A comprehensive library for computational molecular biology

Navigation

Verified details

These details have been verified by PyPI
Project links
GitHub Statistics
Maintainers
Avatar for padix-key from gravatar.com padix-key Avatar for t0mdavid-m from gravatar.com t0mdavid-m

Unverified details

These details have not been verified by PyPI
Project links
Meta
  • License Expression: BSD-3-Clause
    SPDX License Expression
  • Author: The Biotite contributors
  • Requires: Python >=3.12
  • Provides-Extra: test , lint
Classifiers
Report project as malware

Project description

Biotite at PyPI Python version Test status The Biotite Project

Biotite project

Biotite is your Swiss army knife for bioinformatics. Whether you want to identify homologous sequence regions in a protein family or you would like to find disulfide bonds in a protein structure: Biotite has the right tool for you. This package bundles popular tasks in computational molecular biology into a uniform Python library. It can handle a major part of the typical workflow for sequence and biomolecular structure data:

  • Searching and fetching data from biological databases

  • Reading and writing popular sequence/structure file formats

  • Analyzing and editing sequence/structure data

  • Visualizing sequence/structure data

  • Interfacing external applications for further analysis

Biotite internally stores most of the data as NumPy ndarray objects, enabling

  • fast C-accelerated analysis,

  • intuitive usability through NumPy-like indexing syntax,

  • extensibility through direct access of the internal NumPy arrays.

As a result the user can skip writing code for basic functionality (like file parsers) and can focus on what their code makes unique - from small analysis scripts to entire bioinformatics software packages.

If you use Biotite in a scientific publication, please cite:

Kunzmann, P. & Hamacher, K. BMC Bioinformatics (2018) 19:346.
https://doi.org/10.1186/s12859-018-2367-z

Installation

Biotite requires the following packages:

  • numpy

  • requests

  • msgpack

  • networkx

Some functions require some extra packages:

  • matplotlib - Required for plotting purposes.

Biotite can be installed via Conda…

$ conda install -c conda-forge biotite

… or pip

$ pip install biotite

Usage

Here is a small example that downloads two protein sequences from the NCBI Entrez database and aligns them:

import biotite.sequence.align as align
import biotite.sequence.io.fasta as fasta
import biotite.database.entrez as entrez

# Download FASTA file for the sequences of avidin and streptavidin
file_name = entrez.fetch_single_file(
    uids=["CAC34569", "ACL82594"], file_name="sequences.fasta",
    db_name="protein", ret_type="fasta"
)

# Parse the downloaded FASTA file
# and create 'ProteinSequence' objects from it
fasta_file = fasta.FastaFile.read(file_name)
avidin_seq, streptavidin_seq = fasta.get_sequences(fasta_file).values()

# Align sequences using the BLOSUM62 matrix with affine gap penalty
matrix = align.SubstitutionMatrix.std_protein_matrix()
alignments = align.align_optimal(
    avidin_seq, streptavidin_seq, matrix,
    gap_penalty=(-10, -1), terminal_penalty=False
)
print(alignments[0])
MVHATSPLLLLLLLSLALVAPGLSAR------KCSLTGKWDNDLGSNMTIGAVNSKGEFTGTYTTAV-TA
-------------------DPSKESKAQAAVAEAGITGTWYNQLGSTFIVTA-NPDGSLTGTYESAVGNA

TSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFS----ESTTVFTGQCFIDRNGKEV-LKTMWLLRSSVN
ESRYVLTGRYDSTPATDGSGT--ALGWTVAWKNNYRNAHSATTWSGQYV---GGAEARINTQWLLTSGTT

DIGDDWKATRVGINIFTRLRTQKE---------------------
-AANAWKSTLVGHDTFTKVKPSAASIDAAKKAGVNNGNPLDAVQQ

More documentation, including a tutorial, an example gallery and the API reference is available at https://www.biotite-python.org/.

Contribution

Interested in improving Biotite? Have a look at the contribution guidelines. Feel free to join our community chat on Discord.

Project details

Verified details

These details have been verified by PyPI
Project links
GitHub Statistics
Maintainers
Avatar for padix-key from gravatar.com padix-key Avatar for t0mdavid-m from gravatar.com t0mdavid-m

Unverified details

These details have not been verified by PyPI
Project links
Meta
  • License Expression: BSD-3-Clause
    SPDX License Expression
  • Author: The Biotite contributors
  • Requires: Python >=3.12
  • Provides-Extra: test , lint
Classifiers

Release history Release notifications | RSS feed

This version

1.7.1

1.6.0

1.5.0

1.4.0

1.3.0

1.2.0

1.1.0

1.0.1

1.0.0

0.41.2

0.41.1

0.41.0 yanked

Reason this release was yanked:

