gl-smartsort

A tiny Python package that canonicalizes GL Strings by smart sorting:

• recursively sorts within delimiter levels in precedence: ?, ^, |, +, ~, /
• orders blocks by gene/locus (left of *)
• orders alleles numerically (not lexically) within a locus (e.g., A*01:11 before A*01:103)
• breaks ties on expression suffixes deterministically (e.g., A*01:01 before A*01:01N)
• supports the GL String 1.1 ? (possible gene locations) delimiter

As of v0.2.0, the sorting is performed by the standards-conformant glstring library (GL String 1.1 parser + AST); gl-smartsort is a thin wrapper that calls glstring.smart_sort(gl, legacy=True) to preserve the historical ordering convention. This package is a Python port of SmartSort.pm (2012-11-14).

Install (local)

From the project directory:

python -m pip install -U pip
python -m pip install -e .

Usage (Python)

from gl_smartsort import smart_sort

print(smart_sort("A*01:103+A*01:11"))
# A*01:11+A*01:103

Usage (CLI)

Sort a single GL string:

gl-smartsort "B*07:02^A*02:01"

Or sort from stdin (one per line):

cat gl.txt | gl-smartsort

Provenance

This package is a Python port of the original Perl implementation SmartSort.pm (2012-11-14), authored by Martin J. Maiers. Both the original Perl implementation and this Python port were written by the same author. As of v0.2.0 the sorting is delegated to the independently developed, standards- conformant glstring library (Apache-2.0); no third-party source code is vendored into this package.

License

Licensed under the Apache License, Version 2.0 (Apache-2.0). See the LICENSE and NOTICE files for details.

Copyright 2012 Martin J. Maiers and National Marrow Donor Program (NMDP).