bio-hmmer3_report 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 "jeweler", "~> 1.8.3"
+  gem "bundler", ">= 1.0.21"
+  gem "bio", ">= 1.4.2"
+  gem "rdoc", "~> 3.12"
+end

data/LICENSE.txt

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+Copyright (c) 2012 Christian Zmasek and 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-hmmer3_report
+
+[![Build Status](https://secure.travis-ci.org/wwood/bioruby-hmmer3_report.png)](http://travis-ci.org/wwood/bioruby-hmmer3_report)
+
+Parser class for hmmsearch and hmmscan in the HMMER 3 package.
+
+## Examples
+
+# Description
+
+
+    # Input from string:
+    data = String.new
+    data         << '#                                                                            --- full sequence --- -------------- this domain -------------   hmm coord   ali coord   env coord'
+    data << "\n" << '# target name        accession   tlen query name           accession   qlen   E-value  score  bias   #  of  c-Evalue  i-Evalue  score  bias  from    to  from    to  from    to  acc description of target'
+    data << "\n" << '#------------------- ---------- ----- -------------------- ---------- ----- --------- ------ ----- --- --- --------- --------- ------ ----- ----- ----- ----- ----- ----- ----- ---- ---------------------'
+    data << "\n" << 'Bcl-2                PF00452.13   101 sp|P10415|BCL2_HUMAN -            239   3.7e-30  103.7   0.1   1   1   7.9e-34   4.9e-30  103.3   0.0     1   101    97   195    97   195 0.99 Apoptosis regulator proteins, Bcl-2 family'
+    data << "\n" << 'BH4                  PF02180.11    27 sp|P10415|BCL2_HUMAN -            239   3.9e-15   54.6   0.1   1   1   1.3e-18   8.2e-15   53.6   0.1     2    26     8    32     7    33 0.94 Bcl-2 homology region 4'
+    data << "\n"
+
+    report = Bio::HMMER::HMMER3::Report.new(data)
+    report.hits.each do |hit|
+      puts hit.target_name
+      puts hit.full_sequence_e_value
+    end
+
+
+    # Input from file:
+    report = Bio::HMMER::HMMER3::Report.new(File.open('test/data/HMMER/hmmsearch_domtblout.out'))
+    report.hits.each do |hit|
+      puts hit.target_name
+      puts hit.target_accession
+      puts hit.query_name
+      puts hit.query_accession
+      puts hit.query_length
+      puts hit.full_sequence_e_value
+      puts hit.full_sequence_score
+      puts hit.domain_number
+      puts hit.domain_sum
+      puts hit.domain_c_e_value
+      puts hit.domain_i_e_value
+      puts hit.domain_score
+      puts hit.domain_bias
+      puts hit.hmm_coord_from
+      puts hit.hmm_coord_to
+      puts hit.ali_coord_from
+      puts hit.ali_coord_to
+      puts hit.env_coord_from
+      puts hit.env_coord_to
+      puts hit.acc
+      puts hit.target_description
+    end
+
+
+## References
+
+* HMMER  http://hmmer.janelia.org/
+
+Note: this software is under active development!
+
+## Installation
+
+```sh
+    gem install bio-hmmer3_report
+```
+
+## Usage
+
+```ruby
+    require 'bio-hmmer3_report'
+```
+
+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-hmmer3_report
+
+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-hmmer3_report](http://biogems.info/index.html)
+
+## 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-hmmer3_report"
+  gem.homepage = "http://github.com/wwood/bioruby-hmmer3_report"
+  gem.license = "MIT"
+  gem.summary = %Q{Enables parsing of HMMER version 3 reports}
+  gem.description = %Q{Enables parsing of HMMER version 3 reports}
+  gem.email = "gmail.com after donttrustben"
+  gem.authors = ["Christian Zmasek","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-hmmer3_report #{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-hmmer3_report.rb

