bio-hmmer_model 0.0.1

data/.document

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+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/.travis.yml

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+language: ruby
+rvm:
+  - 1.9.2
+  - 1.9.3
+  - jruby-19mode # JRuby in 1.9 mode
+  - rbx-19mode
+#  - 1.8.7
+#  - jruby-18mode # JRuby in 1.8 mode
+#  - rbx-18mode
+
+# uncomment this line if your project needs to run something other than `rake`:
+# script: bundle exec rspec spec

data/Gemfile

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+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "shoulda", ">= 0"
+  gem "rdoc", "~> 3.12"
+  gem "bundler", "~> 1.0.0"
+  gem "jeweler", "~> 1.8.3"
+  gem "bio", ">= 1.4.2"
+  gem "rdoc", "~> 3.12"
+end

data/LICENSE.txt

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+Copyright (c) 2012 Ben J. Woodcroft
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

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+# bio-hmmer_model
+
+[![Build Status](https://secure.travis-ci.org/wwood/bioruby-hmmer_model.png)](http://travis-ci.org/wwood/bioruby-hmmer_model)
+
+Full description goes here
+
+Note: this software is under active development!
+
+## Installation
+
+```sh
+    gem install bio-hmmer_model
+```
+
+## Usage
+
+```ruby
+    require 'bio-hmmer_model'
+```
+
+The API doc is online. For more code examples see the test files in
+the source tree.
+        
+## Project home page
+
+Information on the source tree, documentation, examples, issues and
+how to contribute, see
+
+  http://github.com/wwood/bioruby-hmmer_model
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+## Cite
+
+If you use this software, please cite one of
+  
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+
+## Biogems.info
+
+This Biogem is published at [#bio-hmmer_model](http://biogems.info/index.html)
+
+## Copyright
+
+Copyright (c) 2012 Ben J. Woodcroft. See LICENSE.txt for further details.
+

data/README.rdoc

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+= bio-hmmer_model
+
+{<img
+src="https://secure.travis-ci.org/wwood/bioruby-hmmer_model.png"
+/>}[http://travis-ci.org/#!/wwood/bioruby-hmmer_model]
+
+Full description goes here
+
+Note: this software is under active development!
+
+== Installation
+
+        gem install bio-hmmer_model
+
+== Usage
+
+== Developers
+
+To use the library 
+
+        require 'bio-hmmer_model'
+
+The API doc is online. For more code examples see also the test files in
+the source tree.
+        
+== Project home page
+
+Information on the source tree, documentation, issues and how to contribute, see
+
+  http://github.com/wwood/bioruby-hmmer_model
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+== Cite
+
+  If you use this software, please cite one of
+ 
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+
+== Biogems.info
+
+This Biogem is published at http://biogems.info/index.html#bio-hmmer_model
+
+== Copyright
+
+Copyright (c) 2012 Ben J. Woodcroft. See LICENSE.txt for further details.
+

data/Rakefile

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+# encoding: utf-8
+
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
+  gem.name = "bio-hmmer_model"
+  gem.homepage = "http://github.com/wwood/bioruby-hmmer_model"
+  gem.license = "MIT"
+  gem.summary = %Q{Parse PFAM HMM definition files}
+  gem.description = %Q{Parse PFAM HMM definition files so that the models can be accessible programmatically}
+  gem.email = "donttrustben near gmail.com"
+  gem.authors = ["Ben J. Woodcroft"]
+  # dependencies defined in Gemfile
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+task :default => :test
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-hmmer_model #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.0.1

data/lib/bio-hmmer_model.rb

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+require 'bio/appl/hmmer/model'

