diff_bed.py - count differences between several bed files

Tags

Genomics Intervals BED Comparison

Purpose

Compute overlap statistics between multiple bed files. For each pairwise comparison, this script outputs the number of intervals (exons) and bases overlapping.

Using the --update option, a table can be incrementally updated with additional comparisons.

The strand of intervals is ignored in comparisons.

Column	Content
set	Name of the set
nexons_total	number of intervals in set
nexons_ovl	number of intervals overlapping
nexons_unique	number of unique intervals
nbases_total	number of bases in gene set
nbases_ovl	number of bases overlapping
nbases_unique	number of unique bases

Usage

For example:

python diff_bed.py *.bed.gz > out.tsv

To update results from a previous run, type:

python diff_bed.py --update=out.tsv *.bed.gz > new.tsv

Type:

python diff_bed.py --help

for command line help.

Command line options

usage: diff-bed [-h] [--version] [-u FILENAME_UPDATE] [-p PATTERN_ID] [-t]
                [--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]
diff-bed: error: argument -?: expected one argument