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