dna.vim : Helps parse DNA sequences and common sequencing files (BAM, PAF, FA, etc.)
| script karma |
Rating 1/1,
Downloaded by 37 |
Comments, bugs, improvements
|
Vim wiki
|
| created by |
| Megan Le |
| |
| script type |
| syntax |
| |
| description |
Repository/screenshots: https://github.com/mktle/dna.vim
This script helps parse commonly used sequencing files (SAM/BAM/PAF/GAF/GFA/FA/FQ... or anything with a DNA sequence) through syntax highlighting and helptext.
1) A/C/G/T/U/N are colored (consistent with IGV colors for ACGT)
2) Using the commands :SAM, :BAM, :GAF, or :PAF in their respective files will tell you the description of the field your cursor is hovering over (with flag decoding for SAM/BAM flags)
3) Operation blocks within CIGAR strings are colored separately from each other
4) Using :Phred will decode the Phred score of the hovered character (e.g., using it on a D will print "D is score 35, 0.0003 probability of error")
5) Sequence names in FASTA/FASTQ files are colored
6) Tags in alignment files are colored |
| |
| install details |
| Add the script to ~/.vim/plugin/ |
| |
script versions (upload new version)
Click on the package to download.
| dna.vim |
1.1 |
2025-06-13 |
7.0 |
Megan Le |
add field helptext, flag/Phred decoding, and file-specific highlighting |
| dna.vim |
1.0 |
2025-05-30 |
7.0 |
Megan Le |
Initial upload |
ip used for rating: 18.97.14.87
|
