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view

View biological sequences, colored by base / amino acid, or by sequence quality

Sequences are displayed on a single line and can be navigated with up/down/left/right arrow keys and by scrolling. They are progressively read into memory while navigating down.

Color palettes can be viewed with st view -p/--list-pal and also configured (as described in this help page).

Usage: st view [OPTIONS] [INPUT]...

Options:
  -h, --help  Print help

General 'view' command options:
  -i, --id-len <CHARS>  Length of IDs in characters. Longer IDs are truncated
                        (default: 10 - 100 depending on ID length)
  -d, --show-desc       Show descriptions along IDs if there is enough space
  -b, --bold            Print the sequence in bold letters. Bold text is always
                        used with `--fg` if quality scores are present
      --fg              Color the sequence (foreground) instead of instead of
                        the background (and additionally printed in bold). The
                        background is simultaneously colored by quality scores
                        if present, unless `-Q/--no-qual` is used
  -Q, --no-qual         Ignore quality scores and color only by the sequence

Colors:
  -p, --list-pal           Show a list of all builtin palettes and exit
      --dna-pal <PAL>      Color mapping for DNA. Palette name (hex code,
                           CSS/SVG color name) or list of
                           'base1:rrggbb,base2:rrggbb,...' (builtin palettes:
                           dna, dna-bright, dna-dark, pur-pyrimid, gc-at)
                           [default: dna]
      --aa-pal <PAL>       Color mapping for amino acids. Palette name (hex
                           code, CSS/SVG color name) or list of
                           'base1:rrggbb,base2:rrggbb,...' (available: rasmol,
                           polarity) [default: rasmol]
      --qscale <PAL>       Color scale to use for coloring according to base
                           quality. Palette name (hex code, CSS/SVG color name)
                           or list of 'base1:rrggbb,base2:rrggbb,...' Palette
                           name or sequence of hex codes from low to high
                           [default: red-blue]
      --textcols <COLORS>  Text colors used with background coloring. Specify
                           as: <dark>,<bright>. Which one is used will be chosen
                           depending on the brightness of the background
                           [default: 333333,eeeeee]
  -t, --truecolor <?>      Use 16M colors, not only 256. This has to be
                           supported by the terminal. Useful if autorecognition
                           fails [possible values: true, false]
See this page for the options common to all commands.

This command allows for viewing sequences in the terminal. The output is colored if the terminal supports colors. On UNIX systems (Linux, Mac OS, ...), the sequences are directly forwarded to the less pager command, which allows for navigating up and down or in horizontal direction. On Windows, this is not done.

The first sequence line in the input is always used to determine the sequence type (DNA/RNA or Protein).

Example view of DNA sequences:

st view seqs.fasta

DNA sequence

st view H1.fasta

View of Histone H1 sequences, colored according to the RasMol scheme.

Histone H1

If quality scores are present (from FASTQ or QUAL files), the background is colored accordingly (configure with --qscale and --qmax):

st view seqs.fastq

Sequence quality

Palettes

There are multiple color schemes/palettes available, which can be configured using --dna-pal, --aa-pal and --qscale.

A visualization of the builtin palettes is obtained with st view --list-pal or st view -p:

Palettes