STRNaming

STRNaming is an algorithm for generating simple, informative names for Short Tandem Repeat (STR) sequences, such as those used in the field of forensic genetics, in a standardised and automated manner.

Requirements

STRNaming requires Python version 3.5 or later.

Installation

The recommended way to install STRNaming is by using the pip package installer. If you have pip installed, you can easily install STRNaming by running the following command:

pip install strnaming

Alternatively, STRNaming can be installed by running:

python setup.py install

Usage

This initial version of STRNaming allows generating allele names for sequence data using the ranges and sequence orientation of the "Flanking Region Report" of the Universal Analysis Software for the ForenSeq DNA Signature Prep Kit (Verogen).

Command-line interface

The command-line help can be accessed by running strnaming --help. In short, an STRNaming command looks like this:

strnaming --ranges uas-frr inputfile.txt outputfile.txt

The input file should have a marker name and a sequence on each line, separated by whitespace (i.e., tabs or spaces).

If no output file is given, the output is written to stdout, which normally shows up in your command line window. If no input file is given either, STRNaming will read input from stdin, allowing you to type the input one line at a time.

Programming interface

It is not recommended to import and use parts of this version of STRNaming directly from other Python code, because the internal API is not stable yet. Instead, use the subprocess module if you want to use STRNaming in your Python project at this time. As an added benefit, it will run in a concurrent process, meaning your code does not (necessarily) have to wait for STRNaming to finish.

To use STRNaming in other software projects, regardless of the programming language, it can be run as a separate subprocess. Write a marker name, a whitespace character, the DNA sequence, and a newline character (\n) to its standard input stream (stdin), and STRNaming will write the same marker name, a tab character, the allele name and a newline character to its standard output stream (stdout). Any errors are reported on the standard error stream (stderr) and will cause the STRNaming process to terminate. By specifying the --unbuffered command-line switch, STRNaming will immediately flush its output stream after every line of output.

Release Notes

Version 1.0.0 (21 december 2020)

Initial release of STRNaming.