bed.plot.py - create genomic snapshots using the IGV Viewer

Tags

Python

Purpose

Create genomic plots in a set of intervals using the IGV snapshot mechanism.

The script can use a running instance of IGV identified by host and port. Alternatively, it can start IGV and load a pre-built session.

Usage

Example:

python bed2plot.py < in.bed

Type:

python script_template.py --help

for command line help.

Command line options

usage: bed2plot [-h] [-s SESSION] [-d SNAPSHOTDIR] [-f {png,eps,svg}]
                [-o HOST] [-p PORT] [-e EXTEND] [-x EXPAND] [--session-only]
                [-n {bed-name,increment}] [--timeit TIMEIT_FILE]
                [--timeit-name TIMEIT_NAME] [--timeit-header]
                [--random-seed RANDOM_SEED] [-v LOGLEVEL]
                [--log-config-filename LOG_CONFIG_FILENAME]
                [--tracing {function}] [-? ?] [-P OUTPUT_FILENAME_PATTERN]
                [-F] [-I STDIN] [-L STDLOG] [-E STDERR] [-S STDOUT]
bed2plot: error: argument -?: expected one argument