genome_bed.py - Create a bed file tiling a genome from a fai file

Tags

Python

This program takes an indexed genome and creates windows of a certain size.

It also takes two input parameters: the window/tile size (bases) and the shift size. By default the shift size is equal to the window size. The default window size is 1000.

Usage

python genome_bed -g <genome.fai> -o <output.bed> -w window size -s shift size

Command line options

usage: genome-bed [-h] [--version] [-g GENOME_FILE] [-w WINDOW] [-s SHIFT]
                  [--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]
genome-bed: error: argument -?: expected one argument