bio-hmmer_model 0.0.1 → 0.0.2

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Files changed (5) hide show
  1. data/Gemfile +1 -1
  2. data/VERSION +1 -1
  3. data/lib/bio/appl/hmmer/model.rb +45 -37
  4. data/test/test_bio-hmmer_model.rb +2 -2
  5. metadata +47 -17
data/Gemfile CHANGED
@@ -8,7 +8,7 @@ source "http://rubygems.org"
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  group :development do
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  gem "shoulda", ">= 0"
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  gem "rdoc", "~> 3.12"
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- gem "bundler", "~> 1.0.0"
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+ gem "bundler", "> 1.0.0"
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  gem "jeweler", "~> 1.8.3"
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  gem "bio", ">= 1.4.2"
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  gem "rdoc", "~> 3.12"
data/VERSION CHANGED
@@ -1 +1 @@
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- 0.0.1
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+ 0.0.2
data/lib/bio/appl/hmmer/model.rb CHANGED
@@ -1,39 +1,40 @@
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- ## Example HMM model file, taken from PFAM 26.
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-
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- # HMMER3/b [3.0 | March 2010]
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- # NAME 1-cysPrx_C
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- # ACC PF10417.4
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- # DESC C-terminal domain of 1-Cys peroxiredoxin
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- # LENG 40
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- # ALPH amino
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- # RF no
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- # CS yes
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- # MAP yes
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- # DATE Mon Sep 26 01:36:52 2011
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- # NSEQ 86
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- # EFFN 26.221497
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- # CKSUM 2893062708
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- # GA 20.40 20.40;
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- # TC 20.40 20.50;
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- # NC 20.30 20.30;
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- # BM hmmbuild HMM.ann SEED.ann
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- # SM hmmsearch -Z 15929002 -E 1000 --cpu 4 HMM pfamseq
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- # STATS LOCAL MSV -7.4458 0.71948
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- # STATS LOCAL VITERBI -7.8857 0.71948
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- # STATS LOCAL FORWARD -4.3017 0.71948
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- # HMM A C D E F G H I K L M N P Q R S T V W Y
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- # m->m m->i m->d i->m i->i d->m d->d
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- # 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
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- # 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
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- # 0.00153 6.88065 7.60300 0.61958 0.77255 0.00000 *
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- # 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
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- # 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
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- # 0.00153 6.88065 7.60300 0.61958 0.77255 0.48576 0.95510
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- # 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
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- # 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
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- # 0.00153 6.88065 7.60300 0.61958 0.77255 0.48576 0.95510
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+
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  module Bio
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  class HMMER
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+ ## Example HMM model file, taken from PFAM 26.
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+ #
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+ # HMMER3/b [3.0 | March 2010]
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+ # NAME 1-cysPrx_C
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+ # ACC PF10417.4
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+ # DESC C-terminal domain of 1-Cys peroxiredoxin
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+ # LENG 40
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+ # ALPH amino
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+ # RF no
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+ # CS yes
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+ # MAP yes
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+ # DATE Mon Sep 26 01:36:52 2011
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+ # NSEQ 86
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+ # EFFN 26.221497
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+ # CKSUM 2893062708
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+ # GA 20.40 20.40;
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+ # TC 20.40 20.50;
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+ # NC 20.30 20.30;
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+ # BM hmmbuild HMM.ann SEED.ann
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+ # SM hmmsearch -Z 15929002 -E 1000 --cpu 4 HMM pfamseq
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+ # STATS LOCAL MSV -7.4458 0.71948
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+ # STATS LOCAL VITERBI -7.8857 0.71948
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+ # STATS LOCAL FORWARD -4.3017 0.71948
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+ # HMM A C D E F G H I K L M N P Q R S T V W Y
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+ # m->m m->i m->d i->m i->i d->m d->d
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+ # 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
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+ # 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
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+ # 0.00153 6.88065 7.60300 0.61958 0.77255 0.00000 *
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+ # 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
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+ # 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
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+ # 0.00153 6.88065 7.60300 0.61958 0.77255 0.48576 0.95510
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+ # 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
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+ # 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
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+ # 0.00153 6.88065 7.60300 0.61958 0.77255 0.48576 0.95510
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  class Model
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  class ParseException<Exception; end
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@@ -52,7 +53,14 @@ module Bio
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  attr_accessor :transitions
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  # Probabilities for matches in the model (first line of each position in the main model part of the HMMER3/b file format)
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- # You probably want to use #match_probability not read this variable directly
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+ # You probably want to use #match_probability not read this variable directly.
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+ #
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+ # For speed reasons, you may want to use this data directly, however.
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+ #
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+ # #match_emissions is an Array of Array objects:
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+ # model#[position][amino_acid_index] => Probability of match
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+ #
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+ # amino_acid_index is an index of #alphabet
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  attr_accessor :match_emissions
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  # Probabilities for inserts in the model (second line of each position in the main model part of the HMMER3/b file format)
@@ -92,7 +100,7 @@ module Bio
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  # Assumes that the letter supplied is in the HMM's alphabet
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  def match_probability(hmm_position, letter)
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  index = @alphabet.index(letter)
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- match_emissions[hmm_position+1][index]
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+ match_emissions[hmm_position-1][index]
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  end
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  # Parse a HMM file fed in through some IO, and return an instantiated
@@ -183,7 +191,7 @@ module Bio
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  # All probability parameters are all stored as negative natural log probabilities with
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  # five digits of precision to the right of the decimal point, rounded. For example,
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  # a probability of 0.25 is stored as − log 0.25 = 1.38629.