Wrong version of NumPy

0.40.0

0.39.0

0.38.0

0.37.0

0.36.1

0.36.0

0.35.0

0.34.1

0.34.0

0.33.0

0.32.0

0.31.0

0.30.0

0.29.0

0.28.0

0.27.0

0.26.0

0.25.0

0.24.0

0.23.0

0.22.0

0.21.0

0.20.1

0.20.0

Download files

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

Source Distribution

biotite-1.7.1.tar.gz (39.9 MB view details)

Uploaded Source

Built Distributions

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

biotite-1.7.1-cp314-cp314-win_amd64.whl (45.3 MB view details)

Uploaded CPython 3.14Windows x86-64

biotite-1.7.1-cp314-cp314-manylinux_2_28_x86_64.whl (57.7 MB view details)

Uploaded CPython 3.14manylinux: glibc 2.28+ x86-64

biotite-1.7.1-cp314-cp314-manylinux_2_28_aarch64.whl (57.3 MB view details)

Uploaded CPython 3.14manylinux: glibc 2.28+ ARM64

biotite-1.7.1-cp314-cp314-macosx_11_0_arm64.whl (45.7 MB view details)

Uploaded CPython 3.14macOS 11.0+ ARM64

biotite-1.7.1-cp313-cp313-win_amd64.whl (45.3 MB view details)

Uploaded CPython 3.13Windows x86-64

biotite-1.7.1-cp313-cp313-manylinux_2_28_x86_64.whl (57.9 MB view details)

Uploaded CPython 3.13manylinux: glibc 2.28+ x86-64

biotite-1.7.1-cp313-cp313-manylinux_2_28_aarch64.whl (57.3 MB view details)

Uploaded CPython 3.13manylinux: glibc 2.28+ ARM64

biotite-1.7.1-cp313-cp313-macosx_11_0_arm64.whl (45.6 MB view details)

Uploaded CPython 3.13macOS 11.0+ ARM64

biotite-1.7.1-cp312-cp312-win_amd64.whl (45.3 MB view details)

Uploaded CPython 3.12Windows x86-64

biotite-1.7.1-cp312-cp312-manylinux_2_28_x86_64.whl (58.0 MB view details)

Uploaded CPython 3.12manylinux: glibc 2.28+ x86-64

biotite-1.7.1-cp312-cp312-manylinux_2_28_aarch64.whl (57.3 MB view details)

Uploaded CPython 3.12manylinux: glibc 2.28+ ARM64

biotite-1.7.1-cp312-cp312-macosx_11_0_arm64.whl (45.6 MB view details)

Uploaded CPython 3.12macOS 11.0+ ARM64

File details

Details for the file biotite-1.7.1.tar.gz.

File metadata

  • Download URL: biotite-1.7.1.tar.gz
  • Upload date:
  • Size: 39.9 MB
  • Tags: Source
  • Uploaded using Trusted Publishing? Yes
  • Uploaded via: twine/6.1.0 CPython/3.13.12

File hashes

Hashes for biotite-1.7.1.tar.gz
Algorithm Hash digest
SHA256 2ae4a5d2c2d5ba08ca5d89a647984c99f45994eb908b614e896ce9e4db3ca800
MD5 1154519bdafbc4861053353820a66b9d
BLAKE2b-256 fc93ed0751d0f16d54ec82735605c776b37c77af7949a3dd230a1226f2b3b4df

See more details on using hashes here.

Provenance

The following attestation bundles were made for biotite-1.7.1.tar.gz:

Publisher: test_and_deploy.yml on biotite-dev/biotite

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

File details

Details for the file biotite-1.7.1-cp314-cp314-win_amd64.whl.

File metadata

  • Download URL: biotite-1.7.1-cp314-cp314-win_amd64.whl
  • Upload date:
  • Size: 45.3 MB
  • Tags: CPython 3.14, Windows x86-64
  • Uploaded using Trusted Publishing? Yes
  • Uploaded via: twine/6.1.0 CPython/3.13.12

File hashes

Hashes for biotite-1.7.1-cp314-cp314-win_amd64.whl
Algorithm Hash digest
SHA256 858b9b947933744f2251a06197cb0a15ec6b64ec0b54bae4fbafecd39725c3ce
MD5 8f879e692d1f1ac4ddb12eecb8ec5f72
BLAKE2b-256 64ba9caf28b59d72f0414c68fca415fe00652718a93ff0743111433cca5c98c1

See more details on using hashes here.

Provenance

The following attestation bundles were made for biotite-1.7.1-cp314-cp314-win_amd64.whl:

Publisher: test_and_deploy.yml on biotite-dev/biotite

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

File details

Details for the file biotite-1.7.1-cp314-cp314-manylinux_2_28_x86_64.whl.

