supporth 0.4.0__tar.gz

supporth-0.4.0/LICENSE

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+MIT License
+
+Copyright (c) 2025 Fabian Moreno-Avitia
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

supporth-0.4.0/MANIFEST.in

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+include RELEASING.md
+include supporth_manual.md

supporth-0.4.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: supporth
+Version: 0.4.0
+Summary: Support-based orthologue integration: runs multiple orthology predictors and unifies their calls into a consensus table
+Author: Fabian Moreno-Avitia
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/fma91/SuppOrth
+Project-URL: Documentation, https://github.com/fma91/SuppOrth#readme
+Project-URL: Issues, https://github.com/fma91/SuppOrth/issues
+Keywords: orthology,comparative-genomics,orthofinder,sonicparanoid,broccoli
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: MacOS
+Classifier: Operating System :: POSIX :: Linux
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: pandas>=1.3
+Requires-Dist: biopython>=1.79
+Requires-Dist: matplotlib>=3.4
+Requires-Dist: venny4py>=1.0
+Provides-Extra: viz
+Requires-Dist: matplotlib>=3.4; extra == "viz"
+Requires-Dist: venny4py>=1.0; extra == "viz"
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Provides-Extra: release
+Requires-Dist: build>=1.2; extra == "release"
+Requires-Dist: twine>=6; extra == "release"
+Dynamic: license-file
+
+![SuppOrth](https://raw.githubusercontent.com/fma91/SuppOrth/stand_alone/img/supporth_banner.png)
+
+# SuppOrth
+
+SuppOrth runs **OrthoFinder, SonicParanoid2 and Broccoli** on your protein FASTA
+files and combines their orthologue predictions. You can also include results
+from an existing **OMA** run.
+
+The output contains unique protein pairs between species, the tools supporting
+each pair, and alignment statistics when available. It accepts two or more
+proteomes and keeps one-to-many and many-to-many relationships.
+
+## Install
+
+Use Python 3.10–3.12 on macOS or Linux. Install SuppOrth, then its predictors:
+
+```sh
+python -m pip install supporth        # Install the SuppOrth command-line application
+suppOrth install                     # Install the three predictors and prepare their dependencies
+suppOrth check                       # Check whether predictors and required binaries are ready
+```
+
+SuppOrth is distributed through [PyPI](https://pypi.org/project/supporth/).
+
+The predictors are installed from their source repositories under `~/.supporth`.
+You need Git and a compiler toolchain. MAFFT and FastME must already be available
+or supplied during installation. SonicParanoid needs an indexed Pfam database;
+preparing it can take several hours. To reuse an existing database:
+
+```sh
+suppOrth install --pfam-db /path/to/profile_db
+```
+
+See the [installation details](https://github.com/fma91/SuppOrth/blob/stand_alone/supporth_manual.md#installation)
+for interpreter selection, shared binaries and custom installation locations.
+
+## Run
+
+Put one protein FASTA per species in a directory:
+
+```sh
+suppOrth run -f proteomes/ -o results/ -t 8
+```
+
+Or pass the files directly:
+
+```sh
+suppOrth run speciesA.faa speciesB.faa speciesC.faa -o results/ -t 8
+```
+
+Use unique protein identifiers across the FASTAs. SuppOrth reads the first
+whitespace-separated field of each header. The predictors run sequentially,
+using the requested thread budget.
+
+By default, a pair is kept if **at least three tools support it**, or its
+alignment identity is **greater than 80%**. Change the thresholds with:
+
+```sh
+suppOrth run -f proteomes/ -o results/ --supportLv 2 --identity_filter 90
+```
+
+Use `--supportLv 1` to keep every predicted cross-species pair. Support counts
+measure agreement between methods; they are not probabilities.
+
+## Include OMA
+
+Run OMA separately with the same protein identifiers, then supply its output:
+
+```sh
+suppOrth run -f proteomes/ -o results/ --oma /path/to/oma_run/Output/
+```
+
+SuppOrth imports OMA's `PairwiseOrthologs` tables as a fourth source of support.
+It does not install or run OMA. See the [OMA guide](https://github.com/fma91/SuppOrth/blob/stand_alone/supporth_manual.md#include-oma-predictions)
+for accepted folders and identifier matching.
+
+## Results
+
+Open these files in `results/`:
+
+- **`suppOrth.tsv`**: protein pairs, support counts, 0/1 tool columns and alignment statistics.
+- **`suppOrth.png` and `suppOrth.svg`**: overlap figures from all predictor calls before filtering.
+- **`provenance.json`**: inputs, options, software versions and run status.
+
+Tool labels are **F** (OrthoFinder), **S** (SonicParanoid), **B** (Broccoli) and
+**O** (OMA). For example, `SupportedBy=F,S,O` means three tools support the pair.
+
+![Protein-pair overlaps](https://raw.githubusercontent.com/fma91/SuppOrth/stand_alone/img/suppOrth.png)
+
+The [SuppOrth manual](https://github.com/fma91/SuppOrth/blob/stand_alone/supporth_manual.md#output)
+includes the first ten rows of an example output, all output files, native
+predictor options, BLAST/DIAMOND selection and maintenance commands.
+
+## More options
+
+OrthoFinder uses DIAMOND, MAFFT and IQ-TREE by default. Select BLAST with
+`--alignment blast`. Pass native predictor arguments in a quoted string:
+
+```sh
+suppOrth run -f proteomes/ -o results/ --opt orthofinder="-I 2.0"
+```
+
+See the [SuppOrth manual](https://github.com/fma91/SuppOrth/blob/stand_alone/supporth_manual.md)
+and [release instructions](https://github.com/fma91/SuppOrth/blob/stand_alone/RELEASING.md).

