Source code for skgenome.subtract

"""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