Version Compatibility

Reference examples tested with: bedtools 2.31+, pandas 2.2+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

GTF/GFF Handling

"Parse gene annotations from GTF/GFF" → Read gene models, extract features by type (gene, exon, CDS), and query attributes from annotation files.

• Python: gffutils.create_db('file.gtf') (gffutils), pyranges.read_gtf() (pyranges)
• CLI: awk on tab-delimited GTF fields

GTF and GFF3 are standard gene annotation formats. Both use 1-based coordinates.

Format Comparison

GTF Format

chr1	HAVANA	gene	11869	14409	.	+	.	gene_id "ENSG00000223972"; gene_name "DDX11L1";
chr1	HAVANA	transcript	11869	14409	.	+	.	gene_id "ENSG00000223972"; transcript_id "ENST00000456328";
chr1	HAVANA	exon	11869	12227	.	+	.	gene_id "ENSG00000223972"; transcript_id "ENST00000456328"; exon_number "1";

GFF3 Format

chr1	HAVANA	gene	11869	14409	.	+	.	ID=ENSG00000223972;Name=DDX11L1
chr1	HAVANA	mRNA	11869	14409	.	+	.	ID=ENST00000456328;Parent=ENSG00000223972
chr1	HAVANA	exon	11869	12227	.	+	.	ID=exon1;Parent=ENST00000456328

Parse GTF with gtfparse (Python)

Installation

pip install gtfparse

Basic Parsing

import gtfparse

# Load entire GTF
df = gtfparse.read_gtf('annotation.gtf')

# View columns
print(df.columns)
# ['seqname', 'source', 'feature', 'start', 'end', 'score', 'strand', 'frame',
#  'gene_id', 'transcript_id', 'gene_name', ...]

# Filter by feature type
genes = df[df['feature'] == 'gene']
transcripts = df[df['feature'] == 'transcript']
exons = df[df['feature'] == 'exon']

# Get specific gene
gene_df = df[df['gene_name'] == 'TP53']

Extract Gene Coordinates

import gtfparse

df = gtfparse.read_gtf('annotation.gtf')

# All genes
genes = df[df['feature'] == 'gene'][['seqname', 'start', 'end', 'strand', 'gene_id', 'gene_name']]

# Convert to BED format (0-based)
genes_bed = genes.copy()
genes_bed['start'] = genes_bed['start'] - 1  # GTF is 1-based, BED is 0-based
genes_bed = genes_bed[['seqname', 'start', 'end', 'gene_name', 'gene_id', 'strand']]
genes_bed.to_csv('genes.bed', sep='\t', header=False, index=False)

Get Exons for Gene

import gtfparse

df = gtfparse.read_gtf('annotation.gtf')

# Get all exons for TP53
tp53_exons = df[(df['gene_name'] == 'TP53') & (df['feature'] == 'exon')]
tp53_exons = tp53_exons[['seqname', 'start', 'end', 'transcript_id', 'exon_number']]
print(tp53_exons)

Parse GFF with gffutils (Python)

Installation

pip install gffutils

Create Database

import gffutils

# Create database (slow first time, fast for subsequent queries)
db = gffutils.create_db('annotation.gff3', 'annotation.db',
                         force=True, merge_strategy='create_unique')

# Or load existing database
db = gffutils.FeatureDB('annotation.db')

Query Features

import gffutils

db = gffutils.FeatureDB('annotation.db')

# Count features by type
for featuretype in db.featuretypes():
    count = db.count_features_of_type(featuretype)
    print(f'{featuretype}: {count}')

# Get all genes
for gene in db.features_of_type('gene'):
    print(f'{gene.id}: {gene.seqid}:{gene.start}-{gene.end}')

# Get gene by ID
gene = db['ENSG00000141510']  # TP53
print(f'{gene.attributes["Name"][0]}: {gene.seqid}:{gene.start}-{gene.end}')

# Get children (transcripts, exons)
for transcript in db.children(gene, featuretype='mRNA'):
    print(f'  Transcript: {transcript.id}')
    for exon in db.children(transcript, featuretype='exon'):
        print(f'    Exon: {exon.start}-{exon.end}')

