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توضیحات

A comprehensive library for computational molecular biology

ویژگی	مقدار
سیستم عامل	-
نام فایل	biotite-0.9.0
نام	biotite
نسخه کتابخانه	0.9.0
نگهدارنده	[]
ایمیل نگهدارنده	[]
نویسنده	-
ایمیل نویسنده	The Biotite contributors <none@none.com>
آدرس صفحه اصلی	https://www.biotite-python.org
آدرس اینترنتی	https://pypi.org/project/biotite/
مجوز	BSD 3-Clause License -------------------- Copyright 2017 - 2021, The Biotite contributors All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

.. image:: https://img.shields.io/pypi/v/biotite.svg :target: https://pypi.python.org/pypi/biotite :alt: Biotite at PyPI .. image:: https://img.shields.io/pypi/pyversions/biotite.svg :alt: Python version .. image:: https://github.com/biotite-dev/biotite/actions/workflows/test_and_deploy.yml/badge.svg :target: https://github.com/biotite-dev/biotite/actions/workflows/test_and_deploy.yml :alt: Test status .. image:: https://www.biotite-python.org/_static/assets/general/biotite_logo_m.png :alt: 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: - **mdtraj** - Required for trajetory file I/O operations. - **matplotlib** - Required for plotting purposes. *Biotite* can be installed via *Conda*... .. code-block:: console $ conda install -c conda-forge biotite ... or *pip* .. code-block:: console $ pip install biotite Usage ----- Here is a small example that downloads two protein sequences from the *NCBI Entrez* database and aligns them: .. code-block:: python 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]) .. code-block:: 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 <https://www.biotite-python.org/contribute.html>`_. Feel free to join or community chat on `Discord <https://discord.gg/cUjDguF>`_.

نیازمندی

مقدار	نام
>=2.12	requests
>=1.14.5	numpy
>=0.5.6	msgpack
>=2.0	networkx
-	pytest

زبان مورد نیاز

مقدار	نام
>=3.7	Python

نحوه نصب

نصب پکیج whl biotite-0.9.0:

pip install biotite-0.9.0.whl

نصب پکیج tar.gz biotite-0.9.0:

pip install biotite-0.9.0.tar.gz