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". Some jvarkit 
      programs also allow the following syntax : "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