dnacol and pcol

Color DNA/RNA bases, protein amino acid codes and quality scores in terminal output

About

This is a python script to color DNA, RNA and protein sequences in the terminal. If called using dnacol, it will read lines from STDIN or from a file and color all strings of DNA/RNA it can find. In addition, it can also color phred-encoded quality scores in FASTQ/SAM files. If called using pcol, it will instead color protein sequences encoded as amino acid one-letter codes.

Screenshots

.. image:: https://raw.githubusercontent.com/koelling/dnacol/master/screenshots_v0.4.png

Format-specific coloring

By default, dnacol will find and color all strings of one or more DNA/RNA letters and pcol will color all strings of the twenty standard amino acid letters. However, they will also recognize a few standard file formats and apply more targeting coloring. When reading a file, these formats will automatically be recognized based on their file extensions. When reading from STDIN, dnacol and pcol will try to identify the format based on the data itself (for FASTQ/SAM/VCF files). The format can also be specified using the --format option.

• SAM format (--format=sam, automatically enabled when filename ends in .sam or a line matching the SAM format is found)

  • Ignore headers, color the SEQ column as DNA and the QUAL column as quality scores

• FASTQ format (--format=fastq, automatically enabled when filename ends in .fastq or .fq or the first four lines match the FASTQ format)

  • Color the second line of every read as DNA
  • Color the fourth line of every read as quality scores

• VCF format (--format=vcf, automatically enabled when filename ends in .vcf or a VCF header line is found)

  • Ignore comments, only color the REF and ALT column

• FASTA format (--format=fasta, automatically enabled when filename ends in .fasta or .fa)

  • Ignore sequence identifiers

Colormaps

The script support different colormaps, which specify a color for each possible letter of the sequence.
These are shown in ``dnacol --help``. When called using ``dnacol``, the script will use the ``dna_brgy`` colormap by default,
while ``pcol`` will use the ``protein`` colormap. You can change the ``dnacol`` colormap using a configuration file (see below).

Options
-------

::

    -w, --wide
        wide output (add spaces around each base)
    -f FORMAT, --format FORMAT
        file format (auto|text|sam|vcf|fastq|fasta)

Configuration
-------------
You can create a configuration file in YAML format called ``/etc/dnacol`` or ``~/.dnacol`` to change the behavior of this script.
At the moment, the only setting available is the colormap to use for DNA sequences.
See see ``dnacol --help`` for examples of the colormaps that are available.

To use the ``gbyr`` instead of the ``brgy`` colormap, set the ``dna_colormap`` option like this:

::
  
  dna_colormap: gbyr

Download/Install
----------------

To install, use ``pip``::

    pip install dnacol

If the system-wide directory is not writable, you can install to your home directory with::

    pip install dnacol --user

Alternatively, you can clone this git
repository and use the provided ``setup.py`` script.

::

    git clone https://github.com/koelling/dnacol.git
    cd dnacol && python setup.py install

``dnacol`` has been tested with Python 2.7 and Python 3.5 and 3.6.

Examples
--------

::

    #read gzipped file
    dnacol examples/phix.fa.gz | head

    #pipe from stdin
    head examples/reads.txt | dnacol --wide

    #use `pcol` for protein sequences
    pcol examples/hras.fa

    #use `less -R` to display colors in less
    dnacol examples/phix.fa.gz | less -R