Initial commit!

.coveragerc

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+[report]
+show_missing = True
+omit =
+    claspy/_version.py
+
+[run]
+branch = True

.github/workflows/cibuild.yml

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+name: CI Build
+
+on: [push]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 4
+      matrix:
+        python-version: ["3.10", "3.11"]
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install
+      run: |
+        python -m pip install --upgrade pip
+        pip install .
+        claspy_db --dest=/home/runner/work/claspy/claspy/claspy/cellosaurus.json
+    - name: Test with pytest
+      run: make test
+    - name: Style check
+      run: make style

.gitignore

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+.vscode/
+__pycache__/
+.coverage
+sandbox/
+claspy.egg-info/
+claspy/cellosaurus.txt
+claspy/cellosaurus.json
+.DS_Store

.pylintrc

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+good-names=fh,db

CHANGELOG.md

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+# Change Log
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+
+## Unreleased
+
+### Changed
+- Improvements to loading profile and database objects (!9)
+- Database search is now restricted based on species inferred from markers in the query profile, not by user-specified species (!8)
+- Summary report is displayed in terminal, full report to a CSV file (!11, !12)
+
+### Fixed
+- Added names of additional valid markers present in ForenSeq but not in Cellosaurus; includes four autosomal, seven X chromosome, and 21 Y chromosome STR markers (!8)
+- Rank order of results with the same score but different numbers of shared alleles (!10)
+
+
+## [0.0.2] 2023-05-25
+
+### Fixed
+- Divide by zero bug when query and reference have no shared alleles (!6)
+- Marker name validation and standardization for human, mouse, and dog (!6)
+- Rank order of results with the same score but different numbers of shared alleles (!6)
+- Handling of string alleles, e.g. X and Y for Amelogenin (!7)
+- Smart natural (not lexicographical) sorting of alleles for display (!7)
+
+
+## [0.0.1] 2023-05-22
+
+Initial release! Includes:
+
+- `claspy_db` for downloading and formatting the Cellosaurus database
+- `claspy` for searching a profile against Cellosaurus and reporting the best results

LICENSE

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+Copyright (c) 2023, DHS; all rights reserved.
+
+This Software was prepared for the Department of Homeland Security
+(DHS) by the Battelle National Biodefense Institute, LLC (BNBI) as
+part of contract HSHQDC-15-C-00064 to manage and operate the National
+Biodefense Analysis and Countermeasures Center (NBACC), a Federally
+Funded Research and Development Center.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+1. Redistributions of source code must retain the above copyright
+notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright
+notice, this list of conditions and the following disclaimer in the
+documentation and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+contributors may be used to endorse or promote products derived from
+this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

MANIFEST.in

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+recursive-include claspy/tests/data/ *

Makefile

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+## #===== development tasks =====#
+
+## help:        print this help message and exit
+help: Makefile
+	@sed -n 's/^## //p' Makefile
+
+## test:        run automated test suite
+test:
+	pytest --cov=claspy claspy
+
+## format:      autoformat Python and Snakemake code
+format:
+	black --line-length=99 setup.py claspy/*.py claspy/tests/*.py
+
+## style:       check code style
+style:
+	black --line-length=99 --check setup.py claspy/*.py claspy/tests/*.py
+
+## hooks:       deploy git pre-commit hooks for development
+hooks:
+	echo "set -eo pipefail" > .git/hooks/pre-commit
+	echo "make style" >> .git/hooks/pre-commit
+	chmod 755 .git/hooks/pre-commit

README.md

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+# Claspy: cell line authentication with STRs in Python
+
+Documentation for Claspy is pending.
+In the mean time, see the following hints.
+
+```
+claspy_db  # Run one time to install Cellosaurus database
+claspy query.csv  # Run to find closest profile to the query in the database
+```
+
+STR profiles should be in tabular/CSV format and look something like this.
+
+```csv
+Sample,Marker,Allele1,Allele2
+sample1,CSF1PO,12,13
+sample1,D13S317,12,
+sample1,D16S539,9,11
+sample1,D18S51,12,15
+sample1,D19S433,13,15
+sample1,D21S11,29,32.2
+sample1,D2S1338,20,23
+sample1,D3S1358,16,17
+sample1,D5S818,10,11
+sample1,D7S820,10,11
+sample1,D8S1179,13,15
+sample1,FGA,18,24
+sample1,Penta D,9,
+sample1,Penta E,17,
+sample1,TH01,9,9.3
+sample1,TPOX,8,
+sample1,vWA,18,19
+```

claspy/__init__.py

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+# -------------------------------------------------------------------------------------------------
+# Copyright (c) 2023, DHS.
+# This file is part of claspy: https://github.com/bioforensics/claspy
+#
+# This software was prepared for the Department of Homeland Security (DHS) by the Battelle National
+# Biodefense Institute, LLC (BNBI) as part of contract HSHQDC-15-C-00064 to manage and operate the
+# National Biodefense Analysis and Countermeasures Center (NBACC), a Federally Funded Research and
+# Development Center.
+# -------------------------------------------------------------------------------------------------
+
+from .markers import validate_names
+from .str_profile import Profile
+from . import db
+from .cli import main, db_main
+from ._version import get_versions
+
+__version__ = get_versions()["version"]
+del get_versions