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+require 'bio/appl/hmmer/hmmer3/report'
+

data/lib/bio/appl/hmmer/hmmer3/report.rb

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+#
+# = bio/appl/hmmer/hmmer3/report.rb - hmmscan/hmmsearch parser
+#
+# Copyright::   Copyright (C) 2011
+#               Christian Zmasek <cmzmasek@yahoo.com>, Ben Woodcroft <https://github.com/wwood>
+# License::     The Ruby License
+#
+# $Id:$
+#
+
+require 'stringio'
+
+module Bio
+  class HMMER
+    # == Description
+    #
+    # Parser class for hmmsearch and hmmscan in the HMMER 3 package. See README of this biogem for more information.
+    class HMMER3
+      class Report
+        def initialize(hmmer_output, format = nil)
+          
+          @hits = Array.new
+          @line_number = 0
+          @format = format
+          if hmmer_output.kind_of?(String)
+            str = StringIO.new(hmmer_output)
+            str.each_line() { |line| parse_line(line) }
+          elsif hmmer_output.kind_of?(IO)
+            hmmer_output.each_line() { |line| parse_line(line) }
+          else
+            raise "Unexpected hmmer_output class: excpected String or IO, found #{hmmer_output.class}"
+          end
+        end
+    
+        attr_reader :hits
+        attr_reader :format
+    
+        private
+    
+        def parse_line(line)
+          @line_number += 1
+          if line  =~ /^#.+this\s+domain/
+            @format = :domtblout
+          elsif line =~ /^#.+best\s+1\s+domain/
+            @format = :tblout
+          elsif line =~ /\S/ && line !~ /^#/
+            if @format == nil
+              if looks_like_per_domain_result?(line)
+                @format = :domtblout
+              else
+                @format = :tblout
+              end
+            end
+            if @format == :domtblout
+              @hits << PerDomainHit.new(line, @line_number)
+            elsif @format == :tblout
+              @hits << PerSequenceHit.new(line, @line_number)
+            else
+              raise ArgumentError, "attempt to parse hmmscan/hmmsearch output style other than \"domtblout\" or \"tblout\""
+            end
+          end
+        end
+    
+        def looks_like_per_domain_result?(line)
+          line =~ /^(\S*)\s+(\S+)\s+(\d+)\s+(\S+)\s+(\S+)\s+(\d+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\d+)\s+(\d+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\S+)\s*(.*)/
+        end
+    
+      end # class Report
+    
+      class Hit
+        def initialize
+          # This is an abstract class. Prevents 'new' being called on this class
+          # and force implementation of 'initialize' in inheriting classes.
+          raise NotImplementedError
+        end
+        attr_reader :target_name
+        attr_reader :target_accession
+        attr_reader :target_description
+        attr_reader :query_name
+        attr_reader :query_accession
+        attr_reader :full_sequence_e_value
+        attr_reader :full_sequence_score
+        attr_reader :full_sequence_bias
+    
+      end # class Hit
+    
+    
+      class PerSequenceHit < Hit
+    
+        # Sets hit data.
+        def initialize(line, line_number)
+    
+          # tblout:
+          #               tn    tacc      qn    qacc fs_eval fs_scor fs_bias   bst_e bst_scor bst_bias   exp     reg     clu      ov     env      dom     rep     inc   desc
+          #                1       2       3       4       5       6       7       8       9      10      11      12      13      14      15       16      17      18     19
+          if  line =~ /^(\S*)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(.*)/
+            @target_name = $1
+            @target_accession = $2
+            @query_name = $3
+            @query_accession = $4
+            @full_sequence_e_value = $5.to_f
+            @full_sequence_score = $6.to_f
+            @full_sequence_bias =  $7.to_f
+            @best_1_domain_e_value = $8.to_f
+            @best_1_domain_score = $9.to_f
+            @best_1_domain_bias =  $10.to_f
+            @domain_number_est_exp = $11.to_i
+            @domain_number_est_reg = $12.to_i
+            @domain_number_est_clu = $13.to_i
+            @domain_number_est_ov  = $14.to_i
+            @domain_number_est_env = $15.to_i
+            @domain_number_est_dom = $16.to_i
+            @domain_number_est_rep = $17.to_i
+            @domain_number_est_inc = $18.to_i
+            @target_description = $19
+          else
+            raise ArgumentError, "line "+ line_number.to_s + " is in an unrecognized format [#{line}]"
+          end
+    
+        end # initialize
+    
+        attr_reader :best_1_domain_e_value
+        attr_reader :best_1_domain_score
+        attr_reader :best_1_domain_bias
+        attr_reader :domain_number_est_exp
+        attr_reader :domain_number_est_reg
+        attr_reader :domain_number_est_clu
+        attr_reader :domain_number_est_ov
+        attr_reader :domain_number_est_env
+        attr_reader :domain_number_est_dom
+        attr_reader :domain_number_est_rep
+        attr_reader :domain_number_est_inc
+    
+      end # class PerSequenceHit
+    
+      class PerDomainHit < Hit
+    
+        # Sets hit data.
+        def initialize(line, line_number)
+    
+          # domtblout:
+          #                tn     acc    tlen   query     acc    qlen  Evalue   score    bias      #       of     c-E    i-E     score   bias      hf      ht      af      at     ef      et     acc  desc
+          #                 1       2       3       4       5       6       7       8       9      10      11      12     13      14      15       16      17      18      19     20      21      22     23
+          if  line =~ /^(\S*)\s+(\S+)\s+(\d+)\s+(\S+)\s+(\S+)\s+(\d+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\d+)\s+(\d+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\S+)\s*(.*)/
+            @target_name = $1
+            @target_accession = $2
+            @target_length = $3.to_i
+            @query_name = $4
+            @query_accession = $5
+            @query_length = $6.to_i
+            @full_sequence_e_value = $7.to_f
+            @full_sequence_score = $8.to_f
+            @full_sequence_bias =  $9.to_f
+            @domain_number = $10.to_i
+            @domain_sum = $11.to_i
+            @domain_c_e_value = $12.to_f
+            @domain_i_e_value = $13.to_f
+            @domain_score = $14.to_f
+            @domain_bias = $15.to_f
+            @hmm_coord_from = $16.to_i
+            @hmm_coord_to = $17.to_i
+            @ali_coord_from = $18.to_i
+            @ali_coord_to = $19.to_i
+            @env_coord_from = $20.to_i
+            @env_coord_to = $21.to_i
+            @acc = $22.to_f
+            @target_description = $23
+          else
+            raise ArgumentError, "line "+ line_number.to_s + " is in a unrecognized format [#{line}]"
+          end
+    
+        end # initialize
+    
+        attr_reader :target_length
+        attr_reader :query_length
+        attr_reader :domain_number
+        attr_reader :domain_sum
+        attr_reader :domain_c_e_value
+        attr_reader :domain_i_e_value
+        attr_reader :domain_score
+        attr_reader :domain_bias
+        attr_reader :hmm_coord_from
+        attr_reader :hmm_coord_to
+        attr_reader :ali_coord_from
+        attr_reader :ali_coord_to
+        attr_reader :env_coord_from
+        attr_reader :env_coord_to
+        attr_reader :acc
+    
+      end # class PerDomainHit
+    end # class HMMER3
+  end # class HMMER
+end # module Bio

