botas-rnaseq 0.1.3__tar.gz

botas_rnaseq-0.1.3/LICENSE

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+MIT License
+
+Copyright (c) 2026 Clabe Wekesa
+
+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.

botas_rnaseq-0.1.3/PKG-INFO

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+Metadata-Version: 2.4
+Name: botas-rnaseq
+Version: 0.1.3
+Summary: BOTAS: Bacterial Operon-aware Transcriptome Alignment System
+Author-email: Clabe Wekesa <simiyu86wekesa@gmail.com>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/clabe-wekesa/botas
+Project-URL: Repository, https://github.com/clabe-wekesa/botas
+Project-URL: Issues, https://github.com/clabe-wekesa/botas/issues
+Project-URL: Documentation, https://github.com/clabe-wekesa/botas#readme
+Keywords: RNA-seq,bacterial transcriptomics,operons,sequence alignment,bioinformatics,circular genomes
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: pysam>=0.22
+Requires-Dist: edlib>=1.3.9
+Requires-Dist: biopython>=1.81
+Provides-Extra: progress
+Requires-Dist: tqdm>=4.66; extra == "progress"
+Provides-Extra: dev
+Requires-Dist: Cython>=3.0; extra == "dev"
+Requires-Dist: pytest>=7.4; extra == "dev"
+Requires-Dist: pytest-cov>=4.1; extra == "dev"
+Requires-Dist: black>=24.0; extra == "dev"
+Requires-Dist: ruff>=0.5; extra == "dev"
+Requires-Dist: mypy>=1.8; extra == "dev"
+Requires-Dist: build>=1.2; extra == "dev"
+Requires-Dist: twine>=5.0; extra == "dev"
+Dynamic: license-file
+
+# BOTAS
+
+## Bacterial Operon-Aware Transcriptome Alignment System
+
+BOTAS is a bacterial RNA-seq analysis framework that integrates read alignment, gene quantification, operon inference, and operon-level quantification within a unified Python package. It is specifically designed for bacterial transcriptomes, providing native support for circular genomes, operon-aware analyses, and strand-specific expression profiling.
+
+Unlike general-purpose RNA-seq aligners developed primarily for eukaryotic transcriptomes, BOTAS addresses the unique characteristics of bacterial genomes, including dense gene organization, polycistronic transcription, operon architecture, and circular chromosomes.
+
+---
+
+## Key Features
+
+- Seed-and-extend alignment engine optimized for bacterial genomes
+- Native support for circular chromosomes and plasmids
+- Paired-end and single-end read alignment
+- Strand-aware gene expression quantification
+- Gene-level and operon-level expression quantification
+- Operon inference from aligned reads
+- Operon-aware transcriptome analysis
+- Optional rRNA filtering
+- Parallel execution for scalable performance
+- Modular and extensible Python architecture
+
+---
+
+## Why BOTAS?
+
+Most RNA-seq aligners were designed for eukaryotic transcriptomes and assume splicing, large introns, and linear chromosomes. These assumptions are inappropriate for bacterial transcriptomes, which are characterized by:
+
+- Densely packed genes
+- Polycistronic transcripts organized into operons
+- Circular chromosomes and plasmids
+- Strong dependence on strand-specific transcription
+
