📚 Tutorial

Import dependencies¶

In [1]:

import polars_bio as pb
import pandas as pd
from polars_bio.range_viz import visualize_intervals

import polars_bio as pb import pandas as pd from polars_bio.range_viz import visualize_intervals

INFO:polars_bio:Creating BioSessionContext

Sample data¶

In [2]:

df1 = pd.DataFrame(
    [["chr1", 1, 5], ["chr1", 3, 8], ["chr1", 8, 10], ["chr1", 12, 14]],
    columns=["chrom", "start", "end"],
)

df2 = pd.DataFrame(
    [["chr1", 4, 8], ["chr1", 10, 11]], columns=["chrom", "start", "end"]
)

df1 = pd.DataFrame( [["chr1", 1, 5], ["chr1", 3, 8], ["chr1", 8, 10], ["chr1", 12, 14]], columns=["chrom", "start", "end"], ) df2 = pd.DataFrame( [["chr1", 4, 8], ["chr1", 10, 11]], columns=["chrom", "start", "end"] )

Overlap¶

In [3]:

overlapping_intervals = pb.overlap(df1, df2, output_type="pandas.DataFrame")

overlapping_intervals = pb.overlap(df1, df2, output_type="pandas.DataFrame")

INFO:polars_bio.operation:Running Overlap operation with algorithm Coitrees and 1 thread(s)...

In [4]:

display(overlapping_intervals)

display(overlapping_intervals)

	chrom_1	start_1	end_1	chrom_2	start_2	end_2
0	chr1	1	5	chr1	4	8
1	chr1	3	8	chr1	4	8

In [5]:

visualize_intervals(overlapping_intervals)

visualize_intervals(overlapping_intervals)

Nearest¶

In [6]:

nearest_intervals = pb.nearest(df1, df2, output_type="pandas.DataFrame")

nearest_intervals = pb.nearest(df1, df2, output_type="pandas.DataFrame")

INFO:polars_bio.operation:Running Nearest operation with algorithm Coitrees and 1 thread(s)...

In [7]:

display(nearest_intervals)

display(nearest_intervals)

	chrom_1	start_1	end_1	chrom_2	start_2	end_2	distance
0	chr1	1	5	chr1	4	8	0
1	chr1	3	8	chr1	4	8	0
2	chr1	8	10	chr1	4	8	6
3	chr1	12	14	chr1	10	11	4

In [8]:

visualize_intervals(nearest_intervals, "nearest pair")

visualize_intervals(nearest_intervals, "nearest pair")