Developing bioSyntax

"HAPPINESS ONLY REAL WHEN SHARED" -C. McCandless

Community Charter

bioSyntax is a community project for scientific syntax highlighting. We encourage you to explore, change and customize it to suit your needs. This page is a collection of resources to help you start that journey. Once you create something helpful, chances are others will find it helpful too, so share it here :)

Like many Open Source projects, we’re volunteers with a common goal. We encourage new and creative solutions but require respectiful and professional conduct with one another. If you have any concerns or issues arise, let us know info{AT}bioSyntax.org or contact any of the core devs.

Like in life; The Fundamental Theorem of Natural Selection applies to Open Source software.

  1. Community Charter
  2. bioSyntax Development Guidelines
    1. Design Principles
    2. Developing syntax-highlighting for <$file-format>
    3. Porting bioSyntax to <$software>
    4. Creating a custom color-theme
    5. Alternative / User Definitions
      1. Submitting an Alternative Language Definition
    6. Other ways to Collaborate
  3. Useful Resources
    1. Regular Expressions
    2. File Specification Files
  4. Syntax Development for less
    1. Resources
    2. Development
  5. Development for vim
    1. Resources
    2. Development
  6. Development for gedit
    1. Resources
    2. Development
  7. Development for sublime
    1. Resources
    2. Development

bioSyntax Development Guidelines

Design Principles

  1. KISS: Keep it simple & sweet.

  2. Grok your data. Syntax highlighting increases legibility, that is the ease with which characters are read. Great syntax highlighting (in science) also reveals the content of the data with a glance. To understand what information is important, you should understand the data structure and how its being applied/used by scientists (opposed to machine parsing). The most valuble asset here is real-life experience working with a file type.

  3. Make it portable. Scientific computing is messy and often not standardized. The syntax you develop may work for your use-cases but not be widely portable. A few steps from the beginning can help you define syntax broadly and accurately.

    • Find and carefully read the Format Specification for you file-type (i.e. SAM Spec). This is your primary guide for what is and is not appropriate within a file-type.
    • Find multiple example files in the central databases (NCBI SRA, EMBL-EBI, RCSB, …).
    • Find multiple example files used by large consortiums or teams (ENCODE, 1000 Genomes Project, RefSeq, …)
    • Find multiple example files output from common software packages (GATK, CLUSTAL, UCSC Genome Browser, Galaxy, …)

Developing syntax-highlighting for <$file-format>

If you work with a scientific file-format and would like to add syntax-highlighting to it, we’d like to help you develop it.

  1. Fork the bioSyntax repository.
  2. Search bioSyntax Issues for the file-format you’re interested in.
    • If it exists; Help develop it.
    • If it doesn’t exist; start an issue for that format. a) Title:”FORMAT DEVELOPMENT: <$file-format>” b) Include a ‘File Specification Definition’ c) Find and include 3-4 example data files (<100 kb) for testing d) In words, write out a ‘sketch’ of how you would like the syntax highlighting to function
  3. Read other examples of syntax-definition files to learn how it functions.
  4. Develop the syntax definition file for your format.
  5. Ideally, once your familiar with the file format and it’s definitions you’ll be able to quickly port it (vim, less, gedit and sublime).
  6. Once you’re happy with the results and it’s working, submit it to the main bioSyntax repository by placing a “pull request”. We’ll review the code and add it to the next release.

Porting bioSyntax to <$software>

The choice of text-editors we included is based on our own use. To port bioSyntax to another program or interface:

  1. Fork the bioSyntax repository.
  2. Search bioSyntax Issues for the software port you’re interested in.
    • If it exists; Help develop.
    • If it doesn’t exist; start an issue for that port. a) Title:”PORT: <$software>” b) Find out and link resources on how syntax-highlighting files are set up for that program c) Write syntax definition files for the bioSyntax core file-types
  3. Once you’re happy with the results and it’s working, submit it to the main bioSyntax repository by placing a “pull request”. We’ll review the code and add it to the next release.

Creating a custom color-theme

If you’re particular about how you want everything to look. Feel free to tweak the theme files. If you develop a theme you think is exceptionally good then we’d be happy to see it. Follow the steps for developing a file format and put in a pull request to add it to bioSyntax.

Alternative / User Definitions

See Also: Alternative Syntax List

To account for the variety of use-cases, there is a collection of alternative syntax highlighting definitions in $bioSyntax/alt-syntax/. These are not installed by default but can replace the respective bioSyntax langauge defintion files.

Submitting an Alternative Language Definition

If you made something useful, chances are others will want to use it too. To add it to bioSyntax:

  1. There’s a quick referene to get you started (this page) and/or open up an issue to discuss your idea.

  2. Develop the language definition file to your satisfaction. Make sure to test it with your own data as well as the $bioSyntax/examples/ toy data.

