bioSyntax TODO

[ababaian]

Open TODO list

A collection of tasks to improve bioSyntax. Feel free to tackle any of these if you'd like to pitch in. If there's no name/ID beside a task, it's open 👍 If there's a name, find that person and ask how to help.

Also any issue labeled with a green help tag is a great place to start collaborating.

Features

• 1) Add Atomic Coloring. JMol / CPK coloring to atoms/elements when they appear in a file-format (PDB).

• 2) Set-up Vim / Sublime / Gedit to only use bioSyntax theme when a bioSyntax format is being used; otherwise use the default or preset theme. Sublime Example.
  See: Issue 7: Sublime Auto-detect [Artem / Alyssa]

• 4) Optimize the Regex Engine for VCF -gedit -sublime -vim(?) to account for catastrophic backtracking. (See vcf-less for a fixed example) Optimize Regex Engine for VCF #36

• 5) Secondary Color Gradient: In BED/WIG files where there can be a score, have one color scheme (like we have) for 0-1000 range. Have a second color gradient (orange?) which recognizes 0.0 - 1.00 (decimal scale). This will support two widely used data-ranges then 0-1 and 0-1000.

• 6) Make 'Infographics' for complex file-types (SAM, VCF, GTF) to help users learn and intepret the file formats. Include things such as PHRED numeric scale, FLAG conversion bits, what each field is etc... Use bioSyntax theme colours as a teaching tool here. Develop built-in help manuals for existing packages #25

• 7) Website / Science art. A fun part of this project has been exploring the design and art side of computational biology. If you've got some artistic talent then there's a bunch of small/large little art projects to spruce the place up, just hit us up.

• 8) For Clustal format (.clustal / .aln), create secondary language definition files for amino-acid based alignments. Currently only nt-sequences are supported.

• 10) Develop either a Rainbow Parentheses or Rainbow Levels script to work with Newick tree format. This will also be used for Nexus files. Develop Rainbow Parentheses/Rainbow Levels Script for Newick Trees #37

• 11) Recruit / find interested non-biology scientists to compile / spearhead what file formats should be developed for the other computational sciences (physics / chemistry / psychology etc...)

• 13) Use less / source-highlight local preferences. When /usr/bin/source-highlight is run, it checks the folder it is run out of for compatible .lang files. To circumvent the need to sudo cp the bioSyntax files we can initialize a local folder ~/.source-highlight/ to which we point the alias scripts and store bioSyntax files in here. While installing source-highlight will require sudo; installing the bioSyntax won't. Check if this is feasible and implement on a branch. Perhaps switch to highlight? Note: This is done for linux installations, not done for mac installs.

• 14) Port for Nano / Pico. [Anicet]

• 15) Found a cool little script on wikipedia for converting PHRED to bars. Can be incorporated into fastq-less script. Sadly not super applicable in other formats at the moment. --> Could exploit the conceal<-->cchar relationship to redraw PHRED scores in vim syntax.

sed -e 'n;n;n;y/!"#$%&'\''()*+,-.\/0123456789:;<=>?@ABCDEFGHIJKL/▁▁▁▁▁▁▁▁▂▂▂▂▂▃▃▃▃▃▄▄▄▄▄▅▅▅▅▅▆▆▆▆▆▇▇▇▇▇██████/' myfile.fastq 

• 16) vim-less. Adapt the built-in less pager in vim for adding syntax highlighting as a non-source-highlight alternative. Add an alias and vimscripts to allow for piping data as well; equals to the sam-less and vcf-less... alias in less. See biostars thread

• 17) Develop a good framework for .Nexus file syntax highlighting. I contacted the original author and we can use http://www.vim.org/scripts/script.php?script_id=964 as a starting point. See what more/less we would like to add. Expand bioSyntax to other (non-biological) file formats #27

• 21) Where possible (?: Vim / Sublime / Less / Gedit), add code-folding for NNNNNNNNN lines in fasta files. (i.e. the start/end of chromosomes in genome files)

• 22) Add .fna file extension to all fasta file extension recognitions. This specifically defines nucleic acid sequences in contrast to the .faa amino acid sequence files Expand bioSyntax to other (non-biological) file formats #27

• 23) Add .gff file extension to all GTF file extension recognitions. This is a more generalized format used by NCBI. Spec File to confirm above statement Expand bioSyntax to other (non-biological) file formats #27

• 24) Create a wikipedia page for bioSyntax and link that page on other appropriate wiki page like Alignment Visualization Software and such.

• 25) Complete CWL language syntax for gedit and less. Expand bioSyntax to other (non-biological) file formats #27

• 27) Create panel of syntax highlighting definitions for ImageJ scripting language. Expand bioSyntax to other (non-biological) file formats #27

• 28) Port bioSyntax to Notepad++ / BBEdit / TextWrangler

New File Formats Definitions for bioSyntax

• See: File Format Matrix
• For 17, 22, 23, 25, 27 - See: Expand bioSyntax to other (non-biological) file formats #27

[ababaian]

Completed Tasks

• 3) Re-write the bed-gedit syntax to use 'Robust Column Selection' [Jeff]

• 9) For genomic coordinates; use 2-color shading to distinguish numeric triplets instead of inserting commas. For, chr13 1,000,123 , color 1 and 000 and 123 differently. Issue [Artem]

• 12) sam-less. In the sequence section, if the chromosome/contig contains "-" characters, it throws off the column index. Fix regex selection. [ Artem TALL].

• 18) Add infrastrucure for User-submitted syntax files and what is necessary for submission. Add supporting text to website on dev page. [Artem]. See Issue [ Artem]

• 18-2) fq-vim: allow for N sequence in read.

• 19) Modify gtf-gedit syntax file to Robust Column Selection [@lazypanda10117]

• 20) Create a global release link which is static and all other release URLs can point to. That way this one link can be updated with new releases and everything else updates automatically. (https://www.bioSyntax.org/release)

• 27) Add documentation for how default installation will change standard calling of less (less -NS)

Installer beta3 updates:

• For less: inform user and prompt (Y/N) for software updates and adding alias commands
• Remove all sudo commands which are not absolutely necessary. (Vim installs should be sudo-free).
• On website, include an uninstall instructions. (i.e. delete these files)
• Check sublime install paths in the install script. See: commit