+BOTAS addresses these challenges through native circular-genome support, operon-aware analysis, strand-specific quantification, circular insert-size validation, and integrated gene and operon quantification within a single framework.
+
+---
+
+## Installation
+
+### Install from PyPI
+
+```bash
+pip install botas
+```
+
+### Install the latest development version
+
+```bash
+pip install git+https://github.com/clabe-wekesa/botas.git
+```
+
+### Install from source
+
+```bash
+git clone https://github.com/clabe-wekesa/botas.git
+cd botas
+pip install .
+```
+
+### Development installation
+
+```bash
+pip install -e ".[dev]"
+```
+
+---
+
+## Quick Start
+
+### Paired-end alignment
+
+```bash
+botas align \
+    -r reference.fasta \
+    -1 reads_R1.fastq \
+    -2 reads_R2.fastq \
+    -o aligned.bam
+```
+
+### Single-end alignment
+
+```bash
+botas align \
+    -r reference.fasta \
+    -U reads.fastq \
+    -o aligned.bam
+```
+
+### Gene quantification
+
+```bash
+botas quantify \
+    -b aligned.bam \
+    -g genes.gff \
+    -o gene_counts.tsv
+```
+
+Supported features include:
+
+- Strand-specific counting
+- MAPQ filtering
+- Multi-mapper handling
+- TPM and RPKM calculation
+- Multi-BAM count matrix generation
+
+### Operon inference
+
+```bash
+botas getOperons \
+    -b aligned.bam \
+    -g genes.gff \
+    -o operons.tsv
+```
+
+Operon inference integrates:
+
+- Intergenic distance
+- Strand consistency
+- Coverage similarity
+- Paired-end support
+- Consensus-based merging
+
+---
+
+## Architecture
+
+```text
+botas/
+├── cli/          # Command-line interface
+├── core/         # Alignment engine
+├── data/         # Reference resources
+├── io/           # FASTQ, BAM and reference handling
+├── operons/      # Operon inference
+├── quantify/     # Gene and operon quantification
+└── rrna/         # rRNA detection and filtering
+```
+
+The alignment engine implements:
+
+- K-mer indexing
+- Seed clustering
+- Edit-distance extension using edlib
+- CIGAR reconstruction
+- Mapping quality estimation
+- Circular coordinate normalization
+
+---
+
+## Design Principles
+
+BOTAS is designed to provide:
+
+- Accurate bacterial RNA-seq alignment
+- Native support for circular genomes
+- Reproducible gene and operon quantification
+- Transparent and interpretable alignment scoring
+- Modular architecture for method development and extension
+- Integration of alignment and operon-level analyses within a unified workflow
+
+---
+
+## Requirements
+
+### Required
+
+- Python ≥ 3.10
+- pysam
+- edlib
+- biopython
+
+### Optional
+
+- tqdm (progress display)
+
+---
+
+## Documentation
+
+Command-line help is available through:
+
+```bash
+botas --help
+botas align --help
+botas quant --help
+botas getOperons --help
+```
+
+---
+
+## Citation
+
+If you use BOTAS in your research, please cite:
+
+> Wekesa, C. S. *BOTAS: Bacterial Operon-Aware Transcriptome Alignment System.*
+
+Citation details will be updated following publication.
+
+---
+
+## License
+
+BOTAS is distributed under the MIT License. See the `LICENSE` file for details.
+
+---
+
+## Author
+
+**Clabe Simiyu Wekesa**
+
+GitHub: https://github.com/clabe-wekesa

