genevalidatorapp 1.4.12

data/spec/database/without_parse_seqids/without_parse_seqids.fa

@@ -0,0 +1,10 @@
+>SI2.2.0_06267 locus=Si_gnF.scaffold02592[1282609..1284114].pep_2 quality=100.00
+MNTLWLSLWDYPGKLPLNFMVFDTKDDLQAAYWRDPYSIPLAVIFEDPQPISQRLIYEIR
+TNPSYTLPPPPTKLYSAPISCRKNKTGHWMDDILSIKTGESCPVNNYLHSGFLALQMITD
+ITKIKLENSDVTIPDIKLIMFPKEPYTADWMLAFRVVIPLYMVLALSQFITYLLILIVGE
+KENKIKEGMKMMGLNDSVF
+>SI2.2.0_13722 locus=Si_gnF.scaffold06207[1925625..1928536].pep_1 quality=100.00
+MSANRLNVLVTLMLAVALLVTESGNAQVDGYLQFNPKRSAVSSPQKYCGKKLSNALQIIC
+DGVYNSMFKKSGQDFPPQNKRHIAHRINGNEEESFTTLKSNFLNWCVEVYHRHYRFVFVS
+EMEMADYPLAYDISPYLPPFLSRARARGMLDGRFAGRRYRRESRGIHEECCINGCTINEL
+TSYCGP

data/spec/database_spec.rb

@@ -0,0 +1,37 @@
+require 'GeneValidatorApp'
+require 'GeneValidatorApp/database'
+require 'rspec'
+
+module GeneValidatorApp
+  describe 'Database' do
+    let 'root' do
+      GeneValidatorApp.root
+    end
+
+    let 'empty_config' do
+      File.join(root, 'spec', 'empty_config.yml')
+    end
+
+    let 'database_dir' do
+      File.join(root, 'spec', 'database')
+    end
+
+    let 'database_dir_no_db' do
+      File.join(root, 'spec', 'database', 'proteins', 'Cardiocondyla_obscurior')
+    end
+
+    let 'app' do
+      GeneValidatorApp.init(config_file: empty_config,
+                            database_dir: database_dir)
+    end
+
+    it 'can tell BLAST+ databases in a directory' do
+    end
+
+    it 'can tell NCBI multipart database name' do
+      #   Database.multipart_database_name?('/home/ben/pd.ben/sequenceserver/db/nr.00').should be_true
+      #   Database.multipart_database_name?('/home/ben/pd.ben/sequenceserver/db/nr').should be_false
+      #   Database.multipart_database_name?('/home/ben/pd.ben/sequenceserver/db/img3.5.finished.faa.01').should be_true
+    end
+  end
+end

data/views/500.slim

@@ -0,0 +1,5 @@
+.alert.alert-danger role="alert"
+  h3.error_header  Oops! Something went Wonky!
+  p  <strong>Apologies, there was an error with your request. Please try again.</strong>
+  p  Error Message: #{request.env['sinatra.error'].message}
+  p  If the error persists, please contact the administrator.

