satellome 1.0.0__tar.gz

satellome-1.0.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+TRF/
+bpe.exe
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
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+# Scrapy stuff:
+.scrapy
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+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
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+# Spyder project settings
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+/site
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+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+.vscode/settings.json
+
+TRF
+test_dataset
+examples_primates.sh
+.claude
+.vscode
+CLAUDE.md
+examples_primates.sh

satellome-1.0.0/LICENSE

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+MIT License
+
+Copyright (c) 2024 Aleksey Komissarov
+
+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.

satellome-1.0.0/MANIFEST.in

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+include README.md
+include LICENSE
+include requirements.txt
+include src/satellome/settings.yaml
+recursive-include src/satellome *.yaml *.yml
+recursive-include scripts *.py *.sh
+recursive-include tests *.py
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]
+recursive-exclude * .DS_Store

satellome-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: satellome
+Version: 1.0.0
+Summary: A comprehensive tool for satellite DNA analysis in T2T genome assemblies
+Home-page: https://github.com/aglabx/Satellome
+Author: Aleksey Komissarov
+Author-email: Aleksey Komissarov <ad3002@gmail.com>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/aglabx/satellome
+Project-URL: Documentation, https://github.com/aglabx/satellome/wiki
+Project-URL: Repository, https://github.com/aglabx/satellome
+Project-URL: Issues, https://github.com/aglabx/satellome/issues
+Classifier: Development Status :: 4 - Beta
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.6
+Classifier: Programming Language :: Python :: 3.7
+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: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.6
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: PyExp
+Requires-Dist: pandas
+Requires-Dist: numpy
+Requires-Dist: scikit-learn
+Requires-Dist: pyyaml
+Requires-Dist: simplejson
+Requires-Dist: intervaltree
+Requires-Dist: tqdm
+Requires-Dist: requests
+Requires-Dist: plotly
+Requires-Dist: kaleido
+Requires-Dist: editdistance
+Requires-Dist: networkx
+Dynamic: author
+Dynamic: home-page
+Dynamic: license-file
+Dynamic: requires-python
+
+# Satellome
+
+A comprehensive bioinformatics tool for analyzing satellite DNA (tandem repeats) in telomere-to-telomere (T2T) genome assemblies.
+
+## Overview
+
+Satellome integrates Tandem Repeat Finder (TRF) to identify, classify, and visualize repetitive DNA sequences, with a particular focus on centromeric and telomeric regions. It provides a complete pipeline from raw genome sequences to detailed visualizations and reports of tandem repeat patterns.
+
+The tool is designed to work with various genome assembly projects including:
+- T2T (Telomere-to-Telomere) Consortium assemblies
+- DNA Zoo chromosome-length assemblies
+- VGP (Vertebrate Genome Project) assemblies
+- NCBI RefSeq and GenBank assemblies
+
+## Features
+
+- **Tandem Repeat Detection**: Automated detection using TRF with optimized parameters
+- **Smart Classification**: Categorizes repeats into microsatellites, complex repeats, and other types
+- **Rich Visualizations**: Generates karyotype plots, 3D visualizations, and distance matrices
+- **Annotation Integration**: Supports GFF3 and RepeatMasker annotations
+- **Parallel Processing**: Efficient handling of multiple genomes
+- **Smart Pipeline**: Automatically skips completed steps (override with `--force`)
+
+## Installation
+
+### Prerequisites
+
+- Python 3.9 or higher
+- Conda (recommended) or pip
+- TRF (Tandem Repeat Finder) binary
+
+### Quick Setup
+
+1. **Clone the repository**
+```bash
+git clone https://github.com/aglabx/satellome.git
+cd satellome
+```
+
+2. **Create conda environment**
+```bash
+conda create -n satellome python=3.9
+conda activate satellome
+```
+
+3. **Install dependencies**
+```bash
+pip install -r requirements.txt
+```
+
+4. **Install satellome**
+```bash
+pip install -e .  # Development mode
+# or
+pip install .     # Production mode
+```
+
+5. **Download TRF binary**
+```bash
+# Linux
+wget https://github.com/Benson-Genomics-Lab/TRF/releases/download/v4.09.1/trf409.linux64
+chmod +x trf409.linux64
+mv trf409.linux64 trf
+
+# macOS
+wget https://github.com/Benson-Genomics-Lab/TRF/releases/download/v4.09.1/trf409.macosx
+chmod +x trf409.macosx
+mv trf409.macosx trf
+```
+
+## Usage
+
+### Basic Command
+
+```bash
+satellome -i genome.fasta -o output_dir -p project_name -t 8
+```
+
+### Advanced Options
+
+```bash
+# With GFF3 annotations
+satellome -i genome.fasta -o output_dir -p project_name -t 8 --gff annotations.gff3
+
+# With RepeatMasker annotations
+satellome -i genome.fasta -o output_dir -p project_name -t 8 --rm repeatmasker.out
+
+# Force rerun all steps
+satellome -i genome.fasta -o output_dir -p project_name -t 8 --force
+
+# Custom TRF binary path
