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