data/lib/bio/appl/hmmer/model.rb

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+## Example HMM model file, taken from PFAM 26.
+
+# HMMER3/b [3.0 | March 2010]
+# NAME  1-cysPrx_C
+# ACC   PF10417.4
+# DESC  C-terminal domain of 1-Cys peroxiredoxin
+# LENG  40
+# ALPH  amino
+# RF    no
+# CS    yes
+# MAP   yes
+# DATE  Mon Sep 26 01:36:52 2011
+# NSEQ  86
+# EFFN  26.221497
+# CKSUM 2893062708
+# GA    20.40 20.40;
+# TC    20.40 20.50;
+# NC    20.30 20.30;
+# BM    hmmbuild HMM.ann SEED.ann
+# SM    hmmsearch -Z 15929002 -E 1000 --cpu 4 HMM pfamseq
+# STATS LOCAL MSV       -7.4458  0.71948
+# STATS LOCAL VITERBI   -7.8857  0.71948
+# STATS LOCAL FORWARD   -4.3017  0.71948
+# HMM          A        C        D        E        F        G        H        I        K        L        M        N        P        Q        R        S        T        V        W        Y
+#             m->m     m->i     m->d     i->m     i->i     d->m     d->d
+#   COMPO   2.25274  4.33630  2.74834  2.65826  3.87771  2.70273  3.95751  3.25125  2.56848  2.82101  4.06536  3.21194  2.50202  2.97228  3.39798  2.99665  2.70159  2.62185  3.52465  3.78187
+#           2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+#           0.00153  6.88065  7.60300  0.61958  0.77255  0.00000        *
+#       1   0.35002  6.53529  7.25102  7.30399  7.52698  2.51105  7.66616  7.05965  7.14684  6.75377  3.79371  6.32251  6.23186  7.14685  7.02553  1.76469  5.22656  6.02391  8.86510  7.90937      1 - H
+#           2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+#           0.00153  6.88065  7.60300  0.61958  0.77255  0.48576  0.95510
+#       2   3.84702  5.95842  6.58626  5.97181  2.06407  5.79758  6.11757  2.43011  5.76033  0.58540  3.17079  5.96610  6.11889  5.84497  5.74893  5.11667  4.83456  2.97676  3.47925  3.13829      2 - H
+#           2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+#           0.00153  6.88065  7.60300  0.61958  0.77255  0.48576  0.95510
+module Bio
+  class HMMER
+    class Model
+      class ParseException<Exception; end
+
+      TAGS = %w(NAME ACC DESC LENG ALPH RF CS MAP DATE NSEQ EFFN CKSUM GA TC NC BM SM STATS_LOCAL_MSV)
+      TAGS.each do |info|
+        attr_accessor info.downcase.to_sym
+      end
+
+      # An array of 4 element arrays from STATS lines (e.g. STATS LOCAL FORWARD   -4.3017  0.71948) => ['LOCAL','FORWARD',-4.3017,0.71948]
+      attr_accessor :stats
+
+      # Letters used in the model (amino acids). The order of this array is the same as the order
+      attr_accessor :alphabet
+
+      # ["m->m", "m->i", "m->d", "i->m", "i->i", "d->m", "d->d"]
+      attr_accessor :transitions
+
+      # Probabilities for matches in the model (first line of each position in the main model part of the HMMER3/b file format)
+      # You probably want to use #match_probability not read this variable directly
+      attr_accessor :match_emissions
+
+      # Probabilities for inserts in the model (second line of each position in the main model part of the HMMER3/b file format)
+      attr_accessor :insert_emissions
+
+      # Probabilities for state transitions in the model (third line of each position in the main model part of the HMMER3/b file format)
+      attr_accessor :state_transitions
+      
+      # A reader interface for multiple HMMs into individual model objects
+      #
+      # === Examples
+      # 
+      #   # Iterator
+      #   Bio::HMMER::Model.models(big_hmm_text) do |mode|
+      #     model
+      #   end
+      #
+      #   # Array
+      #   reports = Bio::HMMER::Model.models(reports_text)
+      #
+      def self.models(multiple_model_text)
+        ary = []
+        multiple_model_text.each_line("\n//\n") do |report|
+          if block_given?
+            yield Bio::HMMER::Model.parse(report)
+          else
+            ary << Bio::HMMER::Model.parse(report)
+          end
+        end
+        return ary
+      end
+
+      # Return the probability given in the HMM of the match probability of a particular position.
+      #
+      # Note that the hmm_position is 1-based - the first position is 1, not 0
+      #
+      # Assumes that the letter supplied is in the HMM's alphabet
+      def match_probability(hmm_position, letter)
+        index = @alphabet.index(letter)
+        match_emissions[hmm_position+1][index]
+      end
+
+      # Parse a HMM file fed in through some IO, and return an instantiated
+      # Bio::HMMER::Model with all the informations filled in
