dnacol 0.3.1

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

Tested with Python 2.7 and Python 3.6. To install, clone this git repository and use the provided setup.py script. When installed correctly, dnacol will simply be available as dnacol in the command line.

#download
git clone https://github.com/koelling/dnacol.git

#install
cd dnacol && python setup.py install

#or: install to home directory (if system-wide directory is not writable)
cd dnacol && python setup.py install --user

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