File metadata

File hashes

Hashes for biotite-1.7.1-cp314-cp314-manylinux_2_28_x86_64.whl
Algorithm Hash digest
SHA256 d34184f23facc4a35bc0ac7914162f6fc5b6c68bf7fbf3187c1966cf53ce9918
MD5 ff9d341a873ae2c2f0e59a602c889b73
BLAKE2b-256 3edccfbc0d38bded4f481d46be88c7ce00c0cd6f9455fb7d728484b2006ff4fe

See more details on using hashes here.

Provenance

The following attestation bundles were made for biotite-1.7.1-cp314-cp314-manylinux_2_28_x86_64.whl:

Publisher: test_and_deploy.yml on biotite-dev/biotite

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

File details

Details for the file biotite-1.7.1-cp314-cp314-manylinux_2_28_aarch64.whl.

File metadata

File hashes

Hashes for biotite-1.7.1-cp314-cp314-manylinux_2_28_aarch64.whl
Algorithm Hash digest
SHA256 d47443b507c6968cb6823ec0cc0bdca1baed6d11ce08bcc015b8a5409d943bf9
MD5 d5491a014cf71e63342ae5f1c83797d2
BLAKE2b-256 678b66ef1cda70d5b4f5d71c959b19f5bc22dde7e428f53a748f7f64ed02b6ae

See more details on using hashes here.

Provenance

The following attestation bundles were made for biotite-1.7.1-cp314-cp314-manylinux_2_28_aarch64.whl:

Publisher: test_and_deploy.yml on biotite-dev/biotite

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

File details

Details for the file biotite-1.7.1-cp314-cp314-macosx_11_0_arm64.whl.

File metadata

File hashes

Hashes for biotite-1.7.1-cp314-cp314-macosx_11_0_arm64.whl
Algorithm Hash digest
SHA256 327f008ec9539624d05161f34ac279b76f4ca303bd98cc9b49d6557dad7cc5c9
MD5 59b5c730cdc89c47a8b17e338e4fa923
BLAKE2b-256 c107aa395daa14c9078178875fecb688f8a7e185ac42eeb2296d1d4e17902b57

See more details on using hashes here.

Provenance

The following attestation bundles were made for biotite-1.7.1-cp314-cp314-macosx_11_0_arm64.whl:

Publisher: test_and_deploy.yml on biotite-dev/biotite

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

File details

Details for the file biotite-1.7.1-cp313-cp313-win_amd64.whl.

File metadata

  • Download URL: biotite-1.7.1-cp313-cp313-win_amd64.whl
  • Upload date:
  • Size: 45.3 MB
  • Tags: CPython 3.13, Windows x86-64
  • Uploaded using Trusted Publishing? Yes
  • Uploaded via: twine/6.1.0 CPython/3.13.12

File hashes

Hashes for biotite-1.7.1-cp313-cp313-win_amd64.whl
Algorithm Hash digest
SHA256 965824257f716a77de3df35616cdaf302483a9ab8df98dc1dd0096c987342c49
MD5 0d155906cc5a4aff4cc430cdb134f538
BLAKE2b-256 44c793a55ec59b8677e89c54f103a1b5017c75cec322b36bf738f27381513273

See more details on using hashes here.

Provenance

The following attestation bundles were made for biotite-1.7.1-cp313-cp313-win_amd64.whl:

Publisher: test_and_deploy.yml on biotite-dev/biotite

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

File details

Details for the file biotite-1.7.1-cp313-cp313-manylinux_2_28_x86_64.whl.

File metadata

File hashes

Hashes for biotite-1.7.1-cp313-cp313-manylinux_2_28_x86_64.whl
Algorithm Hash digest
SHA256 085976013c62977eb29c5180cdffbc4b49633f35172b64c99e56eb7007d9f516
MD5 7f5f909d52fa4adf62784fd0d91a6d23
BLAKE2b-256 7f3451e095d4d4475bc64b793efd362b33d8c88658ac7b8a0b41c632d598b6d8

See more details on using hashes here.

Provenance

The following attestation bundles were made for biotite-1.7.1-cp313-cp313-manylinux_2_28_x86_64.whl:

Publisher: test_and_deploy.yml on biotite-dev/biotite

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

File details

Details for the file biotite-1.7.1-cp313-cp313-manylinux_2_28_aarch64.whl.

File metadata

File hashes

Hashes for biotite-1.7.1-cp313-cp313-manylinux_2_28_aarch64.whl
Algorithm Hash digest
SHA256 4f99104e7ebc1b2ab8ff7910736321e1205c85dba532826877ff263c65bd85ff
MD5 2d34f7efae9dace3b3632235a8e028b8
BLAKE2b-256 851666398b9eced43ca1f421dd46f013d1c9a3b8e159e2de62ec0e11604a29c9

See more details on using hashes here.

