metagene 0.0.7

Metagene Profiling Analysis and Visualization

Metagene

Metagene Profiling Analysis and Visualization

A Python package for performing metagene analysis on genomic sites. This tool allows you to analyze the distribution of genomic features relative to gene regions (5'UTR, CDS, 3'UTR) and create publication-ready metagene profile plots.

Installation

Install metagene using pip:

pip install metagene

Or using uv:

uv add metagene

Quick Start

Command Line Interface

Basic metagene analysis using a built-in reference:

# Using built-in human genome reference (GRCh38)
metagene -i sites.tsv.gz -r GRCh38 --with-header -m 1,2,3 -w 5 \
         -o output.tsv -s scores.tsv -p plot.png

Using a custom GTF file:

# Using custom GTF annotation
metagene -i sites.bed -g custom.gtf.gz -m 1,2,3 -w 5 \
         -o output.tsv -s scores.tsv -p plot.png

Python API

import polars as pl
from metagene import (
    load_sites, load_reference, map_to_transcripts, 
    normalize_positions, plot_profile
)

# Load your genomic sites
sites_df = load_sites("sites.tsv.gz", with_header=True, meta_col_index=[0, 1, 2])

# Load reference genome annotation
reference = load_reference("GRCh38")  # or load_gtf("custom.gtf.gz")

# Perform metagene analysis
annotated_df = map_to_transcripts(sites_df, reference)
final_df, gene_splits = normalize_positions(annotated_df, strategy="median")

# Generate plot
plot_profile(final_df, gene_splits, "metagene_plot.png")

print(f"Analyzed {len(final_df)} sites")
print(f"Gene splits - 5'UTR: {gene_splits[0]:.3f}, CDS: {gene_splits[1]:.3f}, 3'UTR: {gene_splits[2]:.3f}")

Input Formats

TSV Format (Tab-separated values)

ref	pos	strand	score	pvalue
chr1	1000000	+	0.85	0.001
chr1	2000000	-	0.72	0.005

BED Format

chr1	999999	1000000	score1	0.85	+
chr1	1999999	2000000	score2	0.72	-

Column Specification

• Use -m/--meta-columns to specify coordinate columns (1-based indexing)
• Use -w/--weight-columns to specify score/weight columns
• Use --with-header if your file has a header line

Built-in References

Metagene includes pre-processed gene annotations for major model organisms:

Species	Assembly	Reference
Human	GRCh38/hg38	GRCh38, hg38
	GRCh37/hg19	GRCh37, hg19
Mouse	GRCm39/mm39	GRCm39, mm39
	GRCm38/mm10	GRCm38, mm10
	mm9/NCBIM37	mm9, NCBIM37
Arabidopsis	TAIR10	TAIR10
Rice	IRGSP-1.0	IRGSP-1.0
Model Organisms	Various	dm6, ce11, WBcel235, sacCer3, etc.

Managing References

List all available references:

metagene --list

This will show all 23+ available references organized by species:

Human:
  GRCh37          - Human genome GRCh37 (Ensembl release 75)
  GRCh38          - Human genome GRCh38 (Ensembl release 110)
  hg19            - Human genome hg19 (UCSC 2021)
  hg38            - Human genome hg38 (UCSC 2022)

Mouse:
  GRCm38          - Mouse genome GRCm38 (Ensembl release 102)
  GRCm39          - Mouse genome GRCm39 (Ensembl release 110)
  mm10            - Mouse genome mm10 (UCSC 2021)
  mm39            - Mouse genome mm39 (UCSC 2024)
  mm9             - Mouse genome mm9 (UCSC 2020)

... and more

Download a specific reference:

metagene --download GRCh38

Download all references (requires ~10GB disk space):

metagene --download all

CLI Examples

Basic Analysis

# Analyze sites with built-in human reference
metagene -i sites.tsv.gz -r GRCh38 --with-header \
         -m 1,2,3 -w 5 -o output.tsv -p plot.png

Note: References are automatically downloaded on first use.

Advanced Options

# Full analysis with custom parameters
metagene -i sites.bed -r GRCh38 \
         -m 1,2,3 -w 5,6 -n "score1,score2" \
         --bins 200 --region all \
         --score-transform log2 --normalize \
         -o annotated.tsv -s statistics.tsv -p metagene.pdf

Custom GTF Reference

# Use your own GTF annotation
metagene -i sites.tsv.gz -g annotation.gtf.gz --with-header \
         -m 1,2,3 -w 4 -o output.tsv -p plot.png

API Reference

Core Functions

• load_sites(file, with_header=False, meta_col_index=[0,1,2]) - Load genomic sites
• load_reference(name) - Load built-in reference genome
• load_gtf(file) - Load custom GTF annotation
• map_to_transcripts(sites, reference) - Annotate sites with gene information
• normalize_positions(annotated_sites, strategy="median") - Normalize to relative positions
• plot_profile(data, gene_splits, output_file) - Generate metagene plot

Analysis Workflow

# 1. Load data
sites = load_sites("input.tsv", with_header=True, meta_col_index=[0,1,2])
reference = load_reference("GRCh38")

# 2. Annotate and normalize  
annotated = map_to_transcripts(sites, reference)
normalized, splits = normalize_positions(annotated)

# 3. Visualize
plot_profile(normalized, splits, "output.png")

Demo

The plot shows the distribution of genomic sites across normalized gene regions:

• 5'UTR (0.0 - first split): 5' untranslated region
• CDS (first split - second split): Coding sequence
• 3'UTR (second split - 1.0): 3' untranslated region