+      #
+      # e.g. PF10417.4 has length 40 (as of PFAM v26):
+      #
+      #    Bio::Hmmer::Model.parse(File.open('test/data/PF10417.4.hmm')).leng => 40
+      def self.parse(io)
+        model = Bio::HMMER::Model.new
+
+        lines = nil
+        if io.kind_of?(String)
+          lines = io.split("\n")
+        else
+          lines = io.read.split("\n")
+        end
+
+        unless lines[0].match(/^HMMER3\/b/)
+          raise ParseException, "Only HMMER3/b files are currently supported, sorry. The first line of the HMMER model file causing the problem is #{lines[0]}"
+        end
+        lineno = 1
+
+        # Majority of tags at the top of the model
+        while TAGS.include?(lines[lineno].split(/ +/)[0])
+          splits = lines[lineno].strip.split(/ +/)
+          lit = splits[0].downcase
+          tag = TAGS.select{|t| t==lit}[0]
+          value = splits[1..(splits.length-1)].join(' ')
+
+          # cast appropriately
+          value = value.to_i if %w(leng nseq cksum).include?(lit)
+          value = value.to_f if %w(effn).include?(lit)
+          value = [splits[1].to_f, splits[2].to_f] if %w(ga tc nc).include?(lit)
+
+          model.send("#{lit}=".to_sym,value)
+          lineno += 1
+        end
+
+        # STATS_LOCAL_MSV STATS_LOCAL_VITERBI STATS_LOCAL_FORWARD
+        while matches = lines[lineno].match(/^STATS ([^ ]+) ([^ ]+) +([\-\d\.]+) +([\-\d\.]+)$/)
+          model.stats ||= []
+          model.stats.push [matches[1], matches[2], matches[3].to_f, matches[4].to_f]
+          lineno += 1
+        end
+
+        # Next expect HMM   A C D ...
+        splits = lines[lineno].strip.split(/ +/)
+        unless splits[0]=='HMM'
+          raise ParseException, "Unexpected HMM file line encountered, expected the beginning of the main model section e.g. HMM          A        C        D        E ...: #{lines[lineno]}"
+        end
+        model.alphabet = splits[1..(splits.length-1)]
+        lineno += 1
+
+        # m->m     m->i     m->d     i->m     i->i     d->m     d->d
+        splits = lines[lineno].strip.split(/ +/)
+        unless splits.length == 7
+          raise ParseException, "Unexpected line in HMM file, expected '            m->m     m->i     m->d     i->m     i->i     d->m     d->d', found #{lines[lineno]}"
+        end
+        model.transitions = splits
+        lineno += 1
+
+        #skip the next lines since my application does not require these
+        splits = lines[lineno].strip.split(/ +/)
+        lineno += 1 if splits[0]=='COMPO'
+        lineno += 2
+
+        model.match_emissions = []
+        model.insert_emissions = []
+        model.state_transitions = []
+
+        # Iterate through the model, one line at a time
+        model_iterate = 0
+        while !(lines[lineno].match(/^\/\//))
+          splits = lines[lineno].strip.split(/ +/)
+
+          unless splits.length > model.alphabet.length
+            raise ParseException, "Unexpected line format encountered in the main model: #{lines[lineno]}"
+          end
+
+          # Check that the state numbers are in order
+          model_iterate += 1
+          unless splits[0].to_i == model_iterate
+            raise ParseException, "Unexpected model state number: #{splits[0]}"
+          end
+          probabilities = splits[1..model.alphabet.length].collect do |s|
+          # From the HMMER manual:
+          # All probability parameters are all stored as negative natural log probabilities with
+          # five digits of precision to the right of the decimal point, rounded. For example,
+          # a probability of 0.25 is stored as − log 0.25 = 1.38629.
+            10.0**-(s.to_f)
+          end
+          model.match_emissions.push probabilities
+          lineno += 1
+
+          splits = lines[lineno].strip.split(/ +/)
+          unless splits.length == model.alphabet.length
+            raise ParseException, "Unexpected line format encountered in the main model: #{lines[lineno]}"
+          end
+          model.insert_emissions.push splits.collect{|s| 10.0**-(s.to_f)}
+          lineno += 1
+
+          splits = lines[lineno].strip.split(/ +/)
+          unless splits.length == model.transitions.length
+            raise ParseException, "Unexpected line format encountered in the main model: #{lines[lineno]}"
+          end
+          model.state_transitions.push splits.collect{|s| 10.0**-(s.to_f)}
+          lineno += 1
+        end
+
+        return model
+      end
+    end
+  end
+end

