BedClusterName

Clusters a BED file into a set of BED files using the 4th column of the bed name.

Usage

This program is now part of the main jvarkit tool. See jvarkit for compiling.

Usage: java -jar dist/jvarkit.jar bedclustername  [options] Files

Usage: bedclustername [options] Files
  Options:
    -C, --contig, --chromosome
      group by chromosome.
      Default: false
    -F, --format
      An existing directory or a filename ending with the '.zip' or '.tar' or 
      '.tar.gz' suffix.
      Default: BED
      Possible Values: [BED, BED_GZ, INTERVAL_LIST, INTERVAL_LIST_GZ]
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -J, --jobs
      number of clusters. (or specify --size or --window-size/--window-shif)
      Default: -1
    -m, --manifest
      Manifest Bed file output containing chrom/start/end of each gene
    --md5-dir, --sub-dir
      prevent the creation of too many files in the same directory. Create 
      some intermediate directories based on filename's md5.
      Default: false
    --merge-distance, --merge
      if greater than -1 Merge overlapping record for the same name within a 
      distance of 'x'. 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
  * -o, --out
      An existing directory or a filename ending with the '.zip' or '.tar' or 
      '.tar.gz' suffix.
    -R, --reference
      For sorting and /or 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...)
    -S, --size
      number of bases max per bin. (or specify --jobs or 
      --window-size/--window-shif). 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

Creation Date

2050428

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/bedclustername/BedClusterName.java

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 bedclustername ? 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

$ gunzip -c src/test/resources/Homo_sapiens.GRCh37.87.gtf.gz | awk -F '\t' '$3=="exon"' | \
    java -jar dist/jvarkit.jar gtf2bed -c 'gene_name' |\
    java -jar dist/jvarkit.jar bedclustername -o jeter.zip  --size 100 --merge 1

$ unzip -l jeter.zip 
Archive:  jeter.zip
  Length      Date    Time    Name
---------  ---------- -----   ----
     7332  2025-04-28 14:37   cluster.000000001.bed
     1740  2025-04-28 14:37   cluster.000000002.bed
     1456  2025-04-28 14:37   cluster.000000003.bed
---------                     -------
    10528                     3 files


$ unzip -p jeter.zip cluster.000000002.bed | head
22  41697718    41697776    ZC3H7B
22  41716664    41716717    ZC3H7B
22  41721567    41721601    ZC3H7B
22  41721724    41721922    ZC3H7B
22  41723209    41723368    ZC3H7B
22  41726026    41726107    ZC3H7B
22  41728174    41732847    ZC3H7B
22  41734316    41734359    ZC3H7B
22  41735004    41735195    ZC3H7B
22  41735819    41736141    ZC3H7B