Skip to content

Intersecting two pandas DataFrames #332

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 1 commit into
base: master
Choose a base branch
from
Open

Intersecting two pandas DataFrames #332

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
38 changes: 38 additions & 0 deletions pybedtools/contrib/pandas_utils.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,38 @@
import pybedtools


def intersect_dfs(df1, df2, intersect_kwargs=None, read_table_names=None, other_read_table_kwargs=None):
"""
Intersect two pandas DataFrames using pybedtools.intersect.

@param df1: file A
@type df1: pandas.DataFrame
@param df2: file B
@type df2: pandas.DataFrame
@param intersect_kwargs: kwargs passed to pybedtools.intersect
@type intersect_kwargs: dict
@param read_table_names: list of column names passed to pandas.read_table (instead of the default ones given by
pybedtools)
@type read_table_names: list[str]
@param other_read_table_kwargs: kwargs passed to pandas.read_table other than `header` and `names`
@type other_read_table_kwargs: dict
@return: intersected_df
@rtype: pandas.DataFrame
"""
bed1 = pybedtools.BedTool.from_dataframe(df1)
bed2 = pybedtools.BedTool.from_dataframe(df2)

intersect_kwargs = {} if intersect_kwargs is None else intersect_kwargs

intersected_bed = bed1.intersect(bed2, **intersect_kwargs)

read_table_kwargs = {}
if read_table_names is not None:
read_table_kwargs["header"] = None
read_table_kwargs["names"] = read_table_names
if other_read_table_kwargs is not None:
read_table_kwargs.update(other_read_table_kwargs)

intersected_df = intersected_bed.to_dataframe(**read_table_kwargs)

return intersected_df