data/test/data/PF10417.4.hmm

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+HMMER3/b [3.0 | March 2010]
+NAME  1-cysPrx_C
+ACC   PF10417.4
+DESC  C-terminal domain of 1-Cys peroxiredoxin
+LENG  40
+ALPH  amino
+RF    no
+CS    yes
+MAP   yes
+DATE  Mon Sep 26 01:36:52 2011
+NSEQ  86
+EFFN  26.221497
+CKSUM 2893062708a
+GA    20.40 20.40;
+TC    20.40 20.50;
+NC    20.30 20.30;
+BM    hmmbuild HMM.ann SEED.ann
+SM    hmmsearch -Z 15929002 -E 1000 --cpu 4 HMM pfamseq
+STATS LOCAL MSV       -7.4458  0.71948
+STATS LOCAL VITERBI   -7.8857  0.71948
+STATS LOCAL FORWARD   -4.3017  0.71948
+HMM          A        C        D        E        F        G        H        I        K        L        M        N        P        Q        R        S        T        V        W        Y   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   2.25274  4.33630  2.74834  2.65826  3.87771  2.70273  3.95751  3.25125  2.56848  2.82101  4.06536  3.21194  2.50202  2.97228  3.39798  2.99665  2.70159  2.62185  3.52465  3.78187
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00153  6.88065  7.60300  0.61958  0.77255  0.00000        *
+      1   0.35002  6.53529  7.25102  7.30399  7.52698  2.51105  7.66616  7.05965  7.14684  6.75377  3.79371  6.32251  6.23186  7.14685  7.02553  1.76469  5.22656  6.02391  8.86510  7.90937      1 - H
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00153  6.88065  7.60300  0.61958  0.77255  0.48576  0.95510
+      2   3.84702  5.95842  6.58626  5.97181  2.06407  5.79758  6.11757  2.43011  5.76033  0.58540  3.17079  5.96610  6.11889  5.84497  5.74893  5.11667  4.83456  2.97676  3.47925  3.13829      2 - H
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00153  6.88065  7.60300  0.61958  0.77255  0.48576  0.95510
+      3   3.87133  6.63923  3.89382  3.88785  5.98251  4.95105  3.93438  3.68845  2.69475  3.27020  5.68503  3.97945  5.34053  0.41198  3.17365  4.15121  3.92972  5.02995  7.06168  5.68005      3 - H
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00153  6.88065  7.60300  0.61958  0.77255  0.48576  0.95510
+      4   2.93042  5.61109  6.17679  3.76792  1.81306  5.40034  2.47830  3.66556  3.67201  1.61899  3.02770  5.55617  5.76424  5.48715  4.24305  4.71076  1.71392  2.41572  4.64632  2.89796      4 - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00153  6.88065  7.60300  0.61958  0.77255  0.48576  0.95510
+      5   1.34086  5.78215  5.31499  4.74053  3.99248  3.54064  3.18524  3.62049  4.66792  3.98458  4.89191  3.01845  5.60287  4.93806  3.96254  2.17813  1.60342  1.85688  6.38036  3.93735      5 - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00153  6.88065  7.60300  0.61958  0.77255  0.48576  0.95510
+      6   2.56552  6.58132  0.80265  2.07249  5.92644  4.24713  5.03138  5.41245  3.45173  4.25340  4.14610  3.91228  5.23780  3.17510  3.17192  3.41601  2.89202  4.97199  3.66027  3.57391      6 - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00153  6.88065  7.60300  0.61958  0.77255  0.48576  0.95510
+      7   2.15347  6.58424  3.77072  2.03987  5.93070  4.16570  5.03052  5.41764  1.18262  4.89011  5.62454  3.38929  5.23711  2.51176  2.17951  2.66218  2.90748  4.29580  7.01609  4.55623      7 - T
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02515  6.88065  3.73750  0.61958  0.77255  0.48576  0.95510
+      8   2.80113  6.56430  3.49064  1.98594  3.65677  3.88839  1.75083  5.39731  3.12467  3.87248  5.60466  2.31713  5.21780  2.87689  3.14824  2.90316  2.20859  4.95556  6.99630  2.28921      8 - S
+          2.68638  4.42246  2.77540  2.73144  3.46374  2.40467  3.72515  3.29375  2.67628  2.69375  4.24710  2.90367  2.73760  3.18167  2.89821  2.37847  2.77540  2.98539  4.58497  3.61524
