jvarkit

CytobandToSvg

Creates a svg karyotype .

Usage

Usage: cytoband2svg [options] Files
  Options:
    -C, --cytobands
      Cytoband URI. tab delimited file. no header. 
      chrom/chromStart/chromEnd/name/gieStain. '-'=stdin
      Default: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz
    -H, --height
      Image height
      Default: 700
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
    -t, --title
      title
      Default: <empty string>
    --version
      print version and exit
    -W, -width, --width
      Image width
      Default: 1000

Keywords

• karyotype
• svg
• ideogram

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 cytoband2svg

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/misc/CytobandToSvg.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/misc/CytobandToSvgTest.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 cytoband2svg ? 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

Input

input is a tab delimited file similar to http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz

no header

columns are

• chrom
• chromStart
• chromEnd
• name
• gieStain

Chromosomes will be ordered occording to the first time they’re seen in the file, so you’d better sort them.

$ wget -O - "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz" |\
	gunzip -c |\
	sort -t $'\t' -k1,1V -k2,2n > cytoBand.txt

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