data/views/index.slim

@@ -0,0 +1,66 @@
+section#search
+  h1.page-header
+    span  GeneValidator 
+    span.small  Identify problems with gene predictions
+  form#input action="#{uri('/')}" method="POST"
+    .form-group#input_seq_group
+      label.control-label.input_seq-label for="seq"  Input Sequences:
+      - if @max_characters != 'undefined'
+        textarea#seq.form-control autofocus="" name="seq" placeholder="Paste your sequence(s) here..." rows="10" spellcheck="false" data-maxCharacters="#{@max_characters}"
+      - else
+        textarea#seq.form-control autofocus="" name="seq" placeholder="Paste your sequence(s) here..." rows="10" spellcheck="false" 
+    .clearfix
+    button#adv_params_btn.btn.btn-primary type="button" onclick="changeAdvParamsBtnText()"
+      i.fa.fa-pencil-square-o
+      |   Show Advanced Parameters
+    .clearfix
+    #adv_params.collapse
+      .form-group.form-inline#validations_group
+        br/
+        label.control-label  Advanced Parameters: Validations Types
+        br/
+        label.checkbox-inline.no_indent.col-lg-3.col-md-5.col-sm-6.col-xs-12
+          <input id="lenc" class="check" type="checkbox" name="validations[]" checked="" value="lenc">Length Validation (via clusterization)
+        label.checkbox-inline.no_indent.col-lg-3.col-md-5.col-sm-6.col-xs-12
+          <input id="lenr" class="check" type="checkbox" name="validations[]" checked="" value="lenr"> Length Validation (via ranking)
+        label.checkbox-inline.no_indent.col-lg-3.col-md-5.col-sm-6.col-xs-12
+          <input id="dup" class="check" type="checkbox" name="validations[]" checked="" value="dup"> Duplication Check
+        label.checkbox-inline.no_indent.col-lg-3.col-md-5.col-sm-6.col-xs-12
+          <input id="merge" class="check" type="checkbox" name="validations[]" checked="" value="merge"> Gene Merge Validation
+        label.checkbox-inline.no_indent.col-lg-3.col-md-5.col-sm-6.col-xs-12
+          <input id="align" class="check" type="checkbox" name="validations[]" checked="" value="align"> Multiple Alignment Validation (proteins)
+        label.checkbox-inline.no_indent.col-lg-3.col-md-5.col-sm-6.col-xs-12
+          <input id="frame" class="check" type="checkbox" name="validations[]" checked="" value="frame"> Blast Reading Frame Validation (nucleotides)
+        label#lastValidation.checkbox-inline.no_indent.col-lg-3.col-md-5.col-sm-6.col-xs-12
+          <input id="orf" class="check" type="checkbox" name="validations[]" checked="" value="orf"> Open Reading Frame Validation (nucleotides)
+      .clearfix
+      br/
+      .form-group.form-inline
+        label.control-label  Advanced Parameters: Database
+        br/
+        label.radio-inline.no_indent.col-lg-3.col-md-5.col-sm-6.col-xs-12
+          <input type="radio" name="database" value="#{@default_db.title.chomp}" checked=""> #{@default_db.title.chomp}
+        - unless @non_default_dbs.empty?
+          - @non_default_dbs.each do |db|
+            label.radio-inline.no_indent.col-lg-3.col-md-5.col-sm-6.col-xs-12
+              <input type="radio" name="database" value="#{db.title.chomp}"> #{db.title.chomp}
+      .clearfix
+    .form-group
+      button#input_btn.btn.btn-lg.btn-primary type="submit" value="input"
+        i.fa.fa-search
+        | &nbsp;&nbsp;Analyse Sequences
+      .clearfix
+    .show_examples_text
+      span 
+        a#protein_example onclick="examplarSequence('protein')"
+          | Show a protein example
+      span
+        | &nbsp;&#124;&nbsp;
+      span
+        a#dna_example onclick="examplarSequence('dna')"
+          | Show a DNA example
+section#results
+  #results_box style="display:none;"
+    h1#output_header.page-header
+      span Results
+    #output