supporth-0.4.0/README.md

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+![SuppOrth](https://raw.githubusercontent.com/fma91/SuppOrth/stand_alone/img/supporth_banner.png)
+
+# SuppOrth
+
+SuppOrth runs **OrthoFinder, SonicParanoid2 and Broccoli** on your protein FASTA
+files and combines their orthologue predictions. You can also include results
+from an existing **OMA** run.
+
+The output contains unique protein pairs between species, the tools supporting
+each pair, and alignment statistics when available. It accepts two or more
+proteomes and keeps one-to-many and many-to-many relationships.
+
+## Install
+
+Use Python 3.10–3.12 on macOS or Linux. Install SuppOrth, then its predictors:
+
+```sh
+python -m pip install supporth        # Install the SuppOrth command-line application
+suppOrth install                     # Install the three predictors and prepare their dependencies
+suppOrth check                       # Check whether predictors and required binaries are ready
+```
+
+SuppOrth is distributed through [PyPI](https://pypi.org/project/supporth/).
+
+The predictors are installed from their source repositories under `~/.supporth`.
+You need Git and a compiler toolchain. MAFFT and FastME must already be available
+or supplied during installation. SonicParanoid needs an indexed Pfam database;
+preparing it can take several hours. To reuse an existing database:
+
+```sh
+suppOrth install --pfam-db /path/to/profile_db
+```
+
+See the [installation details](https://github.com/fma91/SuppOrth/blob/stand_alone/supporth_manual.md#installation)
+for interpreter selection, shared binaries and custom installation locations.
+
+## Run
+
+Put one protein FASTA per species in a directory:
+
+```sh
+suppOrth run -f proteomes/ -o results/ -t 8
+```
+
+Or pass the files directly:
+
+```sh
+suppOrth run speciesA.faa speciesB.faa speciesC.faa -o results/ -t 8
+```
+
+Use unique protein identifiers across the FASTAs. SuppOrth reads the first
+whitespace-separated field of each header. The predictors run sequentially,
+using the requested thread budget.
+
+By default, a pair is kept if **at least three tools support it**, or its
+alignment identity is **greater than 80%**. Change the thresholds with:
+
+```sh
+suppOrth run -f proteomes/ -o results/ --supportLv 2 --identity_filter 90
+```
+
+Use `--supportLv 1` to keep every predicted cross-species pair. Support counts
+measure agreement between methods; they are not probabilities.
+
+## Include OMA
+
+Run OMA separately with the same protein identifiers, then supply its output:
+
+```sh
+suppOrth run -f proteomes/ -o results/ --oma /path/to/oma_run/Output/
+```
+
+SuppOrth imports OMA's `PairwiseOrthologs` tables as a fourth source of support.
+It does not install or run OMA. See the [OMA guide](https://github.com/fma91/SuppOrth/blob/stand_alone/supporth_manual.md#include-oma-predictions)
+for accepted folders and identifier matching.
+
+## Results
+
+Open these files in `results/`:
+
+- **`suppOrth.tsv`**: protein pairs, support counts, 0/1 tool columns and alignment statistics.
