bwamem

Python bindings for the BWA-MEM aligner.

Installation

pip install bwamem

Usage

Build Index

from bwamem import BwaIndexer

indexer = BwaIndexer()
index_path = indexer.build_index('reference.fa')

Single-End Alignment

from bwamem import BwaAligner

aligner = BwaAligner('path/to/index')
alignments = aligner.align('ACGATCGCGATCGA')

for aln in alignments:
    print(f'{aln.ctg}:{aln.r_st} strand={aln.strand} mapq={aln.mapq}')

Paired-End Alignment

read1 = 'ACGATCGCGATCGA'
read2 = 'TTCGATCGATCGAT'

paired_alignments = aligner.align(read1, read2)

for pe_aln in paired_alignments:
    print(f'Insert size: {pe_aln.insert_size}, Proper pair: {pe_aln.is_proper_pair}')

Retrieve Sequences from Index

# Get full sequence
seq = aligner.seq('chr1')

# Get subsequence
subseq = aligner.seq('chr1', start=100, end=200)

Monitor Index Building Progress

from bwamem import BwaIndexer

# Progress messages are captured by default (no console spam)
indexer = BwaIndexer(capture_progress=True)
index_path = indexer.build_index('genome.fasta')

# Check progress info
progress = indexer.get_progress()
print(f"Status: {progress['status']}")
print(f"Iterations: {progress['iterations']}")
print(f"Characters processed: {progress['characters_processed']}")

# Get progress percentage (if available)
if indexer.progress_percent:
    print(f"Progress: {indexer.progress_percent:.1f}%")

# Access all captured messages
for msg in progress['messages']:
    print(msg)

Control Index Building Verbosity

from bwamem import BwaIndexer

# Verbosity levels:
# 0 = silent (no output)
# 1 = quiet (only warnings/errors) - default
# 2 = normal (standard BWA messages)
# 3+ = debug (verbose output)

# Silent mode
indexer = BwaIndexer(verbose=0)
indexer.build_index('genome.fasta')

# Normal mode with progress messages shown in console
indexer = BwaIndexer(verbose=2, capture_progress=False)
indexer.build_index('genome.fasta')

# Debug mode with captured progress
indexer = BwaIndexer(verbose=3, capture_progress=True)
indexer.build_index('genome.fasta')

# Custom algorithm and block size
indexer = BwaIndexer(algorithm='bwtsw', block_size=50000000)
indexer.build_index('genome.fasta')

Read FASTA/FASTQ Files

from bwamem import fastx_read, read_paired_fastx

# Single-end (supports both FASTA and FASTQ)
for read in fastx_read('sequences.fasta.gz'):
    print(f'{read.name}: {read.sequence}')

# Paired-end
for read1, read2 in read_paired_fastx('R1.fastq', 'R2.fastq'):
    print(f'{read1.name}, {read2.name}')

Custom Options

# Specify alignment parameters
aligner = BwaAligner('path/to/index', options='-x ont2d -A 1 -B 0')

# Set custom insert size for paired-end reads
aligner = BwaAligner('path/to/index', insert_model=(500, 50))
paired_alignments = aligner.align(read1, read2)

Alignment Attributes

Each Alignment object contains the following attributes:

Attribute	Description
`ctg`	Contig/reference name
`r_st`	Reference start position (0-based)
`r_en`	Reference end position (property)
`strand`	Strand: +1 for forward, -1 for reverse
`q_st`, `q_en`	Query start/end positions
`mapq`	Mapping quality score
`cigar`	CIGAR as list of `[length, op]` pairs
`cigar_str`	CIGAR string (property)
`NM`	Edit distance
`score`	Alignment score
`is_primary`	Primary alignment flag

Calculated properties (computed on demand): r_en, cigar_str, blen, mlen

CIGAR operations: 0=M (match), 1=I (insertion), 2=D (deletion), 3=N (skip), 4=S (soft-clip), 5=H (hard-clip)

PairedAlignment contains: read1, read2 (Alignment objects), is_proper_pair (bool), insert_size (int or None)

License

Python bindings: Mozilla Public License 2.0
BWA: GNU General Public License v3.0

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

bwamem-0.0.54.tar.gz (1.1 MB view details)

Uploaded Aug 12, 2026 Source

Built Distributions

If you're not sure about the file name format, learn more about wheel file names.

The dropdown lists show the available interpreters, ABIs, and platforms. Enable javascript to be able to filter the list of wheel files.

bwamem-0.0.54-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (384.1 kB view details)

Uploaded Aug 12, 2026 CPython 3.13manylinux: glibc 2.17+ x86-64

bwamem-0.0.54-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (384.0 kB view details)

Uploaded Aug 12, 2026 CPython 3.12manylinux: glibc 2.17+ x86-64

File details

Details for the file bwamem-0.0.54.tar.gz.

File metadata

Download URL: bwamem-0.0.54.tar.gz
Upload date: Aug 12, 2026
Size: 1.1 MB
Tags: Source
Uploaded using Trusted Publishing? Yes
Uploaded via: twine/7.0.0 CPython/3.13.14

File hashes

Hashes for bwamem-0.0.54.tar.gz
Algorithm	Hash digest
SHA256	`ec2601d5e94936b6bdc1bc4011feea4c189ca851833749210867cbd7a7f2a975`
MD5	`322c702376f0b92126080d48798f1758`
BLAKE2b-256	`0e085d2714bf84ba8336d87812c893fec552632cf148cbda537ab92a5eea4e93`

See more details on using hashes here.

