jvarkit
BedCluster
Clusters a BED file into a set of BED files.
Usage
This program is now part of the main jvarkit tool. See jvarkit for compiling.
Usage: java -jar dist/jvarkit.jar bedcluster [options] Files
Usage: bedcluster [options] Files
Options:
-C, --contig, --chromosome
group by chromosome.
Default: false
--compress
Compress bed with bgz.
Default: false
--consecutive
When using option --size only use consecutive ordered region. Default is
to find the best region anywhere.
Default: false
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
--interval-list
Save as htsjdk interval list (https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/util/IntervalList.html)
instead of bed.
Default: false
-J, --jobs
number of clusters. (or specify --size)
Default: -1
-m, --manifest
Manifest Bed file output containing chrom/start/end of each gene
--merge
Merge overlapping bed records before clustering
Default: false
--names
Print BED name (4th column of input bed)
Default: false
* -o, --out
An existing directory or a filename ending with the '.zip' or '.tar' or
'.tar.gz' suffix.
-R, --reference
For sorting, writing interval_list,A SAM Sequence dictionary source: it
can be a *.dict file, a fasta file indexed with 'picard
CreateSequenceDictionary' or 'samtools dict', or any hts file containing
a dictionary (VCF, BAM, CRAM, intervals...)
--sex, --par
Detects human dictionary ans splits pseudo-autosomal regions and group
by sex.
Default: false
-S, --size
number of bases max per bin. (or specify --jobs). A distance specified
as a positive integer.Commas are removed. The following suffixes are
interpreted : b,bp,k,kb,m,mb,g,gb
Default: -1
--version
print version and exit
Keywords
- bed
- chromosome
- contig
See also in Biostars
Creation Date
20200130
Source code
Unit Tests
Contribute
- Issue Tracker: http://github.com/lindenb/jvarkit/issues
- Source Code: http://github.com/lindenb/jvarkit
License
The project is licensed under the MIT license.
Citing
Should you cite bedcluster ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md
The current reference is:
http://dx.doi.org/10.6084/m9.figshare.1425030
Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030
Example
$ java -jar dist/bedcluster.jar -j 10 -m jeter.mf -o jeter.zip --compress --contig test.bed
$ head jeter.mf
#chrom start end filename number_of_records sum-length avg-length stddev-size
1 57460450 59012406 1_57460451_59012406.000000001.bed.gz 1 1551956 1551956 0
1 48998526 50489585 1_48998527_50489585.000000002.bed.gz 1 1491059 1491059 0
1 901876 248790491 1_901877_248790491.000000003.bed.gz 49 1393594 28440 41317
1 1567473 248154506 1_1567474_248154506.000000004.bed.gz 50 1393602 27872 39042
1 470970 229841608 1_470971_229841608.000000005.bed.gz 51 1393594 27325 37502
1 160445 248041507 1_160446_248041507.000000006.bed.gz 51 1393602 27325 37487
1 5647427 246685894 1_5647428_246685894.000000007.bed.gz 51 1393601 27325 37433
1 34553 245778447 1_34554_245778447.000000008.bed.gz 51 1393601 27325 37186
1 696290 247495148 1_696291_247495148.000000009.bed.gz 52 1393594 26799 35931
$ unzip -l jeter.zip | head
Archive: jeter.zip
Length Date Time Name
--------- ---------- ----- ----
76 2020-01-31 12:45 1_57460451_59012406.000000001.bed.gz
74 2020-01-31 12:45 1_48998527_50489585.000000002.bed.gz
487 2020-01-31 12:45 1_901877_248790491.000000003.bed.gz
494 2020-01-31 12:45 1_1567474_248154506.000000004.bed.gz
494 2020-01-31 12:45 1_470971_229841608.000000005.bed.gz
511 2020-01-31 12:45 1_160446_248041507.000000006.bed.gz
511 2020-01-31 12:45 1_5647428_246685894.000000007.bed.gz
unzip -p jeter.zip 1_5647428_246685894.000000007.bed.gz | gunzip -c |head
1 5647427 5728355
1 8921060 8939308
1 11128527 11133154
1 13216355 13219581
1 16787442 16794976
1 20465818 20476879
1 21737952 21739786
1 26145130 26159432
1 37627163 37627235
1 38021842 38022108