BEDOps
Manipulate tabular genomic files.
: Bedtools
BEDOPS [1]is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster.
The Code: is hosted at https://github.com/bedops/bedops [2]
A picture-rich operation manual is hosted at https://bedops.readthedocs.org/[3]
BEDOps is a competitor of Bedtools with interesting complementary concepts but overall lower performance
bedextract
bedmap
bedops
closest-features
# Sorting
sort-bed
bbms / bbms.py
# Compression and extraction
starch
unstarch
starchcat
# Data conversion
wig2bed
$ bedops
citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract
version: 2.3.0
authors: Shane Neph & Scott Kuehn
USAGE: bedops [process-flags] <operation> <File(s)>*
Every input file must be sorted per the sort-bed utility.
Each operation requires a minimum number of files as shown below.
There is no fixed maximum number of files that may be used.
Input files must have at least the first 3 columns of the BED specification.
The program accepts BED and starch file formats.
May use '-' for a file to indicate reading from standard input (BED format only).
Process Flags:
--chrom <chromosome> Process data for given <chromosome> only.
--ec Error check input files (slower).
--header Accept headers (VCF, GFF, SAM, BED, WIG) in any input file.
--help Print this message and exit successfully.
--help-<operation> Detailed help on <operation>.
An example is --help-c or --help-complement
--range L:R Add 'L' bp to all start coordinates and 'R' bp to end
coordinates. Either value may be + or - to grow or
shrink regions. With the -e/-n operations, the first
(reference) file is not padded, unlike all other files.
--range S Pad input file(s) coordinates symmetrically by S.
This is shorthand for: --range -S:S.
--version Print program information.
Operations: (choose one of)
-c, --complement [-L] File1 [File]*
-d, --difference ReferenceFile File2 [File]*
-e, --element-of [-number% | -number (in bp)] ReferenceFile File2 [File]*
by default, -e -100% is used.
-i, --intersect File1 File2 [File]*
-m, --merge File1 [File]*
-n, --not-element-of [-number% | -number (in bp)] ReferenceFile File2 [File]*
by default, -n -100% is used.
-p, --partition File1 [File]*
-s, --symmdiff File1 File2 [File]*
-u, --everything File1 [File]*
Example: bedops --range 10 -u file1.bed
NOTE: Only operations -e|n|u preserve all columns (no flattening)
References:
- ↑
Shane Neph, M Scott Kuehn, Alex P Reynolds, Eric Haugen, Robert E Thurman, Audra K Johnson, Eric Rynes, Matthew T Maurano, Jeff Vierstra, Sean Thomas, Richard Sandstrom, Richard Humbert, John A Stamatoyannopoulos
BEDOPS: high-performance genomic feature operations.
Bioinformatics: 2012, 28(14);1919-20
[PubMed:22576172] ##WORLDCAT## [DOI] (I p) - ↑ https://github.com/bedops/bedops
- ↑ https://bedops.readthedocs.org/