data/test/data/HMMER/hmmscan_domtblout.out

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+#                                                                              --- full sequence --- -------------- this domain -------------   hmm coord   ali coord   env coord
+# target name        accession   tlen query name             accession   qlen   E-value  score  bias   #  of  c-Evalue  i-Evalue  score  bias  from    to  from    to  from    to  acc description of target
+#------------------- ---------- -----   -------------------- ---------- ----- --------- ------ ----- --- --- --------- --------- ------ ----- ----- ----- ----- ----- ----- ----- ---- ---------------------
+#comment             PF08016.5    426 jgi|Nemve1|7|gw.28.1.1 -           1604   5.9e-19   67.4  70.5   1   8   0.00053       1.1    7.3   0.4   220   264   142   191   134   200 0.73 Polycystin cation channel
+Ion_trans            PF00520.24   201 jgi|Nemve1|7|gw.28.1.1 -           1604  6.3e-169  557.4  95.3   1   4   1.5e-41     3e-38  130.8  11.1     3   171   140   307   139   346 0.81 Ion transport protein
+Ion_trans            PF00520.24   201 jgi|Nemve1|7|gw.28.1.1 -           1604  6.3e-169  557.4  95.3   2   4   9.1e-45   1.8e-41  141.3  13.1     4   200   479   664   476   665 0.97 Ion transport protein
+Ion_trans            PF00520.24   201 jgi|Nemve1|7|gw.28.1.1 -           1604  6.3e-169  557.4  95.3   3   4   5.2e-45     1e-41  142.1  14.0     1   201   900  1117   900  1117 0.96 Ion transport protein
+Ion_trans            PF00520.24   201 jgi|Nemve1|7|gw.28.1.1 -           1604  6.3e-169  557.4  95.3   4   4   9.2e-51   1.8e-47  160.9  11.3     1   201  1217  1423  1217  1423 0.97 Ion transport protein
+PKD_channel          PF08016.5    426 jgi|Nemve1|7|gw.28.1.1 -           1604   5.9e-19   67.4  70.5   1   8   0.00053       1.1    7.3   0.4   220   264   142   191   134   200 0.73 Polycystin cation channel

