gffkit 0.1.0__tar.gz

gffkit-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Qunjie Zhang
+
+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.

gffkit-0.1.0/MANIFEST.in

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+include README.md
+include LICENSE
+recursive-include src/gffkit *.py

gffkit-0.1.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: gffkit
+Version: 0.1.0
+Summary: Region-aware GFF annotation integration toolkit
+Author: Qunjie Zhang
+License: MIT
+Project-URL: Homepage, https://github.com/qunjie-zhang/gffkit
+Project-URL: Repository, https://github.com/qunjie-zhang/gffkit
+Project-URL: Issues, https://github.com/qunjie-zhang/gffkit/issues
+Keywords: GFF3,GTF,genome annotation,bioinformatics,UTR,gene annotation
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+
+# gffkit
+
+`gffkit` is a lightweight toolkit for region-aware GFF/GTF annotation integration.
+It combines three utilities:
+
+1. `detect-bridge`: detect suspicious merged-gene artifacts caused by bridge transcripts.
+2. `complement`: complement/merge annotations, with optional region-swap mode.
+3. `add-utr`: reconstruct `five_prime_UTR` and `three_prime_UTR` features from exon/CDS coordinates.
+
+## Installation
+
+```bash
+pip install gffkit
+```
+
+
+## Quick start
+
+### Full integration pipeline
+
+```bash
+gffkit integrate \
+  --annotation-a EviAnn.gff3 \
+  --annotation-b ANNEVO.gff3 \
+  --outdir gffkit_out \
+  --prefix sample
+```
+
+Outputs:
+
+- `gffkit_out/sample.suspicious.tsv`
+- `gffkit_out/sample.merged.gff3`
+- `gffkit_out/sample.final.withUTR.gff3`
+
+### Step-by-step usage
+
+```bash
+# 1. Detect suspicious merged genes in Annotation A
+gffkit detect-bridge -i EviAnn.gff3 -o suspicious.tsv
+
+# 2. Use A as the global reference, but switch to B in suspicious regions
+gffkit complement \
+  --ref EviAnn.gff3 \
+  --add ANNEVO.gff3 \
+  --swap_region_tsv suspicious.tsv \
+  --swap_region_flank 100 \
+  --output merged.gff3
+
+# 3. Add UTR features
+gffkit add-utr -i merged.gff3 -o final.annotation.withUTR.gff3
+```
+
+## Command overview
+
+```bash
+gffkit --help
+gffkit detect-bridge --help
+gffkit complement --help
+gffkit add-utr --help
+gffkit integrate --help
+```
+
+## Annotation integration strategy
+
+- Annotation A, for example EviAnn/RNA-seq-supported GFF, is used as the global primary reference.
+- Annotation B, for example ANNEVO/deep-learning GFF, is used as the local primary reference only in suspicious merged-gene regions.
+- UTR features are reconstructed after merging using an exon-minus-CDS strategy.
+
+## License
+
+MIT License.

gffkit-0.1.0/README.md

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+# gffkit
+
+`gffkit` is a lightweight toolkit for region-aware GFF/GTF annotation integration.
+It combines three utilities:
+
+1. `detect-bridge`: detect suspicious merged-gene artifacts caused by bridge transcripts.
+2. `complement`: complement/merge annotations, with optional region-swap mode.
+3. `add-utr`: reconstruct `five_prime_UTR` and `three_prime_UTR` features from exon/CDS coordinates.
+
+## Installation
+
+```bash
+pip install gffkit
+```
+
+
+## Quick start
+
+### Full integration pipeline
+
+```bash
+gffkit integrate \
+  --annotation-a EviAnn.gff3 \
+  --annotation-b ANNEVO.gff3 \
+  --outdir gffkit_out \
+  --prefix sample
+```
+
+Outputs:
+
+- `gffkit_out/sample.suspicious.tsv`
+- `gffkit_out/sample.merged.gff3`
+- `gffkit_out/sample.final.withUTR.gff3`
+
+### Step-by-step usage
+
+```bash
+# 1. Detect suspicious merged genes in Annotation A
+gffkit detect-bridge -i EviAnn.gff3 -o suspicious.tsv
+
+# 2. Use A as the global reference, but switch to B in suspicious regions
+gffkit complement \
+  --ref EviAnn.gff3 \
+  --add ANNEVO.gff3 \
+  --swap_region_tsv suspicious.tsv \
+  --swap_region_flank 100 \
+  --output merged.gff3
+
+# 3. Add UTR features
+gffkit add-utr -i merged.gff3 -o final.annotation.withUTR.gff3
+```
+
+## Command overview
+
+```bash
+gffkit --help
+gffkit detect-bridge --help
+gffkit complement --help
+gffkit add-utr --help
+gffkit integrate --help
+```
+
+## Annotation integration strategy
+
+- Annotation A, for example EviAnn/RNA-seq-supported GFF, is used as the global primary reference.
+- Annotation B, for example ANNEVO/deep-learning GFF, is used as the local primary reference only in suspicious merged-gene regions.
+- UTR features are reconstructed after merging using an exon-minus-CDS strategy.
+
+## License
+
+MIT License.

gffkit-0.1.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=68", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "gffkit"
+version = "0.1.0"
+description = "Region-aware GFF annotation integration toolkit"
+readme = "README.md"
+requires-python = ">=3.8"
+license = {text = "MIT"}
+authors = [
+  {name = "Qunjie Zhang"}
+]
+keywords = ["GFF3", "GTF", "genome annotation", "bioinformatics", "UTR", "gene annotation"]
+classifiers = [
+  "Development Status :: 3 - Alpha",
+  "Intended Audience :: Science/Research",
+  "Topic :: Scientific/Engineering :: Bio-Informatics",
+  "License :: OSI Approved :: MIT License",
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3.8",
+  "Programming Language :: Python :: 3.9",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Operating System :: OS Independent",
+]
+dependencies = []
+
+[project.urls]
+Homepage = "https://github.com/qunjie-zhang/gffkit"
+Repository = "https://github.com/qunjie-zhang/gffkit"
+Issues = "https://github.com/qunjie-zhang/gffkit/issues"
+
+[project.scripts]
+gffkit = "gffkit.main:main"
+gffkit-detect-bridge = "gffkit.detect_bridge_merged_genes:main"
+gffkit-complement = "gffkit.complement_annotations:main"
+gffkit-add-utr = "gffkit.add_utr:main"
+
+[tool.setuptools]
+package-dir = {"" = "src"}
+
+[tool.setuptools.packages.find]
+where = ["src"]

gffkit-0.1.0/setup.cfg

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

gffkit-0.1.0/src/gffkit/__init__.py

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+"""gffkit: region-aware GFF annotation integration utilities."""
+
+__version__ = "0.1.0"

gffkit-0.1.0/src/gffkit/__main__.py

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+from .main import main
+
+if __name__ == "__main__":
+    raise SystemExit(main())