+satellome -i genome.fasta -o output_dir -p project_name -t 8 --trf /path/to/trf
+
+# Parallel processing of multiple genomes
+python scripts/run_satellome_parallel.py -i genomes_list.txt -o results_dir -t 32
+```
+
+### Parameters
+
+- `-i, --input`: Input FASTA file (required)
+- `-o, --output`: Output directory (required)
+- `-p, --project`: Project name (required)
+- `-t, --threads`: Number of threads (default: 1)
+- `--gff`: GFF3 annotation file (optional)
+- `--rm`: RepeatMasker output file (optional)
+- `--trf`: Path to TRF binary (default: "trf")
+- `--force`: Force rerun all steps
+
+## Output Structure
+
+```
+output_dir/
+├── genome_name.trf                   # Main TRF output file
+├── genome_name.1kb.trf               # Repeats >1kb
+├── genome_name.3kb.trf               # Repeats >3kb
+├── genome_name.10kb.trf              # Repeats >10kb
+├── genome_name.micro.trf             # Microsatellites (1-9 bp monomers)
+├── genome_name.complex.trf           # Complex repeats (>9 bp monomers)
+├── genome_name.pmicro.trf            # Potential microsatellites
+├── genome_name.tssr.trf              # Tandem simple sequence repeats
+├── genome_name.*.gff3                # GFF3 format files for each category
+├── genome_name.*.fa                  # FASTA files with repeat sequences
+├── distances.tsv.*                   # Distance matrices with various extensions
+├── images/
+│   ├── *.png                         # Karyotype and other visualizations
+│   └── *.svg                         # Vector graphics versions
+└── reports/
+    ├── satellome_report.html         # Comprehensive HTML report
+    └── annotation_report.txt         # Annotation intersection report (if GFF provided)
+```
+
+## Classification System
+
+Satellome classifies tandem repeats into four categories:
+
+1. **micro**: Microsatellites (monomer length 1-9 bp)
+2. **complex**: Complex repeats (monomer length >9 bp)
+3. **pmicro**: Potential microsatellites
+4. **tssr**: Tandem simple sequence repeats
+
+## Utility Scripts
+
+### Format Conversion
+```bash
+# Convert TRF to FASTA
+python scripts/trf_to_fasta.py -i repeats.trf -o repeats.fasta
+
+# Convert TRF to GFF3
+python scripts/trf_to_gff3.py -i repeats.trf -o repeats.gff3
+
+# Extract coordinates
+python scripts/trf_to_coordinates.py -i repeats.trf -o coordinates.txt
+```
+
+### Analysis Tools
+```bash
+# Extract large tandem repeats
+python scripts/trf_get_large.py -i repeats.trf -m 1000 -o large_repeats.trf
+
+# Get microsatellite statistics
+python scripts/trf_get_micro_stat.py -i repeats.trf -o micro_stats.txt
+
+# Check telomeric repeats
+python scripts/check_telomeres.py -i genome.fasta -t repeats.trf
+```
+
+## Example Workflow
+
+### 1. Download Test Dataset
+```bash
+# Download S. cerevisiae genome
+curl -OJX GET "https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/accession/GCF_000146045.2/download?include_annotation_type=GENOME_FASTA,GENOME_GFF&filename=GCF_000146045.2.zip" -H "Accept: application/zip"
+unzip GCF_000146045.2.zip
+```
+
+### 2. Run Analysis
+```bash
+# Run satellome pipeline
+satellome -i ncbi_dataset/data/GCF_000146045.2/GCF_000146045.2_R64_genomic.fna \
+          -o results \
+          -p scerevisiae \
+          -t 8 \
+          --gff ncbi_dataset/data/GCF_000146045.2/genomic.gff
+
+# View results
+open results/scerevisiae_report.html
+```
+
+### 3. Analyzing DNA Zoo Assemblies
+```bash
+# Download a DNA Zoo assembly (example: Aardvark)
+wgethttps://dnazoo.s3.wasabisys.com/Acinonyx_jubatus/aciJub1_HiC.fasta.gz
+gzip -d aciJub1_HiC.fasta.gz
+
+# Run satellome on DNA Zoo assembly
+satellome -i aciJub1_HiC.fasta \
+          -o dnazoo_results \
+          -p cheetah \
+          -t 8
+```
+
+## Configuration
+
+The pipeline uses `settings.yaml` for tool parameters. Key settings include:
+
+- TRF parameters (match/mismatch scores, indel penalties)
+- Minimum/maximum repeat lengths
+- Classification thresholds
+- Visualization parameters
+
+## Testing
+
+Run the test suite:
+```bash
+python tests/test_overlapping.py
+python test_standalone.py
+python test_chromosome_sorting.py
+```
+
+## Contributing
+
+1. Fork the repository
+2. Create a feature branch (`git checkout -b feature/amazing-feature`)
+3. Commit your changes (`git commit -m 'Add amazing feature'`)
+4. Push to the branch (`git push origin feature/amazing-feature`)
+5. Open a Pull Request
+
+## Citation
+
+If you use Satellome in your research, please cite:
+
+```
+Komissarov A. et al. (2024). Satellome: A comprehensive tool for satellite DNA 
+analysis in T2T genome assemblies. [Publication details]
+```
+
+## License
+
+This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.
+
+## Support
+
+- **Issues**: [GitHub Issues](https://github.com/aglabx/satellome/issues)
+- **Documentation**: [Wiki](https://github.com/aglabx/satellome/wiki)
+- **Email**: ad3002@gmail.com
+
+## Acknowledgments
+
+- [Tandem Repeat Finder](https://github.com/Benson-Genomics-Lab/TRF) by Gary Benson
+- [T2T Consortium](https://www.genome.gov/about-nhgri/telomere-to-telomere) for inspiring this work
+- [DNA Zoo](https://www.dnazoo.org/) for providing chromosome-length assemblies
+- [Vertebrate Genome Project](https://vertebrategenomesproject.org/) for high-quality reference genomes