+          0.08325  2.53369  7.57941  0.05811  2.87434  0.31315  1.31356
+      9   3.67343  6.62372  3.20082  3.78669  5.96999  0.74714  3.75850  5.45722  1.80122  4.92893  5.66524  3.21819  2.84224  3.41116  3.78606  2.95389  4.34013  5.01524  7.05453  5.64184     10 - S
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00153  6.88065  7.60300  0.61958  0.77255  0.48576  0.95510
+     10   3.21404  3.48620  3.03457  1.73535  5.74395  3.52290  5.07435  2.86188  2.95191  2.95215  5.50841  3.62375  5.27254  3.44019  3.63863  3.10323  3.87986  1.13875  6.91964  3.76446     11 - -
+          2.68643  4.42250  2.77544  2.72940  3.46202  2.40538  3.72519  3.29379  2.67766  2.69380  4.24715  2.90372  2.73765  3.18026  2.89826  2.37912  2.77544  2.98543  4.58502  3.61528
+          0.09911  2.36599  7.60300  0.04871  3.04621  0.48576  0.95510
+     11   0.81344  5.64580  3.63796  5.54324  4.74573  5.41633  5.76051  4.05227  5.34764  2.74708  3.63724  5.56139  5.78596  5.49305  5.38286  3.58302  4.49282  1.13230  6.27718  4.18122     13 - B
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00153  6.88065  7.60300  0.61958  0.77255  0.48576  0.95510
+     12   2.92335  1.31603  6.54313  5.94804  5.01326  5.76683  6.14640  2.64759  5.74905  2.61283  3.71581  5.94050  6.11509  5.88615  5.76526  5.09324  0.86787  3.03657  6.61717  5.44029     14 - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00153  6.88065  7.60300  0.61958  0.77255  0.48576  0.95510
+     13   7.97163  8.66281  8.18669  8.27762  8.83385  7.25177  8.82321  9.24064  8.47832  8.30564  9.64010  8.56319  0.00412  8.78020  8.23540  8.32884  8.41649  8.80697  9.14062  9.07281     15 - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00153  6.88065  7.60300  0.61958  0.77255  0.48576  0.95510
+     14   0.53695  3.18676  5.90049  2.79980  4.76925  5.36000  4.09457  3.67946  5.15267  3.12557  4.78754  5.42693  5.73354  5.33928  5.26588  3.06565  4.46799  2.17269  6.28830  5.10419     16 - T
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00153  6.88065  7.60300  0.61958  0.77255  0.48576  0.95510
+     15   4.20766  8.06890  1.39679  4.30245  7.34968  1.60060  6.07138  6.93033  3.10545  6.35822  7.22635  0.92322  6.12791  3.03067  5.85026  4.27534  5.62075  6.44254  8.49748  6.90055     17 - T
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00153  6.88065  7.60300  0.61958  0.77255  0.48576  0.95510
+     16   8.36163  8.74018  8.24824  8.33878  8.10367  7.33021  8.66656  9.17581  8.51070  8.18478  9.58516  8.64891  7.95525  8.80122  8.24969  8.76783  8.72273  8.89727  0.00437  8.15746     18 - T
+          2.68625  4.42232  2.77526  2.73130  3.46361  2.40519  3.72216  3.29361  2.67747  2.69362  4.24696  2.90353  2.73746  3.18153  2.89807  2.37893  2.77526  2.98525  4.58484  3.61510
+          0.14538  3.63140  2.21799  0.14648  1.99322  0.48576  0.95510
+     17   3.69846  6.48547  3.69888  2.69569  4.84057  3.45359  3.46826  3.17175  1.65546  4.79030  4.47760  3.00063  5.14501  2.18109  2.05274  3.68996  2.51802  2.03497  6.91881  3.72948     20 - .
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00171  6.76600  7.48834  0.61958  0.77255  0.13711  2.05477
+     18   2.99839  6.59188  2.99815  2.45942  5.93846  4.85056  3.62975  4.41816  2.48472  4.89729  5.63244  4.31756  0.67957  2.88749  3.15963  4.04064  3.78739  4.98339  7.02309  5.61207     21 - T
+          2.69022  4.42629  2.77822  2.71594  3.45737  2.40917  3.72898  3.28928  2.68145  2.69530  4.25094  2.89793  2.73745  3.17930  2.90205  2.38291  2.77098  2.98806  4.56381  3.61719
