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A command-line and manager tool for calculating statistics for region set files (BED files) and managing them in the BEDbase database.

Main features:

1) bedmaker - pipeline to convert supported file types into BED format and bigBed format.
2) bedqc - pipeline to flag bed files for further evaluation to determine whether they should be included in the downstream analysis.
3) bedstat - pipeline for obtaining statistics about bed files.
4) bedbuncher - pipeline designed to create bedsets (sets of BED files) that will be retrieved from bedbase.
5) index - pipeline to create vectors of bedfiles and insert them into vector database for further search.
6) Other delete and update tools that manage bed and bedset files in the BEDbase database.

Mainly pipelines are intended to be run from command line but nevertheless, they are also available as a python function, so that user can implement them to his own code (e.g. automatic uploading tools).

Installation

To install bedboss use this command: 

pip install bedboss
or install the latest version from the GitHub repository: 
pip install git+https://github.com/databio/bedboss.git

BEDboss dependencies

Before running any of the pipelines, you need to install the required dependencies.

To check if all dependencies are installed, you can run the following command:

bedboss check-requirements

All dependencies can be using this how to documentation: How to install dependencies

BEDbase configuration file

To run most of the pipelines, you need to create a BEDbase configuration file.

How to create a BEDbase configuration file is described in the configuration section.

Pipelines information

bedmaker

bedmaker - pipeline to convert supported file types* into BED format and bigBed format. Currently supported formats:

  • bedGraph
  • bigBed
  • bigWig
  • wig

bedqc

flag bed files for further evaluation to determine whether they should be included in the downstream analysis. Currently, it flags bed files that are larger than 2G, has over 5 milliom regions, and/or has mean region width less than 10 bp. This threshold can be changed in bedqc function arguments.

bedstat

pipeline for obtaining statistics about bed files

It produces BED file Statistics:

  • GC content.The average GC content of the region set.
  • Number of regions. The total number of regions in the BED file.
  • Median TSS distance. The median absolute distance to the Transcription Start Sites (TSS)
  • Mean region width. The average region width of the region set.
  • Exon percentage. The percentage of the regions in the BED file that are annotated as exon.
  • Intron percentage. The percentage of the regions in the BED file that are annotated as intron.
  • Promoter proc percentage. The percentage of the regions in the BED file that are annotated as promoter-prox.
  • Intergenic percentage. The percentage of the regions in the BED file that are annotated as intergenic.
  • Promoter core percentage. The percentage of the regions in the BED file that are annotated as promoter-core.
  • 5' UTR percentage. The percentage of the regions in the BED file that are annotated as 5'-UTR.
  • 3' UTR percentage. The percentage of the regions in the BED file that are annotated as 3'-UTR.

bedbuncher

Pipeline designed to create bedsets (sets of BED files) that will be retrieved from bedbase.

Example bedsets:

Bedbuncher calculates statistics: - Bedset statistics (currently means and standard deviations).