Compressed Files

Handle gzip, bzip2, and BGZF compressed sequence files with Biopython.

Required Imports

import gzip
import bz2
from Bio import SeqIO
from Bio import bgzf  # For BGZF (indexable compression)

Reading Compressed Files

Gzip (.gz)

with gzip.open('sequences.fasta.gz', 'rt') as handle:
    for record in SeqIO.parse(handle, 'fasta'):
        print(record.id, len(record.seq))

Important: Use 'rt' (read text) mode, not 'rb' (read binary).

Bzip2 (.bz2)

with bz2.open('sequences.fasta.bz2', 'rt') as handle:
    for record in SeqIO.parse(handle, 'fasta'):
        print(record.id, len(record.seq))

BGZF (Block Gzip)

BGZF files can be read like regular gzip, but also support indexing:

# Read like normal gzip (auto-detected)
for record in SeqIO.parse('sequences.fasta.bgz', 'fasta'):
    print(record.id)

# Or explicitly with bgzf module
with bgzf.open('sequences.fasta.bgz', 'rt') as handle:
    for record in SeqIO.parse(handle, 'fasta'):
        print(record.id)

Writing Compressed Files

Gzip (.gz)

with gzip.open('output.fasta.gz', 'wt') as handle:
    SeqIO.write(records, handle, 'fasta')

Bzip2 (.bz2)

with bz2.open('output.fasta.bz2', 'wt') as handle:
    SeqIO.write(records, handle, 'fasta')

BGZF (.bgz)

with bgzf.open('output.fasta.bgz', 'wt') as handle:
    SeqIO.write(records, handle, 'fasta')

BGZF: Indexable Compression

BGZF is the only compressed format that supports SeqIO.index() and SeqIO.index_db().

BGZF (Block GZip Format) is a variant of gzip that allows random access. It's used by BAM files and tabix-indexed files.

Create Indexable Compressed File

from Bio import SeqIO, bgzf

# Write as BGZF (can be indexed later)
records = SeqIO.parse('input.fasta', 'fasta')
with bgzf.open('output.fasta.bgz', 'wt') as handle:
    SeqIO.write(records, handle, 'fasta')

Index a BGZF File

# SeqIO.index() works with BGZF!
records = SeqIO.index('sequences.fasta.bgz', 'fasta')
seq = records['target_id'].seq
records.close()

# SeqIO.index_db() also works
records = SeqIO.index_db('index.sqlite', 'sequences.fasta.bgz', 'fasta')

Convert Gzip to BGZF

from Bio import SeqIO, bgzf
import gzip

# Read from gzip, write to BGZF
with gzip.open('input.fasta.gz', 'rt') as in_handle:
    with bgzf.open('output.fasta.bgz', 'wt') as out_handle:
        SeqIO.write(SeqIO.parse(in_handle, 'fasta'), out_handle, 'fasta')

Code Patterns

Read Gzipped FASTQ

with gzip.open('reads.fastq.gz', 'rt') as handle:
    records = list(SeqIO.parse(handle, 'fastq'))
print(f'Loaded {len(records)} reads')

Count Records in Gzipped File

with gzip.open('sequences.fasta.gz', 'rt') as handle:
    count = sum(1 for _ in SeqIO.parse(handle, 'fasta'))
print(f'{count} sequences')

Fast Count with Low-Level Parser

from Bio.SeqIO.FastaIO import SimpleFastaParser
import gzip

with gzip.open('sequences.fasta.gz', 'rt') as handle:
    count = sum(1 for _ in SimpleFastaParser(handle))

Convert Compressed to Uncompressed

with gzip.open('input.fasta.gz', 'rt') as in_handle:
    records = SeqIO.parse(in_handle, 'fasta')
    SeqIO.write(records, 'output.fasta', 'fasta')

Convert Uncompressed to Compressed

records = SeqIO.parse('input.fasta', 'fasta')
with gzip.open('output.fasta.gz', 'wt') as out_handle:
    SeqIO.write(records, out_handle, 'fasta')

Auto-Detect Compression

from pathlib import Path
from Bio import SeqIO, bgzf
import gzip
import bz2

def open_sequence_file(filepath, format):
    filepath = Path(filepath)
    suffix = filepath.suffix.lower()
    if suffix == '.gz':
        # Could be gzip or bgzf - bgzf handles both
        handle = bgzf.open(filepath, 'rt')
    elif suffix == '.bgz':
        handle = bgzf.open(filepath, 'rt')
    elif suffix == '.bz2':
        handle = bz2.open(filepath, 'rt')
    else:
        handle = open(filepath, 'r')
    return SeqIO.parse(handle, format)

Process Large Gzipped File (Memory Efficient)

with gzip.open('large.fastq.gz', 'rt') as handle:
    for record in SeqIO.parse(handle, 'fastq'):
        if len(record.seq) >= 100:
            process(record)

Compress Existing File (Raw Copy)

import shutil

with open('sequences.fasta', 'rb') as f_in:
    with gzip.open('sequences.fasta.gz', 'wb') as f_out:
        shutil.copyfileobj(f_in, f_out)

Compression Comparison

Format	Extension	Indexable	Speed	Compression
Gzip	.gz	No	Fast	Good
BGZF	.bgz	Yes	Fast	Good
Bzip2	.bz2	No	Slow	Better
LZMA	.xz	No	Slowest	Best

When to Use Each Format

Use Case	Recommended Format
Archive (no random access needed)	gzip or bzip2
Need to index compressed file	BGZF
BAM files and tabix	BGZF (native)
Maximum compression	bzip2 or xz
Best speed	gzip or BGZF

Common Errors

Error	Cause	Solution
TypeError: a bytes-like object is required	Used 'rb' mode	Use 'rt' for text mode
UnicodeDecodeError	Wrong encoding	Try gzip.open(file, 'rt', encoding='latin-1')
gzip.BadGzipFile	Not a gzip file	Check file extension matches actual format
OSError: Not a gzipped file	Corrupt or wrong format	Verify file integrity
SeqIO.index() fails on .gz	Regular gzip not indexable	Convert to BGZF first

Decision Tree

Working with compressed sequence files?
├── Just reading sequentially?
│   └── Use gzip.open() or bz2.open() with 'rt' mode
├── Need to index the compressed file?
│   └── Convert to BGZF, then use SeqIO.index()
├── Writing compressed output?
│   ├── Will need to index later? → Use bgzf.open()
│   └── Just archiving? → Use gzip.open() or bz2.open()
└── Converting between formats?
    └── Parse with SeqIO, write to new handle

Related Skills

• read-sequences - Core parsing functions used with compressed handles
• write-sequences - Write to compressed output files
• batch-processing - Process multiple compressed files
• alignment-files - BAM files use BGZF natively; samtools handles compression