Macroape is abbreviation for MAtrix CompaRisOn by Approximate P-value Estimation. It's a bioinformatic tool for evaluating similarity measure between a pair of Position Weight Matrices. Used approach and application described in manual at https://docs.google.com/document/pub?id=1_jsxhMNzMzy4d2d_byAd3n6Szg5gEcqG_Sf7w9tEqWw

Add this line to your application's Gemfile:

gem 'macroape'

And then execute:

$ bundle

Or install it yourself as:

$ gem install macroape

For more information read manual at https://docs.google.com/document/pub?id=1_jsxhMNzMzy4d2d_byAd3n6Szg5gEcqG_Sf7w9tEqWw

MacroAPE have 7 command line tools:

• find_threshold <PWM file> [<pvalue(by default: 0.0005)>...]
• find_pvalue <PWM file> <threshold>...

• eval_similarity <first PWM file> <second PWM file>
• eval_alignment <first PWM file> <second PWM file> <shift of second matrix> <orientation of second matrix(direct|revcomp)>

• preprocess_collection <folder with motif files> <collection output file>
• scan_collection <query PWM file> <collection file>

• align_motifs <pwm_leader> <pwm_2> <pwm_3> ...

Also you can use -h option to print help for a tool in console. There are lots of different command line options. Most useful option is -d <discretization=1|10|100|1000>. You can vary precision/speed rate by specifing a discretization. For more information look through a manual. Some of tools also can process PCMs in addition to PWMs.

require 'macroape'
background = [1,1,1,1]
discretization = 10
pwm_first = Bioinform::PWM.new(File.read('first_pwm.pat')).background(background).discrete(discretization)
pwm_second = Bioinform::PWM.new(File.read('first_pwm.pat')).background(background).discrete(discretization)

cmp = Macroape::PWMCompare.new(pwm_first, pwm_second)
first_threshold = pwm_first.threshold(pvalue)
second_threshold = pwm_second.threshold(pvalue)

similarity_info = cmp.jaccard(first_threshold, second_threshold)
puts "Jaccard similarity: #{similarity_info[:similarity]}"

For more details look a source code of utilities in lib/macroape/cli/ folder

1. Fork it
2. Create your feature branch (git checkout -b my-new-feature)
3. Commit your changes (git commit -am 'Added some feature')
4. Push to the branch (git push origin my-new-feature)
5. Create new Pull Request

If you're developing both macroape and bioinform - it may be useful to know that test_helper and spec_helper expands require path in such a way that if you have two "cousin" folders: macroape and bioinform then macroape specs will require bioinform from development folder not from gem. It can save you lots of time not to rebuild-reinstall bioinform gem each time it get some changes

Copyright (c) 2011-2014 Ilya Vorontsov, Ivan Kulakovskiy, Vsevolod Makeev