WibToBedGraph

Extract Wib files to bedgraph or wig

Usage

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

Usage: java -jar dist/jvarkit.jar wib2bedgraph  [options] Files

Usage: wib2bedgraph [options] Files
  Options:
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
  * -r, --regions
      An interval as the following syntax : "chrom:start-end" or 
      "chrom:middle+extend"  or "chrom:start-end+extend" or 
      "chrom:start-end+extend-percent%".A program might use a Reference 
      sequence to fix the chromosome name (e.g: 1->chr1)
      Default: <empty string>
  * --tabix
      A wib associated indexed tabix file.e.g: wget 
      "https://hgdownload.soe.ucsc.edu/gbdb/hg38/multiz100way/phastCons100way.wib" 
      && wget -O - "https://hgdownload.cse.ucsc.edu/goldenpath/hg38/database/phastCons100way.txt.gz" 
      | gunzip -c | bgzip > phastCons100way.txt.gz && tabix --force -0 -s 2 -e 
      3 -e 4 phastCons100way.txt.gz

      Default: <empty string>
    --version
      print version and exit
  * --wib
      The wib file itself e.g: wget 
      'https://hgdownload.soe.ucsc.edu/gbdb/hg38/multiz100way/phastCons100way.wib' 
      . 
      Default: <empty string>
    --wig
      output WIG format instead of BED graph
      Default: false

Keywords

• wib
• wig
• bed

Creation Date

20230819

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/wib/WibToBedGraph.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 wib2bedgraph ? 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/jvarkit.jar wib2bedgraph --tabix ~/phastCons100way.txt.gz --wib ~/phastCons100way.wib -r "chr2:1-125168903" | head

chr2 11391 11392 0.14969291 chr2 11392 11393 0.14667717 chr2 11393 11394 0.14064567 chr2 11394 11395 0.13461417 chr2 11395 11396 0.12858267 chr2 11396 11397 0.13461417 chr2 11397 11398 0.14366141 chr2 11398 11399 0.14969291 chr2 11399 11400 0.1557244 chr2 11400 11401 0.15874015

$ java -jar dist/jvarkit.jar wib2bedgraph --tabix ~/phastCons100way.txt.gz --wib ~/phastCons100way.wib -r "chr2:1-125168903" --wig | head

variableStep chrom=chr2 span=1 11392 0.14969291 11393 0.14667717 11394 0.14064567 11395 0.13461417 11396 0.12858267 11397 0.13461417 11398 0.14366141 11399 0.14969291 11400 0.1557244 ```