📚 Tutorial
Import dependencies¶
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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¶
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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¶
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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)...
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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 |
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visualize_intervals(overlapping_intervals)
visualize_intervals(overlapping_intervals)
Nearest¶
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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)...
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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 | 0 |
| 3 | chr1 | 12 | 14 | chr1 | 10 | 11 | 1 |
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visualize_intervals(nearest_intervals, "nearest pair")
visualize_intervals(nearest_intervals, "nearest pair")
