bed2annotator.py - convert bed to annotator format

Tags

Python

Purpose

This script converts a bed file into annotator compatible regions. Depending on the option –section this script will create:

segments

a segments file

annotations

a file with annotations. Each bed track is a separate annotation.

workspace

a file with a workspace

Usage

Example:

python bed2annotator2tsv.py --help

Type:

python bed2annotator2tsv.py --help

for command line help.

Command line options

usage: bed2annotator [-h] [-g GENOME_FILE] [-f FEATURES] [-i FILES]
                     [-a ANNOTATIONS] [--map-tsv-file INPUT_FILENAME_MAP]
                     [-l MAX_LENGTH] [-m]
                     [-s {segments,annotations,workspace}] [--subset SUBSETS]
                     [--timeit TIMEIT_FILE] [--timeit-name TIMEIT_NAME]
                     [--timeit-header] [--random-seed RANDOM_SEED]
                     [-v LOGLEVEL] [--log-config-filename LOG_CONFIG_FILENAME]
                     [--tracing {function}] [-? ?] [-I STDIN] [-L STDLOG]
                     [-E STDERR] [-S STDOUT]
bed2annotator: error: argument -?: expected one argument