data/test/data/HMMER/hmmscan_tblout.out

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+#                                                               --- full sequence ---- --- best 1 domain ---- --- domain number estimation ----
+# target name        accession  query name           accession    E-value  score  bias   E-value  score  bias   exp reg clu  ov env dom rep inc description of target
+#------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ -----   --- --- --- --- --- --- --- --- ---------------------
+wnt                  PF00110.12 sp|P56705|WNT4_HUMAN -           9.7e-130  418.5  23.4  1.1e-129  418.3  16.2   1.0   1   0   0   1   1   1   1 wnt family

data/test/data/HMMER/hmmsearch_domtblout.out

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+#                                                                            --- full sequence --- -------------- this domain -------------   hmm coord   ali coord   env coord
+# target name        accession   tlen query name           accession   qlen   E-value  score  bias   #  of  c-Evalue  i-Evalue  score  bias  from    to  from    to  from    to  acc description of target
+#------------------- ---------- ----- -------------------- ---------- ----- --------- ------ ----- --- --- --------- --------- ------ ----- ----- ----- ----- ----- ----- ----- ---- ---------------------
+wnt                  PF00110.12   310 sp|P56705|WNT4_HUMAN -            351  1.2e-125  418.5  23.4   1   1  2.2e-129  1.3e-125  418.3  16.2     2   310    43   351    42   351 0.97 wnt family
+MEF2_binding         PF09047.3     35 sp|P56705|WNT4_HUMAN -            351      0.17   11.2   1.0   1   1   6.4e-05      0.38   10.1   0.7     3    21    31    50    30    51 0.84 MEF2 binding

data/test/data/HMMER/hmmsearch_domtblout_empty.out

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+#                                                                            --- full sequence --- -------------- this domain -------------   hmm coord   ali coord   env coord
+# target name        accession   tlen query name           accession   qlen   E-value  score  bias   #  of  c-Evalue  i-Evalue  score  bias  from    to  from    to  from    to  acc description of target
+#------------------- ---------- ----- -------------------- ---------- ----- --------- ------ ----- --- --- --------- --------- ------ ----- ----- ----- ----- ----- ----- ----- ---- ---------------------

data/test/data/HMMER/hmmsearch_tblout.out

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+#                                                               --- full sequence ---- --- best 1 domain ---- --- domain number estimation ----
+# target name        accession  query name           accession    E-value  score  bias   E-value  score  bias   exp reg clu  ov env dom rep inc description of target
+#------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ -----   --- --- --- --- --- --- --- --- ---------------------
+wnt                  PF00110.12 sp|P56705|WNT4_HUMAN -           9.7e-130  418.5  23.4  1.1e-129  418.3  16.2   1.0   1   2   3   4   5   6   7 wnt family

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-hmmer3_report'
+
+class Test::Unit::TestCase
+end

