloged(df,
view_df,
raise_errors=False,
df_view_col="view_region",
view_name_col="name"):
"""
Tests if all region names in `df[df_view_col]` are present in
`view_df[view_name_col]`.
Expand Down Expand Up @@ -137,23 +128,19 @@ def is_cataloged(

if not _verify_columns(view_df, [view_name_col], return_as_bool=True):
if raise_errors:
raise ValueError(
f"Could not find \
raise ValueError(f"Could not find \
`{view_name_col}` \
column in view_df")
return False

if not set(df[df_view_col].copy().dropna().values).issubset(
set(view_df[view_name_col].values)
):
set(view_df[view_name_col].values)):
if raise_errors:
missing_regions = set(df[df_view_col].values).difference(
set(view_df[view_name_col].values)
)
set(view_df[view_name_col].values))
raise ValueError(
f"The following regions in df[df_view_col] not in "
f"view_df[view_name_col]: \n{missing_regions}"
)
f"view_df[view_name_col]: \n{missing_regions}")
return False

return True
Expand Down Expand Up @@ -187,21 +174,18 @@ def is_overlapping(df, cols=None):

total_interval_len = np.sum((df[ek1] - df[sk1]).values)
total_interval_len_merged = np.sum(
(
df_merged[ek1] - df_merged[sk1]
).values)
(df_merged[ek1] - df_merged[sk1]).values)

if total_interval_len > total_interval_len_merged:
return True
else:
return False


def is_viewframe(
region_df,
raise_errors=False,
view_name_col="name",
cols=None):
def is_viewframe(region_df,
raise_errors=False,
view_name_col="name",
cols=None):
"""
Checks that `region_df` is a valid viewFrame.
Expand Down Expand Up @@ -240,9 +224,8 @@ def is_viewframe(

ck1, sk1, ek1 = _get_default_colnames() if cols is None else cols

if not _verify_columns(
region_df, [ck1, sk1, ek1, view_name_col], return_as_bool=True
):
if not _verify_columns(region_df, [ck1, sk1, ek1, view_name_col],
return_as_bool=True):
if raise_errors:
raise TypeError("Invalid view: invalid column names")
return False
Expand All @@ -260,10 +243,8 @@ def is_viewframe(
if len(set(region_df[view_name_col])) < \
len(region_df[view_name_col].values):
if raise_errors:
raise ValueError(
"Invalid view: entries in \
region_df[view_name_col] must be unique"
)
raise ValueError("Invalid view: entries in \
region_df[view_name_col] must be unique")
return False

if is_overlapping(region_df, cols=cols):
Expand Down Expand Up @@ -320,12 +301,10 @@ def is_contained(
ck2, sk2, ek2 = _get_default_colnames() if cols_view is None else cols_view
if df_view_col is None:
try:
df_view_assigned = ops.overlap(
df,
view_df,
cols1=cols,
cols2=cols_view
)
df_view_assigned = ops.overlap(df,
view_df,
cols1=cols,
cols2=cols_view)
# ek2 = end_ is the default value
assert (df_view_assigned[ek2 + "_"].isna()).sum() == 0
# sk2 = start_ is the default value
Expand All @@ -342,20 +321,17 @@ def is_contained(
return True

if not is_cataloged(
df, view_df, df_view_col=df_view_col, view_name_col=view_name_col
):
df, view_df, df_view_col=df_view_col, view_name_col=view_name_col):
if raise_errors:
raise ValueError("df not cataloged in view_df")
return False

df_trim = trim(
df,
view_df=view_df,
df_view_col=df_view_col,
view_name_col=view_name_col,
cols=cols,
cols_view=cols_view
)
df_trim = trim(df,
view_df=view_df,
df_view_col=df_view_col,
view_name_col=view_name_col,
cols=cols,
cols_view=cols_view)

is_start_trimmed = np.any(df[sk1].values != df_trim[sk1].values)
is_end_trimmed = np.any(df[ek1].values != df_trim[ek1].values)
Expand Down Expand Up @@ -406,11 +382,11 @@ def is_covering(df, view_df, view_name_col="name", cols=None, cols_view=None):
from ..ops import complement

if complement(
df,
view_df=view_df,
view_name_col=view_name_col,
cols=cols,
cols_view=cols_view,
df,
view_df=view_df,
view_name_col=view_name_col,
cols=cols,
cols_view=cols_view,
).empty:
return True
else:
Expand Down Expand Up @@ -469,32 +445,28 @@ def is_tiling(
"""

view_df = construction.make_viewframe(
view_df, view_name_col=view_name_col, cols=cols_view
)
view_df = construction.make_viewframe(view_df,
view_name_col=view_name_col,
cols=cols_view)

if is_overlapping(df, cols=cols):
if raise_errors:
raise ValueError("overlaps")
return False
if not is_covering(
df,
view_df,
view_name_col=view_name_col,
cols=cols,
cols_view=cols_view
):
if not is_covering(df,
view_df,
view_name_col=view_name_col,
cols=cols,
cols_view=cols_view):
if raise_errors:
raise ValueError("not covered")
return False
if not is_contained(
df,
view_df,
df_view_col=df_view_col,
view_name_col=view_name_col,
cols=cols,
cols_view=cols_view
):
if not is_contained(df,
view_df,
df_view_col=df_view_col,
view_name_col=view_name_col,
cols=cols,
cols_view=cols_view):
if raise_errors:
raise ValueError("not contained")
return False
Expand Down

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