wig2bed.py - convert densities to intervals

Purpose

define intervals based on densities within a bigwig file.

The script currently implements the following methods (--method):

threshold

output windows that contain values above a certain threshold.

std-above-mean

output windows that are a certain number of standard deviations above the mean.

multiple-of-mean

output windows that are a certain times above the mean.

Usage

Bigwig files need to be supplied by the –bigwig-file options.

For example:

python wig2bed.py --threshold=10 --method=threshold --genome-file=mm10 --bigwig-file=in.bw > out.bed

Command line options

usage: wig2bed [-h] [-m {threshold,stddev-above-mean,multiple-of-mean}]
               [-g GENOME_FILE] [-t THRESHOLD] [-i bigwig]
               [--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]
wig2bed: error: argument -?: expected one argument