  3. Fork bioSyntax and add your file to $bioSyntax/alt-syntax/<Program>_<File_type>-<ID>.[lang|vim]

     # An example for fasta files for vim which finds an ORF and highlights it
     alt-syntax/vim_fasta-ORF.vim
    
  4. Commit your changes and submit a Pull request to add your changes to bioSyntax. In the pull-request form please include:

    • The name/ID of your syntax(es) and for which program(s) it’s for.
    • A short (<50 word) description of what it does that’s unique.
    • A screenshot of the syntax in action.

Other ways to Collaborate

If you like bioSyntax and would like to help out in other ways, check the bioSyntax Issues to see if you can help solve an open problem. Problems tagged help are often a good place to start with.

Looking for a side-project to work on? Take on one of the projects from the bioSyntax TODO.

Useful Resources

Regular Expressions

File Specification Files

Syntax Development for less

Syntax highlighting in less is non-standard. We use the source-highlight package to accomplish this.

Resources

Development

  1. Language Definition files are stored in $SOURCE_HIGHLIGHT_PATH/<language>.lang
  2. Every <language>.lang file has an associated <language>.style file which assigns the regex variable in .lang to color variables in .outlang.
  3. The main color-theme files are either; biosyntax.outlang or biosyntax-vcf.outlang. This is the only place where colors are set.
  4. Automatic file-extension recognition for less is performed by the $BIOSYNTAX/less/src-hilite-lesspipe.sh script. You’ll have to add explicit support for a new format.

     *.fasta|*.fa|*.mfa)
     source-highlight -f esc --lang-def=fasta.lang --outlang-def=bioSyntax.outlang --style-file=fasta.style -i "$source" ;;
    
  5. To add pipe-capability in less; alias are defined in the users .bashrc or .zshrc. All bioSyntax aliases can be found in the $BIOSYNTAX/less/rc_append.txt file.

     alias fa-less='source-highlight -f esc --lang-def=fasta.lang --outlang-def=bioSyntax.outlang --style-file=fasta.style | less'
    
  • To maximize compatibility; please limit color use to Xterm 8-bit (256 colors)
  • There is currently a 17-color limit in source-highlight as imposed in colors.h.

Development for vim

vim natively supports syntax highlighting.

Resources

Development

  1. Language Definition files are stored in <language>.vim in your vim-syntax folder.
    • Linux/MacOS: ~/.vim/syntax/ folder
    • Windows: $HOME/vimfiles/syntax/<language>.vim
  2. Ensure Syntax Highlighting is enabled: add syntax enable to your ~/.vimrc file.
  3. To make vim recognize a file-extension, a <language>.vim (the same name as your syntax file) should be placed in ~/.vim/ftdetect/ folder (win:$HOME/vimfiles/ftdetect). This file contains a single line to set the filetype on buffer read.

     au BufRead,BufNewFile *.stc set filetype=<language>
    
  4. bioSyntax uses a custom theme file which is stored in ~/.vim/colors/bioSyntax.vim. All Language Definition files must refer or link to colour-variables defined in this theme file.

     # 'ntA' is defined in ~/.vim/colors/bioSyntax.vim
     syntax match ntA "[Aa]"
    
     # To assign 'ntT' colours to a new variable 'ntI',
     # Define the match then
     syntax match ntI "[Ii]"
    
     # Link the new variable to the pre-defined color variable
     highlight link ntI ntT
    
    

Development for gedit

gedit supports syntax highlighting through the gtksourceview library.

Resources

Development

  1. Any Language Definition file for gedit <language>.lang should be placed in the gtksourceview language folder
    • Linux: /usr/share/gtksourceview-3.0/language-specs/<language>.lang
  2. The bioSyntax theme file bioSyntax.xml is in the gtksoureview style folder
    • Linux: /usr/share/gtksourceview-3.0/styles/bioSyntax.xml
  3. In the header for bioSyntax.xml, it will import the parent style kate.xml. This can be modified.

Development for sublime

sublime has native support for syntax highlighting.

Resources

Development

  1. To start an example file for a new format: in Sublime > Tools > Developer > New Syntax. The extension of this file should be <language>.sublime-syntax.
  2. The <language>.sublime-syntax file cannot contain any Tabs; everything is space-indented.
  3. The <language>.sublime-syntax file should be placed in:
    • Linux: ~/.config/sublime-text-3/Packages/User
    • Windows: %APPDATA%/Roaming/Sublime Text 3/Packages/
    • Mac: ~/Library/Application Support/Sublime Text 3/Packages/User/
  4. The language definiton file refers to color definitions as scopes, which are defined in a theme file, Color Scheme - bioSyntax.sublime-package in
    • Linux: /opt/sublime_text/Packages/
    • Windows: C:/Program Files/Sublime Text 3/Packages/
    • Mac: /Applications/Sublime Text.app/Contents/MacOS/Packages/

drawHelix.sh