data/views/layout.slim

@@ -0,0 +1,85 @@
+doctype html
+html lang="en"
+  head
+    meta charset="utf-8"
+    meta content="IE=edge" http-equiv="X-UA-Compatible"
+    meta content="width=device-width, initial-scale=1" name="viewport"
+    meta content="" name="description"
+    meta content="" name="author"
+    title GeneValidator | Identify problems with Gene Predictions
+
+    script type="text/javascript" src="#{uri('web_files/js/jquery.min.js')}"
+    script type="text/javascript" src="#{uri('web_files/js/bootstrap.min.js')}"
+    script type="text/javascript" src="#{uri('web_files/js/jquery.tablesorter.min.js')}"
+    script type="text/javascript" src="#{uri('web_files/js/d3.v3.min.js')}"
+    script type="text/javascript" src="#{uri('web_files/js/plots.min.js')}"
+    script type="text/javascript" src="#{uri('web_files/js/genevalidator.min.js')}"
+    script type="text/javascript" src="#{uri('web_files/js/jquery.cookie.min.js')}"
+    script type="text/javascript" src="#{uri('web_files/js/jquery.validate.min.js')}"
+
+    /! Bootstrap core CSS
+    link href="#{uri('web_files/css/bootstrap1.min.css')}" rel="stylesheet" type="text/css"
+    link href="#{uri('web_files/css/font-awesome.min.css')}" rel="stylesheet" type="text/css"
+    link href="#{uri('web_files/css/custom.min.css')}" rel="stylesheet" type="text/css"
+
+    /! HTML5 shim and Respond.js IE8 support of HTML5 elements and media queries
+    /![if lt IE 9]
+      script src="https://oss.maxcdn.com/libs/html5shiv/3.7.0/html5shiv.js"
+      script src="https://oss.maxcdn.com/libs/respond.js/1.4.2/respond.min.js"
+
+  body#mainbody
+    .navbar.navbar-default.navbar-fixed-top role="navigation"
+      .nav-container
+        .navbar-header
+          button.navbar-toggle data-target=".navbar-responsive-collapse" data-toggle="collapse" type="button" 
+            span.icon-bar
+            span.icon-bar
+            span.icon-bar
+          span.navbar-brand
+            a href="#" GeneValidator
+        .navbar-collapse.collapse.navbar-responsive-collapse
+          ul.nav.navbar-nav
+            li
+              a href="#" Home
+            li
+              a href="https://github.com/IsmailM/GeneValidatorApp" target="_blank"  Source Code
+            li
+              a href="https://ismailm.github.io/GeneValidatorApp-API" target="_blank"  API
+            /!   a href="#"  Documentation
+            /! li
+            /!   a href="#"  Support
+            li
+              a href="http://yannick.poulet.org" target="_blank" Wurm Lab
+          ul.nav.navbar-nav.navbar-right
+            li
+              a.nav_github_icon href="https://github.com/IsmailM/GeneValidatorApp" target="_blank"
+                span.i.fa.fa-2x.fa-github
+    ==yield
+    #spinner.modal aria-hidden="true" aria-labelledby="spinner" role="dialog" tabindex="-1"
+      .modal-dialog
+        .modal-content
+          .modal-body.text-center
+            h2  Calculating...
+            p.results_link  This may take some time. Please leave this page open.
+            i.fa.fa-spinner.fa-5x.fa-spin
+    footer#footer
+      p.text-muted.text-center 
+        | Please cite "Dragan M, Moghul MI, Priyam A & Wurm Y 
+        em 
+          | (in prep) 
+        | GeneValidator: identify problematic gene predictions"
+        br
+        |  Developed at 
+        a href="http://yannick.poulet.org" target="_blank" Wurm Lab
+        | , 
+        a href="http://www.sbcs.qmul.ac.uk" target="_blank" QMUL
+        |  with funding by 
+        a href="http://www.bbsrc.ac.uk/home/home.aspx" target="_blank" BBSRC
+        |  and 
+        a href="https://www.google-melange.com/gsoc/homepage/google/gsoc2013" target="_blank"  Google Summer of Code 2013
+        br
+        | This page was created by 
+        a href="https://github.com/IsmailM/GeneValidatorApp" target="_blank"  GeneValidator Web Application 
+        | v#{GeneValidatorApp::VERSION} (using 
+        a href="https://github.com/monicadragan/GeneValidator" target="_blank"  GeneValidator 
+        | v#{@current_gv_version})