data/test/unit/bio/appl/hmmer/test_hmmer3report.rb

@@ -0,0 +1,240 @@
+#
+#
+#
+# Copyright::   Copyright (C) 2011
+#               Christian Zmasek <cmzmasek@yahoo.com>
+# License::    The Ruby License
+#
+#  $Id:$
+#
+require 'helper'
+
+module Bio
+  module Testreport
+
+    HMMER_TEST_DATA = Pathname.new(File.join('test','data','HMMER')).cleanpath.to_s
+
+    def self.hmmsearch_domtblout_empty
+      File.open(File.join HMMER_TEST_DATA, 'hmmsearch_domtblout_empty.out')
+    end
+
+    def self.hmmsearch_domtblout
+      File.open(File.join HMMER_TEST_DATA, 'hmmsearch_domtblout.out')
+    end
+
+    def self.hmmsearch_tblout
+      File.open(File.join HMMER_TEST_DATA, 'hmmsearch_tblout.out')
+    end
+
+    def self.hmmscan_domtblout
+      File.open(File.join HMMER_TEST_DATA, 'hmmscan_domtblout.out')
+    end
+
+    def self.hmmscan_tblout
+      File.open(File.join HMMER_TEST_DATA, 'hmmscan_tblout.out')
+    end
+
+  end # Testreport
+
+  class Testreport_class_methods < Test::Unit::TestCase
+
+
+    def test_hmmsearch_domtblout_empty
+      filename = Testreport.hmmsearch_domtblout_empty
+
+      assert_instance_of(Bio::HMMER::HMMER3::Report,
+        report = Bio::HMMER::HMMER3::Report.new(filename))
+
+      assert_instance_of(Array,
+        report.hits)
+
+      assert_equal(0, report.hits.length)
+    end #
+
+
+    def test_hmmsearch_domtblout
+      filename = Testreport.hmmsearch_domtblout
+
+      assert_instance_of(Bio::HMMER::HMMER3::Report,
+        report = Bio::HMMER::HMMER3::Report.new(filename))
+
+      assert_instance_of(Array,
+        report.hits)
+
+      assert_instance_of(Bio::HMMER::HMMER3::PerDomainHit,
+        report.hits[0])
+
+      assert_kind_of(Bio::HMMER::HMMER3::Hit,
+        report.hits[0])
+
+      assert_equal(2,report.hits.length)
+      assert_equal("wnt", report.hits[0].target_name)
+      assert_equal("PF00110.12", report.hits[0].target_accession)
+      assert_equal(310, report.hits[0].target_length)
+      assert_equal("sp|P56705|WNT4_HUMAN", report.hits[0].query_name)
+      assert_equal("-", report.hits[0].query_accession)
+      assert_equal(351, report.hits[0].query_length)
+      assert_equal(1.2e-125, report.hits[0].full_sequence_e_value)
+      assert_equal(418.5, report.hits[0].full_sequence_score)
+      assert_equal(23.4, report.hits[0].full_sequence_bias)
+      assert_equal(1, report.hits[0].domain_number)
+      assert_equal(1, report.hits[0].domain_sum)
+      assert_equal(2.2e-129, report.hits[0].domain_c_e_value)
+      assert_equal(1.3e-125, report.hits[0].domain_i_e_value)
+      assert_equal(418.3, report.hits[0].domain_score)
+      assert_equal(16.2, report.hits[0].domain_bias)
+      assert_equal(2, report.hits[0].hmm_coord_from)
+      assert_equal(310, report.hits[0].hmm_coord_to)
+      assert_equal(43, report.hits[0].ali_coord_from)
+      assert_equal(351, report.hits[0].ali_coord_to)
+      assert_equal(42, report.hits[0].env_coord_from)
+      assert_equal(351, report.hits[0].env_coord_to)
+      assert_equal(0.97, report.hits[0].acc)
+      assert_equal("wnt family", report.hits[0].target_description)
+      assert_equal("MEF2_binding", report.hits[1].target_name)
+      assert_equal(0.17, report.hits[1].full_sequence_e_value)
+      assert_equal(6.4e-05, report.hits[1].domain_c_e_value)
+      assert_equal("MEF2 binding", report.hits[1].target_description)
+
+    end # test_hmmsearch_domtblout
+
+    def test_hmmsearch_tblout
+
+      filename = Testreport.hmmsearch_tblout
+
+      assert_instance_of(Bio::HMMER::HMMER3::Report,
+        report = Bio::HMMER::HMMER3::Report.new(filename))
+
+      assert_instance_of(Array,
+        report.hits)
+
+      assert_instance_of(Bio::HMMER::HMMER3::PerSequenceHit,
+        report.hits[0])
+
+      assert_kind_of(Bio::HMMER::HMMER3::Hit,
+        report.hits[0])
+
+      assert_equal(1,report.hits.length)
+      assert_equal("wnt", report.hits[0].target_name)
+      assert_equal("PF00110.12", report.hits[0].target_accession)
+      assert_equal("sp|P56705|WNT4_HUMAN", report.hits[0].query_name)
+      assert_equal("-", report.hits[0].query_accession)
+      assert_equal(9.7e-130, report.hits[0].full_sequence_e_value)
+      assert_equal(418.5, report.hits[0].full_sequence_score)
+      assert_equal(23.4, report.hits[0].full_sequence_bias)
+      assert_equal(1.1e-129, report.hits[0].best_1_domain_e_value)
+      assert_equal(418.3, report.hits[0].best_1_domain_score)
+      assert_equal(16.2, report.hits[0].best_1_domain_bias)
+      assert_equal(1.0, report.hits[0].domain_number_est_exp)
+      assert_equal(1, report.hits[0].domain_number_est_reg)
+      assert_equal(2, report.hits[0].domain_number_est_clu)
+      assert_equal(3, report.hits[0].domain_number_est_ov)
+      assert_equal(4, report.hits[0].domain_number_est_env)
+      assert_equal(5, report.hits[0].domain_number_est_dom)
+      assert_equal(6, report.hits[0].domain_number_est_rep)
+      assert_equal(7, report.hits[0].domain_number_est_inc)
+      assert_equal("wnt family", report.hits[0].target_description)
+
+    end # test_hmmsearch_tblout