+          0.22976  1.58583  7.60300  1.97291  0.14972  0.48576  0.95510
+     19   5.67560  8.14957  4.68756  3.29510  7.67322  0.30855  6.13106  7.08697  3.33475  6.40091  7.34454  2.03781  6.37189  5.29571  3.57570  5.51168  5.91914  6.67738  8.39021  7.07535     32 - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00153  6.88065  7.60300  0.61958  0.77255  0.48576  0.95510
+     20   3.11564  6.58588  1.15869  1.80848  5.93230  4.32155  5.03188  5.41929  1.99229  4.89173  4.57745  3.42776  5.23836  2.53662  3.85675  3.24486  2.23557  4.97725  7.01772  5.60584     33 - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00153  6.88065  7.60300  0.61958  0.77255  0.48576  0.95510
+     21   2.90264  6.58396  1.92097  2.34670  5.93032  3.87471  3.22499  4.13927  1.30840  2.87803  5.62428  2.84437  2.30991  3.44608  3.62101  3.75582  3.43616  4.12541  7.01587  5.60415     34 - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00153  6.88065  7.60300  0.61958  0.77255  0.48576  0.95510
+     22   2.20320  3.15842  4.38124  3.97638  4.71386  2.68775  5.71944  3.39721  5.30007  2.79297  3.57556  5.52289  5.75513  5.44826  5.34016  3.57574  1.79439  0.94404  6.24079  5.06267     35 - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00153  6.88065  7.60300  0.61958  0.77255  0.48576  0.95510
+     23   5.01172  4.38216  7.04818  6.47606  3.22055  6.34573  6.75435  0.75315  6.30899  1.75450  1.88592  6.51683  6.61755  6.40788  6.32578  5.69555  3.87090  2.25957  7.11274  5.97837     36 - B
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.37234  6.88065  1.17165  0.61958  0.77255  0.48576  0.95510
+     24   3.38651  5.31219  5.83861  3.94503  3.77192  5.09499  5.42679  1.75474  5.02553  2.38137  4.43134  3.84059  3.14551  3.76906  5.05370  4.40431  4.16221  0.71619  5.93686  4.75945     37 - E
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.04487  6.51052  3.16078  0.61958  0.77255  2.39092  0.09601
+     25   2.31624  5.58871  4.64082  3.50951  4.73553  3.53859  5.03796  3.49524  4.03684  3.00934  4.69287  4.49825  0.82952  3.38897  4.40706  2.51830  3.35917  2.41660  6.16808  4.92589     38 - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00231  6.46796  7.19030  0.61958  0.77255  2.46713  0.08864
+     26   2.35754  5.82777  3.28470  3.87960  5.06715  3.98102  4.99519  3.87815  3.87509  3.03153  4.96864  2.77329  0.62364  4.20569  4.30418  3.94850  3.25340  3.74554  6.42258  5.13649     39 - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02503  6.46796  3.76485  0.61958  0.77255  0.07104  2.67980
+     27   2.21372  4.45699  3.34406  3.11661  5.90218  4.82815  3.04106  3.63821  1.82407  4.19154  5.60044  3.41835  1.49985  3.72386  4.24338  2.21820  2.25432  4.28135  6.99318  4.45821     40 - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00156  6.85951  7.58185  0.61958  0.77255  0.64481  0.74394
+     28   1.88944  6.55713  3.20264  3.48314  5.89679  3.74697  4.15800  3.29260  2.30922  2.52101  5.59920  3.66079  1.88183  3.31784  3.65404  2.74153  1.99300  2.68916  6.99306  5.58538     41 - S
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00155  6.86571  7.58805  0.61958  0.77255  0.72821  0.65927
+     29   3.13739  6.68690  1.77373  3.57251  6.03047  4.89931  5.11494  5.52047  3.06053  4.99208  5.73151  3.27514  2.89960  3.70403  4.36609  1.49937  1.14896  5.07744  7.11915  5.70034     42 - S
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00155  6.86571  7.58805  0.61958  0.77255  0.72821  0.65927
+     30   2.84531  4.05285  2.30195  2.03484  3.48044  4.36546  3.63394  3.23085  3.84150  3.57338  3.54040  3.30555  2.06987  2.51547  3.62591  3.28259  3.48669  2.68228  6.88358  2.32393     43 - H
