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BEDbase

BEDbuncher

BEDbuncher

Section titled “BEDbuncher”

Bedbuncher is used to create bedset of bed files in the bedbase database.

1) Create bedbase config file

Section titled “1) Create bedbase config file”

How to create config file: configuration section.

2) Create pep with bed file record identifiers.

Section titled “2) Create pep with bed file record identifiers.”

To do so, you need to create a PEP with the following fields: sample_name (where sample_name is record_identifier), or sample_name + record_identifier e.g. sample_table:

sample_namerecord_identifier
sample1asdf3215f34
sample2a23452f34tf

3) Run bedboss bunch

Section titled “3) Run bedboss bunch”

From command line

Section titled “From command line”
Terminal window
bedboss bunch \
  --bedbase-config path/to/bedbase_config.yaml \
  --bedset-name bedset1 \
  --pep path/to/pep.yaml \
  --outfolder path/to/output/dir \
  --heavy \
  --upload-pephub \
  --upload-s3

Run bedboss bunch from within Python

Section titled “Run bedboss bunch from within Python”
from bedboss.bedbuncher.bedbuncher import run_bedbuncher_form_pep


run_bedbuncher_form_pep(
    bedbase_config=bedbase_config,
    bedset_pep=pep,
    output_folder=outfolder,
    bedset_name=bedset_name,
    heavy=heavy,
    upload_pephub=upload_pephub,
    upload_s3=upload_s3,
    no_fail=no_fail,
    force_overwrite=force_overwrite,
)