https://github.com/ggonnella/rgfa

Ruby library for handling GFA files
https://github.com/ggonnella/rgfa

Last synced: 2 months ago
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Ruby library for handling GFA files

• Host: GitHub
• URL: https://github.com/ggonnella/rgfa
• Owner: ggonnella
• License: other
• Created: 2016-07-19T16:23:08.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2017-02-21T20:55:22.000Z (almost 8 years ago)
• Last Synced: 2024-04-26T01:20:34.586Z (9 months ago)
• Language: Ruby
• Size: 6.32 MB
• Stars: 15
• Watchers: 2
• Forks: 2
• Open Issues: 3
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG
  • License: LICENSE

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README

        
The Graphical Fragment Assembly (GFA) is a proposed format which allow

to describe the product of sequence assembly.

This gem implements the proposed specifications for the GFA format

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

as close as possible.

The library allows to create a RGFA 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).

## Installation

The latest release of the gem can be installed from the rubygems repository

using:

```gem install rgfa```

Alternatively this git repository can be cloned or the source code

installed from a release archive, and then the gem created and installed

using:

```rake install```

## Usage

To use the library in your Ruby scripts, just require it as follows:

```require "rgfa"```

Additional functionality, which

requires custom tags and additional conventions, is included in a separate

part of the code named {RGFATools} and can be accessed with:

```require "rgfatools"```

## Documentation

A cheatsheet is available as pdf under

https://github.com/ggonnella/rgfa/blob/master/cheatsheet/rgfa-cheatsheet-1.3.1.pdf

The full API documentation is available as pdf under

https://github.com/ggonnella/rgfa/blob/master/pdfdoc/rgfa-api-1.3.1.pdf

or in HTML format (http://www.rubydoc.info/github/ggonnella/rgfa/master/RGFA).

The main class of the library is {RGFA}, which is a good starting point

when reading the documentation.

## References

Gonnella G, Kurtz S. (2016) RGFA: powerful and convenient handling of assembly graphs. PeerJ 4:e2681 https://doi.org/10.7717/peerj.2681