biogl 3.0.1

A collection of (semi) useful bioinformatics functions

biogl

A collection of useful small bioinformatics functions for working with genomic data formats.

Features

• GFF3/GTF Parsing: Comprehensive parser with type hints and opt-in GFF3 spec compliance
• FASTA Utilities: Functions for parsing and manipulating FASTA files
• Coordinate Operations: Tools for working with genomic coordinates
• Type Safety: Full type hints for better IDE support and static analysis
• Well Tested: Comprehensive test suite with real genomic data

Installation

Using pip (recommended)

python3 -m pip install biogl

Development Installation

git clone https://github.com/grahamlarue/biogl.git
cd biogl
pip install -e ".[dev]"

Quick Start

import biogl

# Parse a GFF3/GTF line
from biogl import GxfParse

line = "chr1\tEnsembl\tgene\t1000\t2000\t.\t+\t.\tID=gene1;Name=TEST"
parsed = GxfParse(line, line_number=1)

print(parsed.region)      # chr1
print(parsed.start)       # 1000
print(parsed.stop)        # 2000
print(parsed.strand)      # 1 (normalized)
print(parsed.name)        # gene1
print(parsed.attributes)  # {'ID': 'gene1', 'Name': 'TEST'}

# Enable GFF3 spec compliance features
parsed = GxfParse(
    line,
    line_number=1,
    url_decode=True,        # Decode percent-encoded values
    case_sensitive=True,    # Case-sensitive attribute matching
    strict_coordinates=True # Validate start <= end
)

# Parse FASTA files
from biogl import fasta_parse

for header, sequence in fasta_parse("genome.fa"):
    print(f"{header}: {len(sequence)} bp")

# Work with coordinates
from biogl import coord_overlap

overlap = coord_overlap(100, 200, 150, 250)  # Returns 50

# Reverse complement
from biogl import rev_comp

seq = "ATCG"
rc = rev_comp(seq)  # Returns "CGAT"

Key Modules

• GxfParse: Parse GFF3/GTF annotation files with full type hints
• fasta_parse: Efficient FASTA file parsing
• coord_overlap: Calculate coordinate overlaps
• rev_comp: Reverse complement DNA sequences
• translate: Translate DNA to protein
• flex_open: Open compressed or uncompressed files transparently
• window: Sliding window generator
• And more...

Breaking Changes in v3.0.0

Important: Version 3.0.0 introduces breaking changes to GxfParse:

• Features without explicit IDs now return None instead of 'feature_None' strings
• Migration: Change if name == 'exon_None' to if name is None

See CHANGELOG.md for full details.

Documentation

For detailed documentation on each module, use Python's built-in help:

from biogl import GxfParse
help(GxfParse)

Requirements

• Python 3.10+
• smart_open

Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

License

MIT License - see LICENSE file for details.

Author

Graham Larue ([e-mail])

Links

• PyPI
• GitHub
• Issues
• Changelog