botas_rnaseq-0.1.3/README.md

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+# BOTAS
+
+## Bacterial Operon-Aware Transcriptome Alignment System
+
+BOTAS is a bacterial RNA-seq analysis framework that integrates read alignment, gene quantification, operon inference, and operon-level quantification within a unified Python package. It is specifically designed for bacterial transcriptomes, providing native support for circular genomes, operon-aware analyses, and strand-specific expression profiling.
+
+Unlike general-purpose RNA-seq aligners developed primarily for eukaryotic transcriptomes, BOTAS addresses the unique characteristics of bacterial genomes, including dense gene organization, polycistronic transcription, operon architecture, and circular chromosomes.
+
+---
+
+## Key Features
+
+- Seed-and-extend alignment engine optimized for bacterial genomes
+- Native support for circular chromosomes and plasmids
+- Paired-end and single-end read alignment
+- Strand-aware gene expression quantification
+- Gene-level and operon-level expression quantification
+- Operon inference from aligned reads
+- Operon-aware transcriptome analysis
+- Optional rRNA filtering
+- Parallel execution for scalable performance
+- Modular and extensible Python architecture
+
+---
+
+## Why BOTAS?
+
+Most RNA-seq aligners were designed for eukaryotic transcriptomes and assume splicing, large introns, and linear chromosomes. These assumptions are inappropriate for bacterial transcriptomes, which are characterized by:
+
+- Densely packed genes
+- Polycistronic transcripts organized into operons
+- Circular chromosomes and plasmids
+- Strong dependence on strand-specific transcription
+
+BOTAS addresses these challenges through native circular-genome support, operon-aware analysis, strand-specific quantification, circular insert-size validation, and integrated gene and operon quantification within a single framework.
+
+---
+
+## Installation
+
+### Install from PyPI
+
+```bash
+pip install botas
+```
+
+### Install the latest development version
+
+```bash
+pip install git+https://github.com/clabe-wekesa/botas.git
+```
+
+### Install from source
+
+```bash
+git clone https://github.com/clabe-wekesa/botas.git
+cd botas
+pip install .
+```
+
+### Development installation
+
+```bash
+pip install -e ".[dev]"
+```
+
+---
+
+## Quick Start
+
+### Paired-end alignment
+
+```bash
+botas align \
+    -r reference.fasta \
+    -1 reads_R1.fastq \
+    -2 reads_R2.fastq \
+    -o aligned.bam
+```
+
+### Single-end alignment
+
+```bash
+botas align \
+    -r reference.fasta \
+    -U reads.fastq \
+    -o aligned.bam
+```
+
+### Gene quantification
+
+```bash
+botas quantify \
+    -b aligned.bam \
+    -g genes.gff \
+    -o gene_counts.tsv
+```
+
+Supported features include:
+
+- Strand-specific counting
+- MAPQ filtering
+- Multi-mapper handling
+- TPM and RPKM calculation
+- Multi-BAM count matrix generation
+
+### Operon inference
+
+```bash
+botas getOperons \
+    -b aligned.bam \
+    -g genes.gff \
+    -o operons.tsv
+```
+
+Operon inference integrates:
+
+- Intergenic distance
+- Strand consistency
+- Coverage similarity
+- Paired-end support
+- Consensus-based merging
+
+---
+
+## Architecture
+
+```text
+botas/
+├── cli/          # Command-line interface
+├── core/         # Alignment engine
+├── data/         # Reference resources
+├── io/           # FASTQ, BAM and reference handling
+├── operons/      # Operon inference
+├── quantify/     # Gene and operon quantification
+└── rrna/         # rRNA detection and filtering
+```
+
+The alignment engine implements:
+
+- K-mer indexing
+- Seed clustering
+- Edit-distance extension using edlib
+- CIGAR reconstruction
+- Mapping quality estimation
+- Circular coordinate normalization
+
+---
+
+## Design Principles
+
+BOTAS is designed to provide:
+
+- Accurate bacterial RNA-seq alignment
+- Native support for circular genomes
+- Reproducible gene and operon quantification
+- Transparent and interpretable alignment scoring
+- Modular architecture for method development and extension
+- Integration of alignment and operon-level analyses within a unified workflow
+
+---
+
+## Requirements
+
+### Required
+
+- Python ≥ 3.10
+- pysam
+- edlib
+- biopython
+
+### Optional
+
+- tqdm (progress display)
+
+---
+
+## Documentation
+
+Command-line help is available through:
+
+```bash
+botas --help
+botas align --help
+botas quant --help
+botas getOperons --help
+```
+
+---
+
+## Citation
+
+If you use BOTAS in your research, please cite:
+
+> Wekesa, C. S. *BOTAS: Bacterial Operon-Aware Transcriptome Alignment System.*
+
+Citation details will be updated following publication.
+
+---
+
+## License
+
+BOTAS is distributed under the MIT License. See the `LICENSE` file for details.
+
+---
+
+## Author
+
+**Clabe Simiyu Wekesa**
+
+GitHub: https://github.com/clabe-wekesa

botas_rnaseq-0.1.3/botas/__init__.py

@@ -0,0 +1,6 @@
+from importlib.metadata import PackageNotFoundError, version
+
+try:
+    __version__ = version("botas-rnaseq")
+except PackageNotFoundError:
+    __version__ = "0.1.3"