Skip to main content

Support for binary sequence formats in Biopython

Project description

BinSeqs - Support for binary sequence formats in Bioython

BinSeqs is a Python package intended to enrich the SeqIO framework from Biopython by adding support for some binary sequence formats.

Deprecation Warning

This code has now been merged into Biopython. Starting from Biopython release 1.75, all you need to do to support the formats below is to load the Bio.SeqIO module.

Consequently, this project will no longer be maintained. It will remain available online but will not be updated. All improvements and bug fixes will occur in the Biopython repository.

You can still use this module until Biopython 1.75 is released and available on your system. After that, loading the incenp.bio.seqio module will be a no-op and a DeprecationWarning will be emitted.

Formats supported

Usage

The BinSeqs parsers and writers are not designed to be used independently and should instead be used through the Biopython's SeqIO module.

Simply import the incenp.bio.seqio module to make the parsers and writers available to Biopython's SeqIO:

from Bio import SeqIO
import incenp.bio.seqio

records = list(SeqIO.parse('snapgene_file.dna', 'snapgene'))
SeqIO.write(records, 'serialcloner_file.xdna', 'xdna')

Copying

BinSeqs is free software and distributed under the terms of a BSD-like license. The full license is included in the LICENSE.txt file of the source distribution.

Homepage

The project is located at https://incenp.org/dvlpt/binseqs.html (homepage) and https://git.incenp.org/damien/binseqs (repository and bug tracker).

Project details


Download files

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

Source Distribution

incenp.binseqs-0.2.1.tar.gz (10.6 kB view details)

Uploaded Source

Built Distribution

incenp.binseqs-0.2.1-py2.py3-none-any.whl (14.2 kB view details)

Uploaded Python 2 Python 3

File details

Details for the file incenp.binseqs-0.2.1.tar.gz.

File metadata

  • Download URL: incenp.binseqs-0.2.1.tar.gz
  • Upload date:
  • Size: 10.6 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/1.12.1 pkginfo/1.5.0.1 requests/2.20.0 setuptools/40.6.3 requests-toolbelt/0.8.0 tqdm/4.29.0 CPython/3.7.0

File hashes

Hashes for incenp.binseqs-0.2.1.tar.gz
Algorithm Hash digest
SHA256 207580b4f76de5fea938989d87c03ac0fcb57ba321b9734880f63c59c9773527
MD5 476d454c31deffa6e33382269a8fa28f
BLAKE2b-256 c85cbf1dee2082a39dc170df40f64155814fcf96363703e0a5ae78f71eda6362

See more details on using hashes here.

File details

Details for the file incenp.binseqs-0.2.1-py2.py3-none-any.whl.

File metadata

  • Download URL: incenp.binseqs-0.2.1-py2.py3-none-any.whl
  • Upload date:
  • Size: 14.2 kB
  • Tags: Python 2, Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/1.12.1 pkginfo/1.5.0.1 requests/2.20.0 setuptools/40.6.3 requests-toolbelt/0.8.0 tqdm/4.29.0 CPython/3.7.0

File hashes

Hashes for incenp.binseqs-0.2.1-py2.py3-none-any.whl
Algorithm Hash digest
SHA256 0a77fcf2e210a1374af551a782926e6b3134929d948b02ed7271a9dbd77002df
MD5 83dec1308d56f0d995534f6e421a1be6
BLAKE2b-256 4e1a250392c10977f8c895e491d4d1b71cbe0cd479bf53ef326967f780e3b550

See more details on using hashes here.

Supported by

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