Self-vs-self sim-error values of 1 rather than 0

[peterjc]

Summary:

pyani 0.2 would have zero on the sim-error matrix diagonal, but 0.3 has ones.

Description:

See pyani-plus/pyani-plus#109

Reproducible Steps:

This is a simplified version of the sample script on the above issue.

$ ls -1
MGV-GENOME-0264574.fas
MGV-GENOME-0266457.fna
OP073605.fasta

$ pyani createdb

$ pyani index -i .

$ pyani anim -i . -o output
...

$ pyani report -o . --formats=stdout --run_matrices 1
...

$ cat matrix_sim_errors_1.tab 
	Genome_id:1	Genome_id:2	Genome_id:3
Genome_id:1	1	222	27
Genome_id:2	222	1	212
Genome_id:3	27	212	1

Current Output:

One on the sim-error matrix diagonal:

$ cat matrix_sim_errors_1.tab 
	Genome_id:1	Genome_id:2	Genome_id:3
Genome_id:1	1	222	27
Genome_id:2	222	1	212
Genome_id:3	27	212	1

Expected Output:

Zero on the sim-error matrix diagonal

$ cat matrix_sim_errors_1.tab 
	Genome_id:1	Genome_id:2	Genome_id:3
Genome_id:1	0	222	27
Genome_id:2	222	0	212
Genome_id:3	27	212	0

pyani Version:

$ pyani --version
pyani version: 0.3.0-alpha

installed dependencies

If you are running a version of pyani v0.3 or later, then please run the command pyani listdeps at the command line, and enter the output below.

``` $ pyani listdeps System information Platorm==macOS-12.7.6-x86_64-i386-64bit Python==3.12.5 | packaged by conda-forge | (main, Aug 8 2024, 18:31:54) [Clang 16.0.6 ] Installed pyani Python dependendencies... Pillow==10.4.0 (/Users/pc40583/mambaforge/envs/pyani-plus_py312/lib/python3.12/site-packages/pillow-10.4.0.dist-info) biopython==1.84 (/Users/pc40583/mambaforge/envs/pyani-plus_py312/lib/python3.12/site-packages/biopython-1.84.dist-info) matplotlib==3.9.2 (/Users/pc40583/mambaforge/envs/pyani-plus_py312/lib/python3.12/site-packages/matplotlib-3.9.2.dist-info) namedlist==1.8 (/Users/pc40583/mambaforge/envs/pyani-plus_py312/lib/python3.12/site-packages/namedlist-1.8.dist-info) networkx==3.3 (/Users/pc40583/mambaforge/envs/pyani-plus_py312/lib/python3.12/site-packages/networkx-3.3.dist-info) numpy==2.1.0 (/Users/pc40583/mambaforge/envs/pyani-plus_py312/lib/python3.12/site-packages/numpy-2.1.0.dist-info) openpyxl==Not Installed (-) pandas==2.2.3 (/Users/pc40583/mambaforge/envs/pyani-plus_py312/lib/python3.12/site-packages/pandas-2.2.3.dist-info) scipy==1.14.1 (/Users/pc40583/mambaforge/envs/pyani-plus_py312/lib/python3.12/site-packages/scipy-1.14.1.dist-info) seaborn==0.13.2 (/Users/pc40583/mambaforge/envs/pyani-plus_py312/lib/python3.12/site-packages/seaborn-0.13.2.dist-info) sqlalchemy==2.0.35 (/Users/pc40583/mambaforge/envs/pyani-plus_py312/lib/python3.12/site-packages/SQLAlchemy-2.0.35.dist-info) tqdm==4.66.5 (/Users/pc40583/mambaforge/envs/pyani-plus_py312/lib/python3.12/site-packages/tqdm-4.66.5.dist-info) Installed pyani development dependendencies... bandit==Not Installed (-) black==24.8.0 (/Users/pc40583/mambaforge/envs/pyani-plus_py312/lib/python3.12/site-packages/black-24.8.0.dist-info) codecov==Not Installed (-) coverage==7.6.1 (/Users/pc40583/mambaforge/envs/pyani-plus_py312/lib/python3.12/site-packages/coverage-7.6.1.dist-info) doc8==Not Installed (-) flake8==Not Installed (-) jinja2==3.1.4 (/Users/pc40583/mambaforge/envs/pyani-plus_py312/lib/python3.12/site-packages/jinja2-3.1.4.dist-info) mypy==Not Installed (-) pydocstyle==Not Installed (-) pylint==Not Installed (-) pytest==8.3.3 (/Users/pc40583/mambaforge/envs/pyani-plus_py312/lib/python3.12/site-packages/pytest-8.3.3.dist-info) pytest-cov==5.0.0 (/Users/pc40583/mambaforge/envs/pyani-plus_py312/lib/python3.12/site-packages/pytest_cov-5.0.0.dist-info) sphinx==Not Installed (-) Installed pyani pip-install dependendencies... pre-commit==3.8.0 (/Users/pc40583/mambaforge/envs/pyani-plus_py312/lib/python3.12/site-packages/pre_commit-3.8.0.dist-info) pytest-ordering==Not Installed (-) sphinx-rtd-theme==Not Installed (-) Installed third-party tool versions... blast+==Darwin_2.16.0+ (/Users/pc40583/mambaforge/envs/pyani-plus_py312/bin/blastn) nucmer==Darwin_3.1 (/Users/pc40583/mambaforge/envs/pyani-plus_py312/bin/nucmer) blastall==Darwin_2.2.26 (/Users/pc40583/mambaforge/envs/pyani-plus_py312/bin/blastall) fastani==Darwin_1.33 (/Users/pc40583/mambaforge/envs/pyani-plus_py312/bin/fastANI) ```

Python Version:

Python 3.12

Operating System:

macOS Intel