Provenance

The following attestation bundles were made for biotite-1.7.1-cp313-cp313-manylinux_2_28_aarch64.whl:

Publisher: test_and_deploy.yml on biotite-dev/biotite

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

File details

Details for the file biotite-1.7.1-cp313-cp313-macosx_11_0_arm64.whl.

File metadata

File hashes

Hashes for biotite-1.7.1-cp313-cp313-macosx_11_0_arm64.whl
Algorithm Hash digest
SHA256 5212116934b9c22515f86a1c23046cf3ecf7c9706464b14f16d72cd993866095
MD5 291c565ff75f81f0f715965745889078
BLAKE2b-256 b1b1b01e44a3d0ceefce400ee857a8baada1a0a5661a8c1222d1b2ec46d606a7

See more details on using hashes here.

Provenance

The following attestation bundles were made for biotite-1.7.1-cp313-cp313-macosx_11_0_arm64.whl:

Publisher: test_and_deploy.yml on biotite-dev/biotite

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

File details

Details for the file biotite-1.7.1-cp312-cp312-win_amd64.whl.

File metadata

  • Download URL: biotite-1.7.1-cp312-cp312-win_amd64.whl
  • Upload date:
  • Size: 45.3 MB
  • Tags: CPython 3.12, Windows x86-64
  • Uploaded using Trusted Publishing? Yes
  • Uploaded via: twine/6.1.0 CPython/3.13.12

File hashes

Hashes for biotite-1.7.1-cp312-cp312-win_amd64.whl
Algorithm Hash digest
SHA256 4a6a2bdeb92adf21e2a94fe0de898aa2dc01ed8c8b8241b4b2fd646c0dabc155
MD5 efdc82e5da4277df375c100ff7907740
BLAKE2b-256 b6b5f69879c3a641063e450901b2d68c2d2cb948fa5edf041b6e6638d942d20b

See more details on using hashes here.

Provenance

The following attestation bundles were made for biotite-1.7.1-cp312-cp312-win_amd64.whl:

Publisher: test_and_deploy.yml on biotite-dev/biotite

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

File details

Details for the file biotite-1.7.1-cp312-cp312-manylinux_2_28_x86_64.whl.

File metadata

File hashes

Hashes for biotite-1.7.1-cp312-cp312-manylinux_2_28_x86_64.whl
Algorithm Hash digest
SHA256 f563bebc5f2cc754b0e3773b75d5c216cfb5e89146f0c68dfec3d1d1d50051fb
MD5 3b7258b35b8b942158a0418a3dad80de
BLAKE2b-256 1d04cb4e8ba80ba81790d02dcc69d7529961140fc114abde927c99e9ba9c9457

See more details on using hashes here.

Provenance

The following attestation bundles were made for biotite-1.7.1-cp312-cp312-manylinux_2_28_x86_64.whl:

Publisher: test_and_deploy.yml on biotite-dev/biotite

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

File details

Details for the file biotite-1.7.1-cp312-cp312-manylinux_2_28_aarch64.whl.

File metadata

File hashes

Hashes for biotite-1.7.1-cp312-cp312-manylinux_2_28_aarch64.whl
Algorithm Hash digest
SHA256 6d7dbc50b1ea807131775d38078383a9513384fad0119f519a399cf701c34cf0
MD5 b02d3d591946fdb833e2766a4314ef96
BLAKE2b-256 99b1d28dbdfef015fc01807e7f34dff35d4a50585a974a761a7bee0ae2ebeea9

See more details on using hashes here.

Provenance

The following attestation bundles were made for biotite-1.7.1-cp312-cp312-manylinux_2_28_aarch64.whl:

Publisher: test_and_deploy.yml on biotite-dev/biotite

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

File details

Details for the file biotite-1.7.1-cp312-cp312-macosx_11_0_arm64.whl.

File metadata

File hashes

Hashes for biotite-1.7.1-cp312-cp312-macosx_11_0_arm64.whl
Algorithm Hash digest
SHA256 1465b43485d29f5f1f80cfb43ee64e68aa0128a248b31cbc04fadfcc20f8288d
MD5 74db6c7f03e4afda9c7e2e001f3fe088
BLAKE2b-256 f063b3f4c33be78c8718c8554417c8383ec89103e5b60904f75262546d3edbfc

See more details on using hashes here.

Provenance

The following attestation bundles were made for biotite-1.7.1-cp312-cp312-macosx_11_0_arm64.whl:

Publisher: test_and_deploy.yml on biotite-dev/biotite

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

Supported by

AWS Cloud computing and Security Sponsor Datadog Monitoring Depot Continuous Integration Fastly CDN Google Download Analytics Pingdom Monitoring Sentry Error logging StatusPage Status page