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00155  6.86571  7.58805  0.61958  0.77255  0.35944  1.19755
+     31   2.51353  6.58971  1.55383  1.18599  5.93603  3.54496  3.47951  5.42313  2.10559  4.89553  5.63016  3.25814  3.39908  2.88891  4.26332  4.03675  3.98036  3.97874  7.02153  5.60941     44 - H
+          2.68526  4.42232  2.77526  2.73130  3.46360  2.40519  3.72501  3.29360  2.67747  2.69361  4.24696  2.90353  2.73746  3.18153  2.89807  2.37893  2.77526  2.98525  4.58483  3.61510
+          0.41436  3.66094  1.15985  0.14993  1.97164  0.48576  0.95510
+     32   2.64576  6.07031  1.54605  1.44482  5.50763  2.80445  4.68696  5.03589  3.45692  3.03452  3.04758  3.69537  4.88236  2.85075  3.42049  2.68168  2.99112  3.82586  6.40738  5.21921     46 - H
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02411  6.50518  3.80208  0.61958  0.77255  0.14040  2.03264
+     33   0.99559  5.75960  3.80383  4.66240  4.88006  1.92352  5.45217  2.56247  3.60153  3.23646  3.65516  5.00555  5.55501  4.86996  3.56896  2.79989  3.02327  2.25754  6.35567  5.14137     47 - H
+          2.68654  4.42261  2.77555  2.73159  3.46390  2.40349  3.72530  3.29390  2.67644  2.69391  4.24726  2.90382  2.73775  3.18182  2.89676  2.37923  2.77555  2.98554  4.58513  3.61539
+          0.07365  2.65244  7.55997  0.68750  0.69882  0.55848  0.84881
+     34   2.86727  6.06081  4.71282  3.18868  4.17348  5.01369  5.23880  2.28013  1.93074  2.57484  3.62659  3.50797  4.50213  2.73001  3.10936  2.28952  3.90008  1.50505  6.60949  4.05291     50 - H
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00156  6.86009  7.58243  0.61958  0.77255  0.32787  1.27459
+     35   2.32905  4.61224  3.01269  2.06747  5.92970  3.35826  5.03066  4.20939  1.04917  3.64984  5.62391  3.67161  5.23721  2.45994  3.00322  3.20748  3.41763  4.97476  3.55155  5.60396     51 - H
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00153  6.88065  7.60300  0.61958  0.77255  0.48576  0.95510
+     36   2.87585  4.91154  2.54924  1.87007  5.93053  3.59140  3.50481  5.41746  2.12488  3.89065  4.13340  3.11693  5.23707  3.59876  1.11976  3.15039  3.65907  4.97548  7.01598  5.60422     52 - H
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00153  6.88065  7.60300  0.61958  0.77255  0.48576  0.95510
+     37   3.53678  5.63373  4.36711  4.02843  2.01540  5.37388  5.69684  3.73636  3.83560  1.61236  2.79741  5.47083  4.39888  4.05090  4.39243  4.67639  3.18260  2.67827  6.25229  1.13296     53 - H
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03560  6.88065  3.38290  0.61958  0.77255  0.48576  0.95510
+     38   4.04702  4.45403  3.01026  2.32609  2.25662  3.12693  5.01840  3.42003  2.39465  1.95502  4.64661  3.38725  2.26699  2.26855  3.86875  3.09204  3.43488  4.88528  3.14992  5.55372     54 - H
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00158  6.84663  7.56898  0.61958  0.77255  0.96729  0.47822
+     39   2.77690  6.55648  3.18529  1.35735  5.90289  2.75594  5.00282  5.38982  1.92066  3.99323  5.59679  2.36969  5.20939  2.72634  4.23008  2.13282  2.65497  3.96756  6.98836  5.57657     55 - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00158  6.84663  7.56898  0.61958  0.77255  0.27145  1.43663
+     40   3.44111  6.58238  3.91808  2.60745  5.92801  1.21566  3.55470  3.24340  2.18352  3.05904  5.62289  3.02983  3.88905  2.93734  3.36536  2.80785  2.40008  3.92248  7.01473  4.20561     56 - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00103  6.88015        *  0.61958  0.77255  0.00000        *
+//

