GenBank Feature Parser Suite

A Biopython-powered Python toolset and AI agent skill for parsing, validating, analyzing, and mining GenBank annotation files (.gbff, .gbk, .gb, .txt).

Architecture & Key Principles

• Standard-Compliant Parsing: Built on Biopython (Bio.SeqIO) for robust flat-file parsing, multi-line qualifier continuation, quote stripping, and partial coordinate handling (BeforePosition/AfterPosition).
• Contig-Boundary Aware: All spatial operations (operon prediction, neighborhood windowing, mobilome island discovery) strictly partition features by contig before coordinate sorting.
• Rich Semantic Cross-References: Automatically extracts GO terms, COG IDs, KEGG KOs, Pfam, Rfam, and EC numbers from both INSDC /EC_number and Bakta/Prokka /db_xref and /note qualifiers.
• 16 Tool Modules: Comprehensive CLI coverage spanning sequence extraction, locus indexing, operon prediction, CRISPR array detection, GFF3 conversion, codon usage bias (RSCU), and phylogenomic marker extraction.

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Installation & Setup

Requires Python 3.8+ and biopython>=1.80.

pip install -r requirements.txt

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Directory Layout

genbank-feature-parser/
├── SKILL.md                        # Agent skill prompt and instructions
├── README.md                       # Documentation & usage guide
├── requirements.txt                # Python dependencies (biopython)
├── .gitignore                      # Git exclusion rules
├── pf_isolate_discovery_analysis.md # Example isolate discovery report
├── pf_supplementary_analysis.md    # Example genomic analysis report
└── scripts/
    ├── genbank_parser.py           # Core canonical parser library (Bio.SeqIO backend)
    ├── genbank_meor.py             # MEOR & biosurfactant biosynthesis discovery engine
    ├── genbank_discover.py         # Genomic island & operon discovery engine
    ├── genbank_functional.py       # Functional annotation (COG/GO/KEGG/EC) tables
    ├── genbank_gff.py              # GenBank to GFF3 converter & validator
    ├── genbank_codon.py            # Codon usage bias & RSCU calculator
    ├── genbank_crispr.py           # CRISPR array & repeat detector
    ├── genbank_phylo.py            # Phylogenomic marker extraction
    ├── genbank_compare.py          # Comparative synteny & ortholog analyzer
    ├── genbank_operons.py          # Intergenic distance operon predictor
    ├── genbank_neighborhood.py     # Genomic locus neighborhood window extractor
    ├── genbank_extract.py          # Feature & sequence extraction tool
    ├── genbank_fasta.py            # FASTA sequence exporter (CDS/gene/genome)
    ├── genbank_locus.py            # Locus tag indexer & feature search
    ├── genbank_metadata.py         # Record metadata & summary stats
    ├── genbank_sequence.py         # Nucleotide & translation fetcher
    └── genbank_validate.py         # Structural syntax & format validator

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Quick Start & Tool Usage Examples

1. Structural Validation

python scripts/genbank_validate.py input.gbff

2. Extract Functional Profiling (GO, COG, KEGG, Pfam, EC)

python scripts/genbank_functional.py input.gbff --format tsv

3. Convert GenBank to GFF3

python scripts/genbank_gff.py input.gbff output.gff3

4. Mine Dark-Matter Operons & Mobilome Islands

python scripts/genbank_discover.py input.gbff --format json

5. Calculate Codon Usage & RSCU

python scripts/genbank_codon.py input.gbff

6. Detect CRISPR Arrays & Cas Genes

python scripts/genbank_crispr.py input.gbff

7. Export Protein FASTA

python scripts/genbank_fasta.py input.gbff output_proteins.faa

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License

MIT License