+- **`suppOrth.png` and `suppOrth.svg`**: overlap figures from all predictor calls before filtering.
+- **`provenance.json`**: inputs, options, software versions and run status.
+
+Tool labels are **F** (OrthoFinder), **S** (SonicParanoid), **B** (Broccoli) and
+**O** (OMA). For example, `SupportedBy=F,S,O` means three tools support the pair.
+
+![Protein-pair overlaps](https://raw.githubusercontent.com/fma91/SuppOrth/stand_alone/img/suppOrth.png)
+
+The [SuppOrth manual](https://github.com/fma91/SuppOrth/blob/stand_alone/supporth_manual.md#output)
+includes the first ten rows of an example output, all output files, native
+predictor options, BLAST/DIAMOND selection and maintenance commands.
+
+## More options
+
+OrthoFinder uses DIAMOND, MAFFT and IQ-TREE by default. Select BLAST with
+`--alignment blast`. Pass native predictor arguments in a quoted string:
+
+```sh
+suppOrth run -f proteomes/ -o results/ --opt orthofinder="-I 2.0"
+```
+
+See the [SuppOrth manual](https://github.com/fma91/SuppOrth/blob/stand_alone/supporth_manual.md)
+and [release instructions](https://github.com/fma91/SuppOrth/blob/stand_alone/RELEASING.md).

supporth-0.4.0/RELEASING.md

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+# Publishing SuppOrth
+
+The version is defined in `src/supporth/__init__.py`. Use a new version for every
+upload; PyPI does not allow a published distribution to be replaced.
+
+## Build and check
+
+Use an existing Python interpreter in a virtual environment:
+
+```sh
+python3.10 -m venv /tmp/supporth-release
+source /tmp/supporth-release/bin/activate
+python -m pip install '.[dev,release]'
+python -m pytest tests
+python -m build
+python -m twine check --strict dist/*
+```
+
+Build from a clean checkout so `dist/` contains only the intended release.
+`python -m build` creates both the source archive and a wheel built from that
+archive. Check installation in another environment, outside the checkout:
+
+```sh
+python3.10 -m venv /tmp/supporth-wheel-check
+/tmp/supporth-wheel-check/bin/python -m pip install dist/supporth-0.4.0-py3-none-any.whl
+/tmp/supporth-wheel-check/bin/python -m pip check
+/tmp/supporth-wheel-check/bin/suppOrth --version
+/tmp/supporth-wheel-check/bin/supporth run --help
+```
+
+These checks validate the Python distribution. Predictor installation and live
+orthology runs require separate checks with the upstream software and Pfam data.
+
+## Upload
+
+Create PyPI and TestPyPI accounts and use their API tokens when Twine asks for
+credentials. Tokens must not be stored in the repository.
+
+```sh
+python -m twine upload --repository testpypi dist/*
+python -m twine upload dist/*
+```
+
+TestPyPI and PyPI are separate services. Confirm the TestPyPI metadata and files
+before uploading to PyPI. Stable releases are installed with
+`python -m pip install supporth`.
+
+The package name must be available or owned by your PyPI account. An apparent
+absence from the public index does not guarantee that PyPI will allow the name.