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- 10.0**-(s.to_f)
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+ Math.exp(-(s.to_f))
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  end
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  model.match_emissions.push probabilities
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  lineno += 1
data/test/test_bio-hmmer_model.rb CHANGED
@@ -5,13 +5,13 @@ class TestBioHmmerModel < Test::Unit::TestCase
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  hmm = Bio::HMMER::Model.parse(File.open('test/data/PF10417.4.hmm'))
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  assert_equal 86, hmm.nseq
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  assert_equal 40, hmm.leng
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- assert_in_delta 0.00000005, hmm.match_emissions[0][3], 1e-8
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+ assert_in_delta 0.000672849, hmm.match_emissions[0][3], 0.000672849/10000
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  assert_equal "hmmsearch -Z 15929002 -E 1000 --cpu 4 HMM pfamseq", hmm.sm
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  assert_equal ['LOCAL','FORWARD',-4.3017,0.71948], hmm.stats[2]
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  end
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  should "give the correct match probability" do
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  hmm = Bio::HMMER::Model.parse(File.open('test/data/PF10417.4.hmm'))
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- assert_in_delta 0.000204904, hmm.match_probability(3, 'I'), 1e-4
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+ assert_in_delta 0.025010739, hmm.match_probability(3, 'I'), 0.025010739/10000
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  end
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  end
metadata CHANGED
@@ -1,7 +1,7 @@
1
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  --- !ruby/object:Gem::Specification
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  name: bio-hmmer_model
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  version: !ruby/object:Gem::Version
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- version: 0.0.1
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+ version: 0.0.2
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  prerelease:
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  platform: ruby
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  authors:
@@ -9,11 +9,11 @@ authors:
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2012-05-18 00:00:00.000000000 Z
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+ date: 2012-05-25 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: shoulda
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- requirement: &77172790 !ruby/object:Gem::Requirement
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+ requirement: !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -21,10 +21,15 @@ dependencies:
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  version: '0'
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  type: :development
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  prerelease: false
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- version_requirements: *77172790
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+ version_requirements: !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ! '>='
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+ - !ruby/object:Gem::Version
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+ version: '0'
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  - !ruby/object:Gem::Dependency
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  name: rdoc
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- requirement: &77172310 !ruby/object:Gem::Requirement
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+ requirement: !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -32,21 +37,31 @@ dependencies:
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  version: '3.12'
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  type: :development
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  prerelease: false
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- version_requirements: *77172310
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+ version_requirements: !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ~>
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+ - !ruby/object:Gem::Version
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+ version: '3.12'
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  - !ruby/object:Gem::Dependency
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  name: bundler
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- requirement: &77187640 !ruby/object:Gem::Requirement
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+ requirement: !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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- - - ~>
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+ - - ! '>'
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  - !ruby/object:Gem::Version
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  version: 1.0.0
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  type: :development
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  prerelease: false
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- version_requirements: *77187640
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+ version_requirements: !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ! '>'
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+ - !ruby/object:Gem::Version
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+ version: 1.0.0
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  - !ruby/object:Gem::Dependency
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  name: jeweler
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- requirement: &77187000 !ruby/object:Gem::Requirement
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+ requirement: !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -54,10 +69,15 @@ dependencies:
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  version: 1.8.3
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  type: :development
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  prerelease: false
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- version_requirements: *77187000
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+ version_requirements: !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ~>
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+ - !ruby/object:Gem::Version
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+ version: 1.8.3
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  - !ruby/object:Gem::Dependency
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  name: bio
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- requirement: &77186340 !ruby/object:Gem::Requirement
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+ requirement: !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -65,10 +85,15 @@ dependencies:
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  version: 1.4.2
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  type: :development
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  prerelease: false
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- version_requirements: *77186340
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+ version_requirements: !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ! '>='
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+ - !ruby/object:Gem::Version
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+ version: 1.4.2
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  - !ruby/object:Gem::Dependency
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  name: rdoc
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- requirement: &77185790 !ruby/object:Gem::Requirement
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+ requirement: !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -76,7 +101,12 @@ dependencies:
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  version: '3.12'
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  type: :development
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  prerelease: false
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- version_requirements: *77185790
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+ version_requirements: !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ~>
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+ - !ruby/object:Gem::Version
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+ version: '3.12'
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  description: Parse PFAM HMM definition files so that the models can be accessible
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  programmatically
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  email: donttrustben near gmail.com
@@ -115,7 +145,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
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  version: '0'
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  segments:
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  - 0
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- hash: -141514351
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+ hash: 67884365
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  required_rubygems_version: !ruby/object:Gem::Requirement
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  none: false
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  requirements:
@@ -124,7 +154,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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  version: '0'
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  requirements: []
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  rubyforge_project:
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- rubygems_version: 1.8.17
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+ rubygems_version: 1.8.24
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  signing_key:
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  specification_version: 3
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  summary: Parse PFAM HMM definition files