Get Introns

import gffutils

db = gffutils.FeatureDB('annotation.db')

# Get introns for a transcript
transcript = db['ENST00000269305']
introns = list(db.interfeatures(db.children(transcript, featuretype='exon'),
                                 new_featuretype='intron'))
for intron in introns:
    print(f'Intron: {intron.start}-{intron.end}')

Convert Formats with gffread (CLI)

Installation

conda install -c bioconda gffread

GTF to GFF3

gffread annotation.gtf -o annotation.gff3

GFF3 to GTF

gffread annotation.gff3 -T -o annotation.gtf

Extract Sequences

# Extract transcript sequences
gffread -w transcripts.fa -g genome.fa annotation.gtf

# Extract CDS sequences
gffread -x cds.fa -g genome.fa annotation.gtf

# Extract protein sequences
gffread -y proteins.fa -g genome.fa annotation.gtf

Filter Features

# Keep only protein-coding genes
gffread annotation.gtf -C -o coding.gtf

# Keep specific gene types
gffread annotation.gtf --keep-genes=protein_coding -o coding.gtf

Extract Regions with bedtools

Get Promoters

# Extract TSS (transcript start sites)
awk '$3 == "transcript"' annotation.gtf | \
    awk -v OFS='\t' '{
        if ($7 == "+") print $1, $4-1, $4, ".", ".", $7;
        else print $1, $5-1, $5, ".", ".", $7;
    }' > tss.bed

# Get promoter regions (2kb upstream of TSS)
bedtools flank -i tss.bed -g genome.txt -l 2000 -r 0 -s > promoters.bed

Get Gene Bodies

# Extract gene coordinates to BED
awk '$3 == "gene"' annotation.gtf | \
    awk -v OFS='\t' '{
        split($0, a, "gene_id \""); split(a[2], b, "\"");
        print $1, $4-1, $5, b[1], ".", $7;
    }' > genes.bed

Get Exons

# Extract unique exons
awk '$3 == "exon"' annotation.gtf | \
    awk -v OFS='\t' '{print $1, $4-1, $5, ".", ".", $7}' | \
    sort -k1,1 -k2,2n | uniq > exons.bed

Python: GTF to BED Conversion

Goal: Convert GTF annotation features to BED format with proper coordinate system translation for use with bedtools operations.

Approach: Load the GTF with gtfparse, filter to the desired feature type (gene, exon, etc.), convert from 1-based inclusive GTF coordinates to 0-based half-open BED coordinates by subtracting 1 from start positions.

import gtfparse
import pandas as pd

def gtf_to_bed(gtf_path, feature_type='gene', output_path=None):
    '''Convert GTF features to BED format.'''
    df = gtfparse.read_gtf(gtf_path)
    features = df[df['feature'] == feature_type].copy()

    # Convert to 0-based coordinates
    bed = pd.DataFrame({
        'chrom': features['seqname'],
        'start': features['start'] - 1,
        'end': features['end'],
        'name': features.get('gene_name', features.get('gene_id', '.')),
        'score': 0,
        'strand': features['strand']
    })

    if output_path:
        bed.to_csv(output_path, sep='\t', header=False, index=False)
    return bed

# Usage
genes_bed = gtf_to_bed('annotation.gtf', 'gene', 'genes.bed')
exons_bed = gtf_to_bed('annotation.gtf', 'exon', 'exons.bed')

Validate GTF/GFF

# Check GTF format
gffread -E annotation.gtf

# Check GFF3 format
gffread -E annotation.gff3

# Detailed validation
gt gff3validator annotation.gff3  # requires genometools

Common Attributes

GTF Attributes

GFF3 Attributes

Memory-Efficient Processing

import gtfparse

# Process large files in chunks (gtfparse loads all into memory)
# For very large files, use gffutils database approach

# Or filter during parsing
df = gtfparse.read_gtf('annotation.gtf',
                        features=['gene', 'exon'])  # Only load specific features

Related Skills

• bed-file-basics - BED format and conversion
• interval-arithmetic - Gene/exon overlap analysis
• proximity-operations - TSS proximity analysis
• differential-expression/de-results - Gene coordinate mapping