bed2graph.py - compute the overlap graph between two bed files

Tags

Python

Purpose

This script ouputs a list of the names of all overlapping intervals between two bed files.

Usage

Type:

python bed2graph.py A.bed.gz B.bed.gz > graph.out

for command line help.

Command line options

usage: bed2graph [-h] [--version] [-o {full,name}] [--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]
bed2graph: error: argument -?: expected one argument