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
circular=False, # Set True for circular wraparound detection
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 fileoptions(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)circular(bool): Detect genes that wrap sequence end to start (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 usequiet(bool): Suppress informational output (default: True)
circular=True cannot be combined with closed_ends=True.
OrphosResult
Result from gene prediction.
Attributes:
output(str): Formatted output (GenBank, GFF, etc.)gene_count(int): Total number of genes predictedsequence_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.
1 maintainer
Metadata
1 maintainer
Release files for orphos 0.4.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
|---|---|---|---|---|
| orphos-0.4.0.tar.gz | 667.6 kB | With provenance | Details for orphos-0.4.0.tar.gz |
Built distributions (wheels)
Total release size: 45.7 MB
Release files / orphos-0.4.0.tar.gz
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|---|---|
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| Tags | Source |
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