STRNaming STR Sequence Nomenclature
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.
STRNaming requires Python version 3.5 or later.
The recommended way to install STRNaming is by using the
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
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).
The command-line help can be accessed by running
strnaming --help. In short,
an STRNaming command looks like this:
strnaming name-sequences --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.
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
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.
STRNaming will automatically download and cache portions of reference sequence from the Ensembl REST API (http://rest.ensembl.org). If you are running STRNaming on a system without internet access, and you need a piece of reference sequence that was not bundled with the STRNaming package, a message will be displayed to manually store the reference sequence in a specific location. To this end, run the following command (on a system with internet access) to download the sequence:
strnaming refseq-cache chr2:1489653..1489689
Upon success, the location of the downloaded cache files will be displayed. These are the files to be copied to the offline system for STRNaming to work.
Version 1.1.4 (7 February 2023)
- Repeat stretches that fall completely in the prefix or suffix are now ignored.
- Sequences that follow the same repeat pattern as the reference sequence are now named much more quickly while consistently using the same structure.
- Added capability to load reference structures from many locations on one chromosome in a single pass.
Version 1.1.3 (18 August 2022)
- Fixed an issue that caused STRNaming to sometimes favour a longer name with the same score.
Version 1.1.2 (10 May 2022)
- Updated CE allele numbering of DYS612 (+6 units).
- Added reference structure for SE33.
- Updated hardcoded reference length adjustment table to suppress second structure 5' of DYS522.
- Added double-click-to-toggle-text-alignment feature to HTML output.
- Fixed mtDNA reference sequence download URL.
Version 1.1.1 (19 July 2021)
- Fixed an issue with CE allele numbering that occurred for reporting ranges that started or ended halfway into a structure with a hardcoded reference length adjustment.
- Updated table of hardcoded reference length adjustments to include more loci.
Version 1.1.0 (15 July 2021)
Naming of some loci has been updated as a result of bug fixes and improvements to the algorithm. Scoring criteria have been updated to minimize unintended side-effects of these changes.
- Fixed a major issue with HPRTB allele numbering: previously, the CE allele number calculated for a given sequence was one higher than it should be.
- Allele names are now permitted to contain repeats of a unit that exceeds the dominant unit length of a locus. This change greatly improves naming of some complex Y-STRs.
- Short repeat stretches that only partially overlap with a significant repeat of a longer unit are no longer discarded. This change may introduce short repeats adjacent to longer repeats of a longer unit, which were previously 'missed' by STRNaming.
- Fixed bug that disallowed making interruptions which could be filled exactly with an 'orphan' repeat, thereby forcing the use of a compatible 'anchor'.
- Reference sequence analysis now guarantees that all repeat units in the final result are actually repeated.
- Reference repeat units only found outside the reported range are now included in the list of preferred units when generating allele names. This change improves naming stability when a significant part of the reference STR structure lies outside the reported range.
- STRNaming will no longer consider names that include an interruption of which the sequence is equal to an adjacent repeat unit (e.g., CCTACCTATCTA).
- The built-in reference sequence cache was introduced, along with the new mandatory ACTION command-line argument.
- Colored output in HTML format is now available by using the --html command-line argument.
- Reference sequence analysis results of almost the entire human genome have been embedded into the package.
Version 1.0.0 (21 December 2020)
Initial release of STRNaming.
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