"""DataFrame-level subtraction operations.
Subtract one set of regions from another, returning the one-way difference.
The functions here operate on pandas DataFrame and Series instances, not
GenomicArray types.
"""
from __future__ import print_function, absolute_import, division
import logging
import numpy as np
import pandas as pd
from .intersect import by_ranges
[docs]def subtract(table, other):
if not len(other):
return table
return pd.DataFrame.from_records(_subtraction(table, other),
columns=table.columns)
def _subtraction(table, other):
for keeper, rows_to_exclude in by_ranges(other, table, 'outer', True):
if len(rows_to_exclude):
logging.debug(" %s:%d-%d : Subtracting %d excluded regions",
keeper.chromosome, keeper.start, keeper.end,
len(rows_to_exclude))
keep_left = (keeper.start < rows_to_exclude.start.iat[0])
keep_right = (keeper.end > rows_to_exclude.end.iat[-1])
if keep_left and keep_right:
# Keep both original edges of the source region
# =========
# -- --
starts = np.r_[keeper.start, rows_to_exclude.end.values]
ends = np.r_[rows_to_exclude.start.values, keeper.end]
elif keep_left:
# Exclusion overlaps only the right side
# =======
# -- ---
starts = np.r_[keeper.start, rows_to_exclude.end.values[:-1]]
ends = rows_to_exclude.start.values
elif keep_right:
# Exclusion overlaps only the left side
# ========
# --- --
starts = rows_to_exclude.end.values
ends = np.r_[rows_to_exclude.start.values[1:], keeper.end]
elif len(rows_to_exclude) > 1:
# Exclusions overlap both edges
# ======
# -- -- ---
starts = rows_to_exclude.end.values[:-1]
ends = rows_to_exclude.start.values[1:]
else:
# Exclusion covers the whole region
continue
for start, end in zip(starts, ends):
if end > start:
yield keeper._replace(start=start, end=end)
else:
logging.debug("Discarding pair: (%d, %d)", start, end)
else:
logging.debug(" %s:%d-%d : No excluded regions",
keeper.chromosome, keeper.start, keeper.end)
yield keeper