orphos 0.1.0

Python bindings for Orphos - a gene prediction tool for microbial genomes

Orphos Python Bindings

Python bindings for Orphos, a fast and accurate gene prediction tool for microbial genomes.

Installation

From Source

You'll need Rust and Python 3.8+ installed. Then:

# Install maturin (the build tool for Python+Rust projects)
pip install maturin

# Build and install in development mode
cd orphos-python
maturin develop --release

# Or build a wheel
maturin build --release
pip install target/wheels/orphos-*.whl

Quick Start

import orphos

# Analyze a FASTA file
result = orphos.analyze_file("genome.fasta")
print(f"Found {result.gene_count} genes in {result.sequence_count} sequences")
print(result.output)  # GenBank formatted output

# Analyze a sequence string
fasta_string = """>seq1
ATGCGATCGATCGATCGATCGATCGATCG...
"""
result = orphos.analyze_sequence(fasta_string)

# Customize options
options = orphos.OrphosOptions(
    mode="meta",           # Use metagenomic mode
    format="gff",          # Output in GFF format
    closed_ends=True,      # Don't allow genes off edges
    translation_table=11   # Use translation table 11
)
result = orphos.analyze_file("genome.fasta", options)

API Reference

analyze_sequence(fasta_content, options=None)

Analyze DNA sequences from a FASTA-formatted string.

Parameters:

• fasta_content (str): FASTA-formatted sequence(s)
• options (OrphosOptions, optional): Configuration options

Returns: OrphosResult

analyze_file(file_path, options=None)

Analyze DNA sequences from a FASTA file.

Parameters:

• file_path (str): Path to the FASTA file
• options (OrphosOptions, optional): Configuration options

Returns: OrphosResult

OrphosOptions

Configuration options for gene prediction.

Attributes:

• mode (str): "single" for single genome mode, "meta" for metagenomic mode (default: "single")
• format (str): Output format - "gbk", "gff", "sco", or "gca" (default: "gbk")
• closed_ends (bool): Don't allow genes to run off edges (default: False)
• mask_n_runs (bool): Mask runs of N's in the sequence (default: False)
• force_non_sd (bool): Force non-Shine-Dalgarno model (default: False)
• translation_table (int, optional): Translation table 1-25 (excluding 7, 8, 17-20)
• num_threads (int, optional): Number of threads to use
• quiet (bool): Suppress informational output (default: True)

OrphosResult

Result from gene prediction.

Attributes:

• output (str): Formatted output (GenBank, GFF, etc.)
• gene_count (int): Total number of genes predicted
• sequence_count (int): Number of sequences analyzed

Examples

Single Genome Mode (Default)

import orphos

# Analyze with default settings
result = orphos.analyze_file("ecoli.fasta")
print(f"Found {result.gene_count} genes")

# Save GenBank output
with open("output.gbk", "w") as f:
    f.write(result.output)

Metagenomic Mode

import orphos

options = orphos.OrphosOptions(mode="meta")
result = orphos.analyze_file("metagenome.fasta", options)

GFF Output Format

import orphos

options = orphos.OrphosOptions(format="gff")
result = orphos.analyze_file("genome.fasta", options)

# Save GFF output
with open("output.gff", "w") as f:
    f.write(result.output)

Custom Translation Table

import orphos

# Use translation table 4 (Mycoplasma/Spiroplasma)
options = orphos.OrphosOptions(translation_table=4)
result = orphos.analyze_file("mycoplasma.fasta", options)

Processing Multiple Files

import orphos
import os

fasta_dir = "genomes"
output_dir = "predictions"
os.makedirs(output_dir, exist_ok=True)

options = orphos.OrphosOptions(format="gff")

for filename in os.listdir(fasta_dir):
    if filename.endswith(".fasta"):
        input_path = os.path.join(fasta_dir, filename)
        output_path = os.path.join(output_dir, filename.replace(".fasta", ".gff"))
        
        result = orphos.analyze_file(input_path, options)
        
        with open(output_path, "w") as f:
            f.write(result.output)
        
        print(f"{filename}: {result.gene_count} genes")

Output Formats

GenBank (gbk)

Standard GenBank feature table format with gene coordinates and annotations.

GFF (gff)

GFF3 format with gene features and attributes.

Simple Coordinates (sco)

Simple tab-delimited format with gene coordinates.

Gene Calls (gca)

Detailed gene call information including scores and training data.

Performance

The Python bindings have minimal overhead compared to the native Rust implementation. Large genomes and metagenomes can be processed efficiently.

License

GPL-3.0-or-later

Citation

If you use Orphos in your research, please cite:

Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Orphos: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010 Mar 8;11:119.