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

java compiler SDK 11. Please check that this java is in the ${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )

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

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 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

141535	143008	taiwan
564463	570304	china
564463	570304	china
564463	564813	canada
564510	569779	estonia
564510	569779	estonia
564510	569170	germany
564633	569139	italy
564660	565200	iran
564733	569130	brazil
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