Awesome
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