+
+    def test_hmmscan_domtblout
+
+      filename = Testreport.hmmscan_domtblout
+
+      assert_instance_of(Bio::HMMER::HMMER3::Report,
+        report = Bio::HMMER::HMMER3::Report.new(filename))
+
+      assert_instance_of(Array,
+        report.hits)
+
+      assert_instance_of(Bio::HMMER::HMMER3::PerDomainHit,
+        report.hits[0])
+
+      assert_kind_of(Bio::HMMER::HMMER3::Hit,
+        report.hits[0])
+
+      assert_equal(5,report.hits.length)
+      assert_equal("Ion_trans", report.hits[0].target_name)
+      assert_equal("PF00520.24", report.hits[0].target_accession)
+      assert_equal(201, report.hits[0].target_length)
+      assert_equal("jgi|Nemve1|7|gw.28.1.1", report.hits[0].query_name)
+      assert_equal("-", report.hits[0].query_accession)
+      assert_equal(1604, report.hits[0].query_length)
+      assert_equal(6.3e-169, report.hits[0].full_sequence_e_value)
+      assert_equal(557.4, report.hits[0].full_sequence_score)
+      assert_equal(95.3, report.hits[0].full_sequence_bias)
+      assert_equal(1, report.hits[0].domain_number)
+      assert_equal(4, report.hits[0].domain_sum)
+      assert_equal(1.5e-41, report.hits[0].domain_c_e_value)
+      assert_equal(3e-38, report.hits[0].domain_i_e_value)
+      assert_equal(130.8, report.hits[0].domain_score)
+      assert_equal(11.1, report.hits[0].domain_bias)
+      assert_equal(3, report.hits[0].hmm_coord_from)
+      assert_equal(171, report.hits[0].hmm_coord_to)
+      assert_equal(140, report.hits[0].ali_coord_from)
+      assert_equal(307, report.hits[0].ali_coord_to)
+      assert_equal(139, report.hits[0].env_coord_from)
+      assert_equal(346, report.hits[0].env_coord_to)
+      assert_equal(0.81, report.hits[0].acc)
+      assert_equal("Ion transport protein", report.hits[0].target_description)
+    end # test_hmmscan_domtblout
+
+    def test_hmmscan_tblout
+      filename = Testreport.hmmscan_tblout
+
+      assert_instance_of(Bio::HMMER::HMMER3::Report,
+        report = Bio::HMMER::HMMER3::Report.new(filename))
+
+      assert_instance_of(Array,
+        report.hits)
+
+      assert_instance_of(Bio::HMMER::HMMER3::PerSequenceHit,
+        report.hits[0])
+
+      assert_kind_of(Bio::HMMER::HMMER3::Hit,
+        report.hits[0])
+
+      assert_equal(1,report.hits.length)
+      assert_equal("wnt", report.hits[0].target_name)
+      assert_equal("PF00110.12", report.hits[0].target_accession)
+      assert_equal("sp|P56705|WNT4_HUMAN", report.hits[0].query_name)
+      assert_equal("-", report.hits[0].query_accession)
+      assert_equal(9.7e-130, report.hits[0].full_sequence_e_value)
+      assert_equal(418.5, report.hits[0].full_sequence_score)
+      assert_equal(23.4, report.hits[0].full_sequence_bias)
+      assert_equal(1.1e-129, report.hits[0].best_1_domain_e_value)
+      assert_equal(418.3, report.hits[0].best_1_domain_score)
+      assert_equal(16.2, report.hits[0].best_1_domain_bias)
+      assert_equal(1.0, report.hits[0].domain_number_est_exp)
+      assert_equal(1, report.hits[0].domain_number_est_reg)
+      assert_equal(0, report.hits[0].domain_number_est_clu)
+      assert_equal(0, report.hits[0].domain_number_est_ov)
+      assert_equal(1, report.hits[0].domain_number_est_env)
+      assert_equal(1, report.hits[0].domain_number_est_dom)
+      assert_equal(1, report.hits[0].domain_number_est_rep)
+      assert_equal(1, report.hits[0].domain_number_est_inc)
+      assert_equal("wnt family", report.hits[0].target_description)
+    end # test_hmmscan_tblout
+    
+    def test_string_input
+      data = String.new
+      data         << '#                                                                            --- full sequence --- -------------- this domain -------------   hmm coord   ali coord   env coord'
+      data << "\n" << '# target name        accession   tlen query name           accession   qlen   E-value  score  bias   #  of  c-Evalue  i-Evalue  score  bias  from    to  from    to  from    to  acc description of target'
+      data << "\n" << '#------------------- ---------- ----- -------------------- ---------- ----- --------- ------ ----- --- --- --------- --------- ------ ----- ----- ----- ----- ----- ----- ----- ---- ---------------------'
+      data << "\n" << 'Bcl-2                PF00452.13   101 sp|P10415|BCL2_HUMAN -            239   3.7e-30  103.7   0.1   1   1   7.9e-34   4.9e-30  103.3   0.0     1   101    97   195    97   195 0.99 Apoptosis regulator proteins, Bcl-2 family'
+      data << "\n" << 'BH4                  PF02180.11    27 sp|P10415|BCL2_HUMAN -            239   3.9e-15   54.6   0.1   1   1   1.3e-18   8.2e-15   53.6   0.1     2    26     8    32     7    33 0.94 Bcl-2 homology region 4'
+      data << "\n"
+  
+      report = Bio::HMMER::HMMER3::Report.new(data)
+      hits = report.hits
+      hits.each do |hit|
+        assert_kind_of Bio::HMMER::HMMER3::PerDomainHit, hit
+      end
+      assert_equal 2, hits.length
+      assert_equal 'Bcl-2', hits[0].target_name
+      assert_equal 'BH4', hits[1].target_name
+    end
+
+  end # Testreport _class_methods
+
+end #  Bio

