jvarkit

WorldMapGenome

Last commit

Genome/Map of the world. Input is a BED file: chrom/start/end/country.

Usage

Usage: worldmapgenome [options] Files
  Options:
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --version
      print version and exit
  * -R
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard CreateSequenceDictionary
    -T
       just list countries and exit.
  * -o
       (file.jpg) ouput file. Required
    -u
       (uri) URL world SVG map.
      Default: http://upload.wikimedia.org/wikipedia/commons/7/76/World_V2.0.svg
    -w
       (int: size) square size
      Default: 1000

Keywords

Compilation

Requirements / Dependencies

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew worldmapgenome

The java jar file will be installed in the dist directory.

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/circular/WorldMapGenome.java

Contribute

License

The project is licensed under the MIT license.

Citing

Should you cite worldmapgenome ? 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

head map.bed

1	141535	143008	taiwan
1	564463	570304	china
1	564463	570304	china
1	564463	564813	canada
1	564510	569779	estonia
1	564510	569779	estonia
1	564510	569170	germany
1	564633	569139	italy
1	564660	565200	iran
1	564733	569130	brazil
1	564776	569431	mexico
$  cat map.bed |\
     java -jar dist/worldmapgenome.jar \
     -u World_V2.0.svg \
     -w 2000 -o ~/ouput.jpg \
     -R human_g1k_v37.fasta

worldmapgenome

See also