supporth-0.4.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=77.0.3"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "supporth"
+dynamic = ["version"]
+description = "Support-based orthologue integration: runs multiple orthology predictors and unifies their calls into a consensus table"
+readme = "README.md"
+license = "MIT"
+license-files = ["LICENSE"]
+requires-python = ">=3.10"
+authors = [{ name = "Fabian Moreno-Avitia" }]
+keywords = ["orthology", "comparative-genomics", "orthofinder", "sonicparanoid", "broccoli"]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Programming Language :: Python :: 3",
+    "Operating System :: MacOS",
+    "Operating System :: POSIX :: Linux",
+]
+
+dependencies = [
+    "pandas>=1.3",
+    "biopython>=1.79",
+    "matplotlib>=3.4",
+    "venny4py>=1.0",
+]
+
+[project.urls]
+Homepage = "https://github.com/fma91/SuppOrth"
+Documentation = "https://github.com/fma91/SuppOrth#readme"
+Issues = "https://github.com/fma91/SuppOrth/issues"
+
+[project.optional-dependencies]
+viz = ["matplotlib>=3.4", "venny4py>=1.0"]
+dev = ["pytest>=7.0"]
+release = ["build>=1.2", "twine>=6"]
+
+[project.scripts]
+suppOrth = "supporth.cli:main"
+supporth = "supporth.cli:main"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.dynamic]
+version = {attr = "supporth.__version__"}
+
+[tool.setuptools.package-data]
+supporth = ["py.typed"]

supporth-0.4.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

supporth-0.4.0/src/supporth/__init__.py

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+"""SuppOrth: support-based integration of complementary orthology predictors."""
+
+__version__ = "0.4.0"
+
+__all__ = ["__version__"]

supporth-0.4.0/src/supporth/adapters/__init__.py

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+"""Predictor adapters: one module per orthology tool."""
+
+from __future__ import annotations
+
+from .base import Adapter, MethodProfile, StageContext
+from .broccoli import Broccoli
+from .oma import OMA
+from .orthofinder import OrthoFinder
+from .sonicparanoid import SonicParanoid
+
+REGISTRY: dict[str, type[Adapter]] = {
+    OrthoFinder.name: OrthoFinder,
+    SonicParanoid.name: SonicParanoid,
+    Broccoli.name: Broccoli,
+    OMA.name: OMA,
+}
+
+# Predictors SuppOrth installs and launches. OMA is not among them: the user
+# supplies an existing standalone run with --oma.
+DEFAULT_ORDER = (OrthoFinder.name, SonicParanoid.name, Broccoli.name)
+
+
+def get(name: str) -> Adapter:
+    key = name.strip().lower()
+    if key not in REGISTRY:
+        known = ", ".join(sorted(REGISTRY))
+        raise KeyError(f"unknown predictor {name!r}; available: {known}")
+    return REGISTRY[key]()
+
+
+def resolve(names: str | None) -> list[Adapter]:
+    """Adapters for a comma-separated selection, kept in run order."""
+    if not names or names.strip().lower() == "all":
+        return [get(n) for n in DEFAULT_ORDER]
+    requested = {n.strip().lower() for n in names.split(",") if n.strip()}
+    if "oma" in requested:
+        raise KeyError(
+            "OMA is not run by suppOrth; pass an existing standalone run with --oma PATH"
+        )
+    unknown = requested - set(REGISTRY)
+    if unknown:
+        raise KeyError(
+            f"unknown predictor(s): {', '.join(sorted(unknown))}; "
+            f"available: {', '.join(sorted(REGISTRY))}"
+        )
+    return [get(n) for n in DEFAULT_ORDER if n in requested]
+
+
+__all__ = [
+    "Adapter",
+    "MethodProfile",
+    "StageContext",
+    "REGISTRY",
+    "DEFAULT_ORDER",
+    "get",
+    "resolve",
+]