bioView

A configurable and easy install command line tool for the readability enhancement of bioinformatic file format: fasta, fastq and sam file.

Installation

This tools is writen in Nim, it can be compiled to a single excutable file. So, it is very easy to install, just download the released excutable file, and add it to your PATH.

Shell configuration

For ease of use, you can append the configuration to your shell config file.

• For Bash shell: bash config
• For Fish shell: fish config

Usage

Usage:
  bioview fq <file> [--config-file=<config_file>] [--hist=<yes/no>] [--color=<yes/no>] [--phred=<33/64>] [--delimiter=<yes/no>]
  bioview fa <file> [--config-file=<config_file>] [--color=<yes/no>] [--type=<dna/rna/protein>]
  bioview sam <file> [--config-file=<config_file>] [--hist=<yes/no>] [--color=<yes/no>] [--phred=<33/64>] [--multiline=<yes/no>]
  bioview color-atla
  bioview example-config
  bioview (-h | --help)

Example:

View fastq file:

$ bioview fq example.fq | less -rS

View fasta file:

$ bioview fa example_dna.fa | less -rS

View fasta file(protein record):

$ bioview fa example_protein.fa | less -rS

View sam file:

$ bioview sam example_sam.sam | less -rS

View sam file(multiline format):

$ bioview sam example_sam.sam --multiline | less -rS

Use '-' to read from stdin:

$ samtools view -h example.bam | bioview sam - | less -rS

bio-less

Use the bio-less function defined in the shell configuration, it let you use bioView more conveniently.

Usage:
  bio-less <*.fq/*.fa/*.sam/*.bam>
  fq-less <*.fq>
  fa-less <*.fa>
  sam-less <*.sam>

For example:

$ bio-less example.fq

This is equal to: bioview fq example.fq | less -rS

$ fq-less example.fq # equal to `bioview fq example.fq | less -rS`
$ samtools view -h example.bam | sam-less - # equal to `samtools view -h example.bam | bioview sam - | less -rS`

Theme

Provide different themes you can choise.

simple (default)

verbose

emoji

see more.

Make your own theme

You can make your own theme through the config file.

Just generate the config templete, and edit it:

$ mkdir -p ~/.config/bioview/config.json
$ bioview example-config > ~/.config/bioview/config.json
$ vim ~/.config/bioview/config.json

Color

The color fields used to specify the color of related item, for example the base color denote the color of base(ATCG), and the fq_config::hist::color denote the color of histogram in the fastq view. The fg and bg field means the color code of the forground color and the background color. You can query the color code through the command:

$ bioview color-atla

It will list all supported forground color and background color. like:

And use the code -1 denote the "non-color".

Histogram

The fq_config::hist and sam_config::hist fields used to specify the color and symbols of the histogram.

default histogram symbols:

▁▁▁▁▁▁▁▁▂▂▂▂▂▃▃▃▃▃▄▄▄▄▄▅▅▅▅▅▆▆▆▆▆▇▇▇▇▇██████

You can also use other symbols, like the emoji:

👿👿👿👿👿😫😫😫😫😫🙁🙁🙁🙁🙁😣😣😣😣😣🙃🙃🙃🙃🙃😑😑😑😑😑🙂🙂🙂🙂🙂😃😃😃😃😃

For align histogram with the base correctly, you should specify the hist::align field.

Development

This project is written by Nim, and tested under unix-like system environment. You need install Nim firstly.

Compile the code

Compilation:

$ git clone https://github.com/Nanguage/bioView.git
$ cd bioView
$ mkdir bin
$ nim c -d:release -o:./bin/bioview src/main.nim

Unit test:

$ ./test.sh # test all moudles
$ ./test.sh fastq_utils # test the fastq_utils.nim moudle

TODO

• upport other file format:
  • GTF/GFF
  • PDB
  • VCF
  • BED/BedGraph/BEDPE
• Fix the color show bug with less.