ruby-edlib's Introduction

ruby-edlib

Edlib - A lightweight and super fast C/C++ library for sequence alignment using edit distance

Installation

gem install edlib

The Gem compiles the edlib source code inside the gem at installation. If you want to use the latest edlib, see Development.

Usage

require "edlib"

a = Edlib::Aligner.new(mode: :hw, task: :path)
a.align("AACG", "TCAACCTG")

# {
#  :edit_distance   => 1,
#  :alphabet_length => 4,
#  :locations       => [[2, 4], [2, 5]],
#  :alignment       => [0, 0, 0, 1],
#  :cigar           => "3=1I"
# }

keyword argument	description
k	edit distance is not larger than k [-1]
mode	global (NW) , prefix (SHW) , infix (HW) ["NW"]
task	DISTANCE, LOC, PATH ["DISTANCE"]
additional_equalities	List of pairs of characters, where each pair defines two characters as equal. [NULL]

a.align("AACG", "TCAACCTG", nice: true)

# {
#   :edit_distance=>1,                                                 
#   :alphabet_length=>4,                                               
#   :locations=>[[2, 4], [2, 5]],                                      
#   :alignment=>[0, 0, 0, 1],                                          
#   :cigar=>"3=1I",                                                    
#   :query_aligned=>"AACG",                                            
#   :match_aligned=>"|||-",                                            
#   :target_aligned=>"AAC-"
# }

Documentation

https://kojix2.github.io/ruby-edlib/

Development

Pull requests welcome!

git clone https://github.com/kojix2/ruby-edlib # Please fork repo
cd ruby-edlib
bundle install
bundle exec rake compile
bundle exec rake test

Use latest edlib

git clone https://github.com/kojix2/ruby-edlib
cd ruby-edlib
bundle install
bundle exec rake edlib:update # Download latest edlib.h and edlib.cpp
bundle exec rake compile
bundle exec rake test

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ruby-edlib's Issues

Can not install it: undefined symbol: __gxx_personality_v0 - /root/.gem/gems/edlib-0.0.1/lib/edlib/edlib.so (LoadError)

require "edlib"

Error is:

 /root/.gem/gems/edlib-0.0.1/lib/edlib.rb:1:in `require_relative': /root/.gem/gems/edlib-0.0.1/lib/edlib/edlib.so:
 undefined symbol: __gxx_personality_v0 - /root/.gem/gems/edlib-0.0.1/lib/edlib/edlib.so (LoadError)

I just compiled upstream edlib from source and it installed fine. Source I used for this was:

https://github.com/Martinsos/edlib/releases

The lib/ I have after compiling the above, has: