jvarkit

CytobandToSvg

Last commit

Creates a svg karyotype .

Usage

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

Usage: java -jar dist/jvarkit.jar cytoband2svg  [options] Files

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/hg38/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

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

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

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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