data/test/helper.rb

@@ -0,0 +1,18 @@
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'test/unit'
+require 'shoulda'
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'bio-hmmer_model'
+
+class Test::Unit::TestCase
+end

data/test/test_bio-hmmer_model.rb

@@ -0,0 +1,17 @@
+require 'helper'
+
+class TestBioHmmerModel < Test::Unit::TestCase
+  should "read a single file OK" do
+    hmm = Bio::HMMER::Model.parse(File.open('test/data/PF10417.4.hmm'))
+    assert_equal 86, hmm.nseq
+    assert_equal 40, hmm.leng
+    assert_in_delta 0.00000005, hmm.match_emissions[0][3], 1e-8
+    assert_equal "hmmsearch -Z 15929002 -E 1000 --cpu 4 HMM pfamseq", hmm.sm
+    assert_equal ['LOCAL','FORWARD',-4.3017,0.71948], hmm.stats[2]
+  end
+  
+  should "give the correct match probability" do
+    hmm = Bio::HMMER::Model.parse(File.open('test/data/PF10417.4.hmm'))
+    assert_in_delta 0.000204904, hmm.match_probability(3, 'I'), 1e-4
+  end
+end

metadata

@@ -0,0 +1,131 @@
+--- !ruby/object:Gem::Specification
+name: bio-hmmer_model
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+  prerelease: 
+platform: ruby
+authors:
+- Ben J. Woodcroft
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2012-05-18 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: shoulda
+  requirement: &77172790 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: *77172790
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: &77172310 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: *77172310
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: &77187640 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.0.0
+  type: :development
+  prerelease: false
+  version_requirements: *77187640
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: &77187000 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.3
+  type: :development
+  prerelease: false
+  version_requirements: *77187000
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: &77186340 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+  type: :development
+  prerelease: false
+  version_requirements: *77186340
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: &77185790 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: *77185790
+description: Parse PFAM HMM definition files so that the models can be accessible
+  programmatically
+email: donttrustben near gmail.com
+executables: []
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.md
+- README.rdoc
+files:
+- .document
+- .travis.yml
+- Gemfile
+- LICENSE.txt
+- README.md
+- README.rdoc
+- Rakefile
+- VERSION
+- lib/bio-hmmer_model.rb
+- lib/bio/appl/hmmer/model.rb
+- test/data/PF10417.4.hmm
+- test/helper.rb
+- test/test_bio-hmmer_model.rb
+homepage: http://github.com/wwood/bioruby-hmmer_model
+licenses:
+- MIT
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
+      - 0
+      hash: -141514351
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.17
+signing_key: 
+specification_version: 3
+summary: Parse PFAM HMM definition files
+test_files: []