metadata

@@ -0,0 +1,133 @@
+--- !ruby/object:Gem::Specification
+name: bio-hmmer3_report
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+  prerelease: 
+platform: ruby
+authors:
+- Christian Zmasek
+- 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: &76510780 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: *76510780
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: &76510420 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: *76510420
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: &76510040 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.3
+  type: :development
+  prerelease: false
+  version_requirements: *76510040
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: &76509650 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.21
+  type: :development
+  prerelease: false
+  version_requirements: *76509650
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: &76524960 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+  type: :development
+  prerelease: false
+  version_requirements: *76524960
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: &76524250 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: *76524250
+description: Enables parsing of HMMER version 3 reports
+email: gmail.com after donttrustben
+executables: []
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.md
+files:
+- .document
+- .travis.yml
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- VERSION
+- lib/bio-hmmer3_report.rb
+- lib/bio/appl/hmmer/hmmer3/report.rb
+- test/data/HMMER/hmmscan_domtblout.out
+- test/data/HMMER/hmmscan_tblout.out
+- test/data/HMMER/hmmsearch_domtblout.out
+- test/data/HMMER/hmmsearch_domtblout_empty.out
+- test/data/HMMER/hmmsearch_tblout.out
+- test/helper.rb
+- test/unit/bio/appl/hmmer/test_hmmer3report.rb
+homepage: http://github.com/wwood/bioruby-hmmer3_report
+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: -284128881
+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: Enables parsing of HMMER version 3 reports
+test_files: []