Metadata-Version: 2.1
Name: strnaming
Version: 1.0.0
Summary: STRNaming STR Sequence Nomenclature
Home-page: https://github.com/Jerrythafast/strnaming
Author: Jerry Hoogenboom
Author-email: jerryhoogenboom@outlook.com
License: LGPLv3+
Description: 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.
        
Keywords: bioinformatics forensics NGS MPS DNA sequencing STR nomenclature
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+)
Classifier: Operating System :: OS Independent
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Legal Industry
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3
Description-Content-Type: text/markdown
