Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

Awesome Lists | Featured Topics | Projects

https://github.com/ggonnella/gfapy

Gfapy: a flexible and extensible software library for handling sequence graphs in Python
https://github.com/ggonnella/gfapy

assembly bioinformatics gfa graphs sequence-analysis

Last synced: 10 days ago
JSON representation

Gfapy: a flexible and extensible software library for handling sequence graphs in Python

Awesome Lists containing this project

README 

        
Gfapy

~~~~~



|travis| |readthedocs| |latesttag| |license|



|bioconda| |pypi| |debian| |ubuntu|



.. sphinx-begin



The Graphical Fragment Assembly (GFA) are formats for the representation

of sequence graphs, including assembly, variation and splicing graphs.

Two versions of GFA have been defined (GFA1 and GFA2) and several sequence

analysis programs have been adopting the formats as an interchange format,

which allow to easily combine different sequence analysis tools.



This library implements the GFA1 and GFA2 specification

described at https://github.com/GFA-spec/GFA-spec/blob/master/GFA-spec.md.

It allows to create a Gfa object from a file in the GFA format

or from scratch, to enumerate the graph elements (segments, links,

containments, paths and header lines), to traverse the graph (by

traversing all links outgoing from or incoming to a segment), to search for

elements (e.g. which links connect two segments) and to manipulate the

graph (e.g. to eliminate a link or a segment or to duplicate a segment

distributing the read counts evenly on the copies).



The GFA format can be easily extended by users by defining own custom

tags and record types. In Gfapy, it is easy to write extensions modules,

which allow to define custom record types and datatypes for the parsing

and validation of custom fields. The custom lines can be connected, using

references, to each other and to lines of the standard record types.



Requirements

~~~~~~~~~~~~



Gfapy has been written for Python 3 and tested using Python version 3.7.

It does not require any additional Python packages or other software.



Installation

~~~~~~~~~~~~



Gfapy is distributed as a Python package and can be installed using

the Python package manager pip, as well as conda (in the Bioconda channel).

It is also available as a package in some Linux distributions (Debian, Ubuntu).



The following command installs the current stable version from the Python

Packages index::



  pip install gfapy



If you would like to install the current development version from Github,

use the following command::



  pip install -e git+https://github.com/ggonnella/gfapy.git#egg=gfapy



Alternatively it is possible to install gfapy using conda. Gfapy is

included in the Bioconda (https://bioconda.github.io/) channel::



  conda install -c bioconda gfapy



Usage

~~~~~



If you installed gfapy as described above, you can import it in your script

using the conventional Python syntax::



  >>> import gfapy



Documentation

~~~~~~~~~~~~~



The documentation, including this introduction to Gfapy, a user manual

and the API documentation is hosted on the ReadTheDocs server,

at the URL http://gfapy.readthedocs.io/en/latest/ and it can be

downloaded as PDF from the URL

https://github.com/ggonnella/gfapy/blob/master/manual/gfapy-manual.pdf.



References

~~~~~~~~~~



Giorgio Gonnella and Stefan Kurtz "GfaPy: a flexible and extensible software

library for handling sequence graphs in Python", Bioinformatics (2017) btx398

https://doi.org/10.1093/bioinformatics/btx398



.. sphinx-end



.. |travis|

   image:: https://travis-ci.com/ggonnella/gfapy.svg?branch=master

   :target: https://travis-ci.com/ggonnella/gfapy

   :alt: Travis



.. |latesttag|

   image:: https://img.shields.io/github/v/tag/ggonnella/gfapy

   :target: https://github.com/ggonnella/gfapy/tags

   :alt: Latest GitHub tag



.. |readthedocs|

   image:: https://readthedocs.org/projects/pip/badge/?version=stable

   :target: https://pip.pypa.io/en/stable/?badge=stable

   :alt: ReadTheDocs



.. |bioconda|

   image:: https://img.shields.io/conda/vn/bioconda/gfapy

   :target: https://bioconda.github.io/recipes/gfapy/README.html

   :alt: Bioconda



.. |pypi|

   image:: https://img.shields.io/pypi/v/gfapy

   :target: https://pypi.org/project/gfapy/

   :alt: PyPI



.. |debian|

   image:: https://img.shields.io/debian/v/gfapy

   :target: https://packages.debian.org/search?keywords=gfapy

   :alt: Debian



.. |ubuntu|

   image:: https://img.shields.io/ubuntu/v/gfapy

   :target: https://packages.ubuntu.com/search?keywords=gfapy

   :alt: Ubuntu



.. |license|

   image:: https://img.shields.io/pypi/l/gfapy

   :target: https://github.com/ggonnella/gfapy/blob/master/LICENSE.txt

   :alt: ISC License

   

.. |requiresio|

   image:: https://requires.io/github/ggonnella/gfapy/requirements.svg?branch=master

   :target: https://requires.io/github/ggonnella/gfapy/requirements/?branch=master

   :alt: Requirements Status