BEDbuncher tutorial

BEDbuncher

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

1) Create bedbase config file

How to create config file: configuration section.

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_name	record_identifier
sample1	asdf3215f34
sample2	a23452f34tf

3) Run bedboss bunch

From command line

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

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,
    )