dnacol 0.3.2

Display FASTA/FASTQ/SAM/VCF files with colored DNA/RNA bases and quality scores in the terminal

Color DNA/RNA bases and quality scores in terminal output

About

This is a python script to color DNA or RNA sequences in the terminal. 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.

Format-specific coloring

By default, dnacol will color all strings of [ACGTUN]+. However, it 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 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

Options

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

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 3.6.

Examples

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

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

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

Screenshots