Skip to content

How to run bedboss as a Python API

Install bedboss

pip install bedboss

Run bedboss all

from bedboss import run_all

run_all(
    sample_name="example_sample_name",
    input_file="example/path/to/input_file",
    input_type="bed",
    outfolder="example/path/to/outfolder",
    genome="hg38",
    bedbase_config="example/path/to/bedbase_config.yaml",
    # + another optional arguments
)

Run bedboss all-pep

from bedboss import run_all_by_pep

run_all_by_pep(
    pep="example/path/to/pep.yaml"
)

Run bedboss make

from bedboss import BedMaker

BedMaker(
    input_file="example/path/to/input_file",
    input_type="bed",
    output_bed="example/path/to/output_bed",
    output_bigbed="example/path/to/output_bigbed",
    sample_name="example_sample_name",
    genome="hg38",
)

Run bedboss stat

from bedboss import bedstat

bedstat( 
    bedfile="example/path/to/bedfile.bed",
    bedbase_config="example/path/to/bedbase_config.yaml",
    genome="hg38",
    outfolder="example/path/to/outfolder",
)

Run bedboss qc

from bedboss import bedqc

bedqc(
    bedfile="example/path/to/bedfile.bed",
    outfolder="example/path/to/outfolder",
)