Provenance

The following attestation bundles were made for bwamem-0.0.54.tar.gz:

Publisher: publish.yml on y9c/bwamem

Attestations: Values shown here reflect the state when the release was signed and may no longer be current.

Statement:
- Statement type: https://in-toto.io/Statement/v1
- Predicate type: https://docs.pypi.org/attestations/publish/v1
- Subject name: bwamem-0.0.54.tar.gz
- Subject digest: ec2601d5e94936b6bdc1bc4011feea4c189ca851833749210867cbd7a7f2a975
- Sigstore transparency entry: 2433376300
- Sigstore integration time: Aug 12, 2026
Source repository:
- Permalink: y9c/bwamem@33cb2eca3e27dd82954d16ddad8661fe48f0ca11
- Branch / Tag: refs/heads/main
- Owner: https://github.com/y9c
- Access: public
Publication detail:
- Token Issuer: https://token.actions.githubusercontent.com
- Runner Environment: github-hosted
- Publication workflow: publish.yml@33cb2eca3e27dd82954d16ddad8661fe48f0ca11
- Trigger Event: push

File details

Details for the file bwamem-0.0.54-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.

File metadata

Download URL: bwamem-0.0.54-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Upload date: Aug 12, 2026
Size: 384.1 kB
Tags: CPython 3.13, manylinux: glibc 2.17+ x86-64
Uploaded using Trusted Publishing? Yes
Uploaded via: twine/7.0.0 CPython/3.13.14

File hashes

Hashes for bwamem-0.0.54-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm	Hash digest
SHA256	`08884a289772143e1bc311d8c2cc52dd3f239f69bd0cab7e1c6f661583375887`
MD5	`e085ecc7925abb3ad433605e28add16a`
BLAKE2b-256	`cdcd733133cfde05f6de1ee31d626dfcad3e7675dc40a0648898f304f6fdffe6`

See more details on using hashes here.

Provenance

The following attestation bundles were made for bwamem-0.0.54-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl:

Publisher: publish.yml on y9c/bwamem

Attestations: Values shown here reflect the state when the release was signed and may no longer be current.

Statement:
- Statement type: https://in-toto.io/Statement/v1
- Predicate type: https://docs.pypi.org/attestations/publish/v1
- Subject name: bwamem-0.0.54-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
- Subject digest: 08884a289772143e1bc311d8c2cc52dd3f239f69bd0cab7e1c6f661583375887
- Sigstore transparency entry: 2433376511
- Sigstore integration time: Aug 12, 2026
Source repository:
- Permalink: y9c/bwamem@33cb2eca3e27dd82954d16ddad8661fe48f0ca11
- Branch / Tag: refs/heads/main
- Owner: https://github.com/y9c
- Access: public
Publication detail:
- Token Issuer: https://token.actions.githubusercontent.com
- Runner Environment: github-hosted
- Publication workflow: publish.yml@33cb2eca3e27dd82954d16ddad8661fe48f0ca11
- Trigger Event: push

File details

Details for the file bwamem-0.0.54-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.

File metadata

Download URL: bwamem-0.0.54-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Upload date: Aug 12, 2026
Size: 384.0 kB
Tags: CPython 3.12, manylinux: glibc 2.17+ x86-64
Uploaded using Trusted Publishing? Yes
Uploaded via: twine/7.0.0 CPython/3.13.14

File hashes

Hashes for bwamem-0.0.54-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm	Hash digest
SHA256	`faba6e5c76d176103202b1343da4af97f01b51bfe5bee2b202de095b5f139cd5`
MD5	`9847afe342a7cdd1b6c1d22888055c65`
BLAKE2b-256	`9c0dd1c6cb1d7e5d8befd5201b9eb2d183a78ab1725b7ea9eb612a4e58775e2b`

See more details on using hashes here.

Provenance

The following attestation bundles were made for bwamem-0.0.54-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl:

Publisher: publish.yml on y9c/bwamem

Attestations: Values shown here reflect the state when the release was signed and may no longer be current.

Statement:
- Statement type: https://in-toto.io/Statement/v1
- Predicate type: https://docs.pypi.org/attestations/publish/v1
- Subject name: bwamem-0.0.54-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
- Subject digest: faba6e5c76d176103202b1343da4af97f01b51bfe5bee2b202de095b5f139cd5
- Sigstore transparency entry: 2433376396
- Sigstore integration time: Aug 12, 2026
Source repository:
- Permalink: y9c/bwamem@33cb2eca3e27dd82954d16ddad8661fe48f0ca11
- Branch / Tag: refs/heads/main
- Owner: https://github.com/y9c
- Access: public
Publication detail:
- Token Issuer: https://token.actions.githubusercontent.com
- Runner Environment: github-hosted
- Publication workflow: publish.yml@33cb2eca3e27dd82954d16ddad8661fe48f0ca11
- Trigger Event: push