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markschl edited this page Aug 15, 2018 · 4 revisions

View biological sequences, coloured by base / amino acid, or by sequence quality. The output is automatically forwarded to the 'less' pager on UNIX.

Usage:
    st view [options] [<input>...]
    st view (-h | --help)

General command options:
    -n, --num-seqs <N>  Number of sequences to select
    -i, --id-len <N>    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.
    -f, --foreground    Color base / amino acid letters instead of background.
                        If base qualities are present, background coloration
                        is shown, and the foreground scheme will be 'dna-bright'
                        (change with --dna-pal).

Pager (UNIX only):
    -n, --no-pager      Disable automatic forwarding to pager
    --pager <pager>     Pager command to use (default: less -RS).
                        This overrides the value of the $ST_PAGER env.
                        variable, if set.
    -b, --break         Break lines in pager, disabling 'horizontal scrolling'.
                        Equivalent to --pager 'less -R'

Coloring:
    --list-pal          List all palettes and exit.
    --dna-pal <pal>     Color mapping for DNA. Palette name or list of
                        <bases>:<color> (hex code or CSS/SVG color name)
                        [default: dna] (available: dna, dna-bright, dna-dark,
                        pur-pyrimid, gc-at).
    --aa-pal <palette>  Color mapping for amino acids. Palette name or list of
                        <letters>:<color> [default: rasmol] (available:
                        rasmol, polarity).
    --qscale <colors>   Color scale to use for coloring according to base
                        quality. Palette name or sequence of hex codes from
                        low to high [default: blue-red] (available: blue-red).
    --qmax <value>      Upper limit of Phred score visualization (-q)
                        [default: 41]
    --textcols <c>      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]
    -c, --truecolor     Use 16M colors, not only 256. This has to be supported
                        by the terminal. Useful if autorecognition did not work.

See this page for the options common to all commands.

Description

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). For each type, there are multiple color schemes / palettes available, which can be configured using --dna-pal and --aa-pal.

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

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