This is a pre-production deployment of Warehouse, however changes made here WILL affect the production instance of PyPI.
Latest Version Dependencies status unknown Test status unknown Test coverage unknown
Project Description

VCFPy

Python 3 VCF library with good support for both reading and writing

Features

  • Support for reading and writing VCF v4.3
  • Interface to INFO and FORMAT fields is based on OrderedDict allows for easier modification than PyVCF (also I find this more pythonic)
  • Read (and jump in) and write BGZF files just using vcfpy

Why another VCF parser for Python!

I’ve been using PyVCF with quite some success in the past. However, the main bottleneck of PyVCF is when you want to modify the per-sample genotype information. There are some issues in the tracker of PyVCF but none of them can really be considered solved. I tried several hours to solve these problems within PyVCF but this never got far or towards a complete rewrite…

For this reason, VCFPy was born and here it is!

What’s the State?

VCFPy is the result of two full days of development plus some maintenance work later now (right now). I’m using it in several projects but it is not as battle-tested as PyVCF.

Why Python 3 Only?

As I’m only using Python 3 code, I see no advantage in carrying around support for legacy Python 2 and maintaining it. At a later point when VCFPy is known to be stable, Python 2 support might be added if someone contributes a pull request.

History

0.7.0 (2016-09-25)

  • Smaller improvements and fixes to documentation
  • Adding Codacy coverage and static code analysis results to README
  • Various smaller code cleanup triggered by Codacy results
  • Adding __eq__, __neq__ and __hash__ to data types (where applicable)

0.6.0 (2016-09-25

  • Refining implementation for breakend and symbolic allele class
  • Removing record.SV_CODES
  • Refactoring parser module a bit to make the code cleaner
  • Fixing small typos and problems in documentation

0.5.0 (2016-09-24)

  • Deactivating warnings on record parsing by default because of performance
  • Adding validation for INFO and FORMAT fields on reading (#8)
  • Adding predefined INFO and FORMAT fields to pyvcf.header (#32)

0.4.1 (2016-09-22)

  • Initially enabling codeclimate

0.4.0 (2016-09-22)

  • Exporting constants for encoding variant types
  • Exporting genotype constants HOM_REF, HOM_ALT, HET
  • Implementing Call.is_phased, Call.is_het, Call.is_variant, Call.is_phased, Call.is_hom_ref, Call.is_hom_alt
  • Removing Call.phased (breaks API, next release is 0.4.0)
  • Adding tests, fixing bugs for methods of Call

0.3.1 (2016-09-21)

  • Work around FORMAT/FT being a string; this is done so in the Delly output

0.3.0 (2016-09-21)

  • Reader and Writer can now be used as context manager (with with)
  • Including license in documentation, including Biopython license
  • Adding support for writing bgzf files (taken from Biopython)
  • Adding support for parsing arrays in header lines
  • Removing example-4.1-bnd.vcf example file because v4.1 tumor derival lacks ID field
  • Adding AltAlleleHeaderLine, MetaHeaderLine, PedigreeHeaderLine, and SampleHeaderLine
  • Renaming SimpleHeaderFile to SimpleHeaderLine
  • Warn on missing FILTER entries on parsing
  • Reordered parameters in from_stream and from_file (#18)
  • Renamed from_file to from_stream (#18)
  • Renamed Reader.jump_to to Reader.fetch
  • Adding header_without_lines function
  • Generally extending API to make it esier to use
  • Upgrading dependencies, enabling pyup-bot
  • Greatly extending documentation

0.2.1 (2016-09-19)

  • First release on PyPI
Release History

Release History

0.7.0

This version

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

Show More

0.6.0

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

Show More

0.5.0

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

Show More

0.4.1

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

Show More

0.4.0

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

Show More

0.3.1

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

Show More

0.3.0

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

Show More

0.2.1

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

Show More

0.1.0

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

Show More

Download Files

Download Files

TODO: Brief introduction on what you do with files - including link to relevant help section.

File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
vcfpy-0.7.0-py2.py3-none-any.whl (33.1 kB) Copy SHA256 Checksum SHA256 py2.py3 Wheel Sep 25, 2016
vcfpy-0.7.0.tar.gz (979.6 kB) Copy SHA256 Checksum SHA256 Source Sep 25, 2016

Supported By

WebFaction WebFaction Technical Writing Elastic Elastic Search Pingdom Pingdom Monitoring Dyn Dyn DNS HPE HPE Development Sentry Sentry Error Logging CloudAMQP CloudAMQP RabbitMQ Heroku Heroku PaaS Kabu Creative Kabu Creative UX & Design Fastly Fastly CDN DigiCert DigiCert EV Certificate Rackspace Rackspace Cloud Servers DreamHost DreamHost Log Hosting