jvarkit

Biostar336589

displays circular map as SVG from BED and REF file

Usage

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

Usage: java -jar dist/jvarkit.jar biostar336589  [options] Files

Usage: biostar336589 [options] Files
  Options:
    -css, --css
      custom svg css file
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -hist, --histogram
      histogram mode: score of each bed item must be defined. Items must not 
      overlap 
      Default: false
    -u, --url, --hyperlink
      creates a hyperlink when a area is clicked. creates a hyperlink when 
      'click' in an area. The URL must contains __CHROM__, __START__ and 
      __END__ that will be replaced by their values. Predefined values are 
      'hg19','hg38','igv'. IGV : 
      "http://localhost:60151/goto?locus=__CHROM__%3A__START__-__END__" , 
      UCSC: "http://genome.ucsc.edu/cgi-bin/hgTracks?org=Human&db=hg19&position=__CHROM__%3A__START__-__END__"
      Default: <empty string>
    -o, --out
      Output file. Optional . Default: stdout
    --score-end-color
      When coloring with bed/score this is the color end.  A named color 
      ('red', 'blue'...) use the syntax 'rgb(int,int,int)'.
      Default: black
    --score-start-color
      When coloring with bed/score this is the color start.  A named color 
      ('red', 'blue'...) use the syntax 'rgb(int,int,int)'.
      Default: white
    --title
      document title
      Default: Biostar336589
    --version
      print version and exit
    --width
      Linear SVG size. When defined, this option switches to a 
      linear(!=circular) view
      Default: -1
  * -R
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard/gatk CreateSequenceDictionary or samtools dict
    -a
      rotate for 'x' seconds. ignore if <=0
      Default: -1
    -as
      arrow size
      Default: 10.0
    -ch
      contig height
      Default: 10.0
    -da
      distance between arcs
      Default: 10.0
    -fh
      arc height
      Default: 10.0
    -md
      min distance in bp between two features on the same arc.
      Default: 100
    -mr
      min internal radius
      Default: 100.0
    -ms
      skip chromosome reference length lower than this value. ignore if <=0
      Default: -1

Keywords

• genome
• browser
• circular
• bed
• svg

See also in Biostars

• https://www.biostars.org/p/336589
• https://www.biostars.org/p/367522

Creation Date

20180907

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/biostar/Biostar336589.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/biostar/Biostar336589Test.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 biostar336589 ? 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 BED file (file or stdin). https://genome.ucsc.edu/FAQ/FAQformat.html#format1

• column 1: chrom
• column 2: start (you’ll get faster results if the input is sorted on chrom/start )
• column 3: end
• column 4 is the name of the feature
• column 5 is the score [0-1000] or ‘.’
• column 6 strand +/-
• column 7 ignored
• column 8 ignored
• column 9 is ‘.’ or R,G,B (as in the bed specification) or it’s treated as a full svg:style (e.g: fill:red;stroke:blue; )

multiple bed files are splitted into ‘tracks’.

Example

https://gist.github.com/lindenb/b6debad569dcb5112e76da893d68dd81

$ wget -O - -q  "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/gap.txt.gz" |\
	gunzip -c | awk '{printf("%s\t%s\t%s\t%s\t%d\t+\t.\t.\t%s\n",$2,$3,$4,$8,rand()*1000,NR%20==0?"255,0,250":".");}' |\
	java -jar dist/biostar336589.jar -R src/test/resources/human_b37.dict   --url 'http://genome.ucsc.edu/cgi-bin/hgTracks?org=Human&db=hg19&position=__CHROM__%3A__START__-__END__' --title gaps -mr 300 -fh 20 > ~/jeter.svg 

$ wget -O - "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz" |\
	gunzip -c | cut -f 3,5,6 |\
	sort -t $'\t' -k1,1V -k2,2n |\
	bedtools merge |\
	java -jar dist/biostar336589.jar -md 10000 \
	 	-R src/test/resources/human_b37.dict > out.svg

https://gist.github.com/lindenb/5250750014441cc36586dd1f47ed0e37

Example

cat src/test/resources/rotavirus_rf.fa.fai  | awk '{if(NR==1) srand(); printf("%s\t0\t%s\t%s\t%d\t%s\n",$1,$2,$1,rand()*1000,rand()<0.5?rand()<0.5?".":"+":"-");}'   > tmp1.bed
cat src/test/resources/rotavirus_rf.fa.fai  | awk '{if(NR==1) srand(); printf("%s\t0\t%s\t%s\t%d\t%s\n",$1,$2,$1,rand()*1000,rand()<0.5?rand()<0.5?".":"+":"-");}'   > tmp2.bed
cat src/test/resources/rotavirus_rf.fa.fai  | awk '{if(NR==1) srand(); printf("%s\t0\t%s\t%s\t%d\t%s\n",$1,$2,$1,rand()*1000,rand()<0.5?rand()<0.5?".":"+":"-");}'   > tmp3.bed


java -jar dist/biostar336589.jar -R src/test/resources/rotavirus_rf.fa -a 60   tmp1.bed tmp2.bed tmp3.bed > out.svg

https://gist.github.com/lindenb/7fd1fa1d3dedcfe38e009387d9f8579c

Screenshot

https://twitter.com/yokofakun/status/1038060108373286912

https://twitter.com/yokofakun/status/1039054467889590272

This site is open source. Improve this page.