jvarkit

UniprotToSvg

plot uniprot to SVG

Usage

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

Usage: java -jar dist/jvarkit.jar uniprot2svg  [options] Files

Usage: uniprot2svg [options] Files
  Options:
    --exclude-type
      Exclude feature/@type matching that regular expression
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --include-type
      Only feature/@type matching that regular expression
  * -o, --output
      An existing directory or a filename ending with the '.zip' or '.tar' or 
      '.tar.gz' suffix.
    --pedigree
      A pedigree file. tab delimited. Columns: family,id,father,mother, 
      sex:(0|.|undefined|unknown:unknown;1|male|M:male;2|female|F:female), 
      phenotype 
      (-9|?|.:unknown;1|affected|case:affected;0|unaffected|control:unaffected) 
    --svg
      produce SVG only (default is HTML+SVG)
      Default: false
    --vcf
      annotated VCF. Whole file is loaded in memory, so you'd better use a 
      small vcf restricted to your proteins.
    --version
      print version and exit

Keywords

• uniprot
• svg

Creation Date

20220608

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/uniprot/UniprotToSvg.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 uniprot2svg ? 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

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