metadata

@@ -0,0 +1,337 @@
+--- !ruby/object:Gem::Specification
+name: genevalidatorapp
+version: !ruby/object:Gem::Version
+  version: 1.4.12
+platform: ruby
+authors:
+- Ismail Moghul
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2015-05-22 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.6'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.6'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.3'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.3'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.2'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.2'
+- !ruby/object:Gem::Dependency
+  name: rack-test
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.6'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.6'
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.4'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.4'
+- !ruby/object:Gem::Dependency
+  name: genevalidator
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.5'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.5'
+- !ruby/object:Gem::Dependency
+  name: sinatra
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.4'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.4'
+- !ruby/object:Gem::Dependency
+  name: sinatra-contrib
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.4'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.4'
+- !ruby/object:Gem::Dependency
+  name: sinatra-cross_origin
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.3'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.3'
+- !ruby/object:Gem::Dependency
+  name: slim
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+- !ruby/object:Gem::Dependency
+  name: slop
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '4.0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '4.0'
+- !ruby/object:Gem::Dependency
+  name: thin
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.6'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.6'
+- !ruby/object:Gem::Dependency
+  name: w3c_validators
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.1'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.1'
+description: A Web App wrapper for GeneValidator, a program for validating gene predictions.
+email:
+- Ismail.Moghul@gmail.com
+executables:
+- genevalidatorapp
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".travis.yml"
+- Gemfile
+- GeneValidatorApp.gemspec
+- LICENSE.txt
+- README.md
+- Rakefile
+- bin/genevalidatorapp
+- config.ru
+- lib/GeneValidatorApp.rb
+- lib/GeneValidatorApp/config.rb
+- lib/GeneValidatorApp/database.rb
+- lib/GeneValidatorApp/genevalidator.rb
+- lib/GeneValidatorApp/logger.rb
+- lib/GeneValidatorApp/version.rb
+- public/GeneValidator/.gitkeep
+- public/web_files/css/bootstrap.min.css
+- public/web_files/css/bootstrap1.min.css
+- public/web_files/css/custom.css
+- public/web_files/css/custom.min.css
+- public/web_files/css/font-awesome.min.css
+- public/web_files/fonts/FontAwesome.otf
+- public/web_files/fonts/fontawesome-webfont.eot
+- public/web_files/fonts/fontawesome-webfont.svg
+- public/web_files/fonts/fontawesome-webfont.ttf
+- public/web_files/fonts/fontawesome-webfont.woff
+- public/web_files/img/gene.png
+- public/web_files/js/bionode-seq.min.js
+- public/web_files/js/bootstrap.min.js
+- public/web_files/js/d3.v3.min.js
+- public/web_files/js/genevalidator.js
+- public/web_files/js/genevalidator.min.js
+- public/web_files/js/jquery.cookie.min.js
+- public/web_files/js/jquery.min.js
+- public/web_files/js/jquery.tablesorter.min.js
+- public/web_files/js/jquery.validate.min.js
+- public/web_files/js/plots.js
+- public/web_files/js/plots.min.js
+- spec/app_spec.rb
+- spec/database/funky_ids/funky_ids.fa
+- spec/database/funky_ids/funky_ids.fa.nhr
+- spec/database/funky_ids/funky_ids.fa.nin
+- spec/database/funky_ids/funky_ids.fa.nog
+- spec/database/funky_ids/funky_ids.fa.nsd
+- spec/database/funky_ids/funky_ids.fa.nsi
+- spec/database/funky_ids/funky_ids.fa.nsq
+- spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta
+- spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.phr
+- spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pin
+- spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pog
+- spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psd
+- spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psi
+- spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psq
+- spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta
+- spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nhr
+- spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nin
+- spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nog
+- spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsd
+- spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsi
+- spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsq
+- spec/database/unformatted/Cardiocondyla_obscurior/Cobs1.4.proteins.fa
+- spec/database/without_parse_seqids/without_parse_seqids.fa
+- spec/database/without_parse_seqids/without_parse_seqids.fa.phr
+- spec/database/without_parse_seqids/without_parse_seqids.fa.pin
+- spec/database/without_parse_seqids/without_parse_seqids.fa.psq
+- spec/database_spec.rb
+- spec/empty_config.yml
+- views/500.slim
+- views/index.slim
+- views/layout.slim
+homepage: https://github.com/wurmlab/GeneValidatorApp
+licenses:
+- AGPL
+metadata: {}
+post_install_message: |2+
+
+  ------------------------------------------------------------------------
+    Thank you for validating your gene predictions with GeneValidator!
+
+    To launch GeneValidatorApp execute 'genevalidatorapp' from command line.
+
+      $ genevalidatorapp [options]
+
+    Visit https://github.com/wurmlab/GeneValidatorApp for more information.
+  ------------------------------------------------------------------------
+
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: 2.0.0
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.4.6
+signing_key: 
+specification_version: 4
+summary: A Web App wrapper for GeneValidator.
+test_files:
+- spec/app_spec.rb
+- spec/database/funky_ids/funky_ids.fa
+- spec/database/funky_ids/funky_ids.fa.nhr
+- spec/database/funky_ids/funky_ids.fa.nin
+- spec/database/funky_ids/funky_ids.fa.nog
+- spec/database/funky_ids/funky_ids.fa.nsd
+- spec/database/funky_ids/funky_ids.fa.nsi
+- spec/database/funky_ids/funky_ids.fa.nsq
+- spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta
+- spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.phr
+- spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pin
+- spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pog
+- spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psd
+- spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psi
+- spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psq
+- spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta
+- spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nhr
+- spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nin
+- spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nog
+- spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsd
+- spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsi
+- spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsq
+- spec/database/unformatted/Cardiocondyla_obscurior/Cobs1.4.proteins.fa
+- spec/database/without_parse_seqids/without_parse_seqids.fa
+- spec/database/without_parse_seqids/without_parse_seqids.fa.phr
+- spec/database/without_parse_seqids/without_parse_seqids.fa.pin
+- spec/database/without_parse_seqids/without_parse_seqids.fa.psq
+- spec/database_spec.rb
+- spec/empty_config.yml