--- !ruby/object:Gem::Specification name: genevalidator version: !ruby/object:Gem::Version version: 1.6.0 platform: ruby authors: - Monica Dragan - Ismail Moghul - Anurag Priyam - Yannick Wurm autorequire: bindir: bin cert_chain: [] date: 2015-05-28 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: 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: bio-blastxmlparser requirement: !ruby/object:Gem::Requirement requirements: - - "~>" - !ruby/object:Gem::Version version: '2.0' type: :runtime prerelease: false version_requirements: !ruby/object:Gem::Requirement requirements: - - "~>" - !ruby/object:Gem::Version version: '2.0' - !ruby/object:Gem::Dependency name: minitest requirement: !ruby/object:Gem::Requirement requirements: - - "~>" - !ruby/object:Gem::Version version: '5.4' type: :runtime prerelease: false version_requirements: !ruby/object:Gem::Requirement requirements: - - "~>" - !ruby/object:Gem::Version version: '5.4' - !ruby/object:Gem::Dependency name: statsample 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' description: | The tool validates the input predicted genes and provides useful information (length validation, gene merge validation, sequence duplication checking, ORF finding) based on the similarities to genes in public databases. email: y.wurm@qmul.ac.uk executables: - genevalidator extensions: [] extra_rdoc_files: [] files: - ".gitignore" - ".travis.yml" - Gemfile - GeneValidator.gemspec - LICENCE.txt - README.md - Rakefile - aux/app_template_footer.erb - aux/app_template_header.erb - aux/files/css/bootstrap.min.css - aux/files/css/font-awesome.min.css - aux/files/css/style.css - aux/files/fonts/FontAwesome.otf - aux/files/fonts/fontawesome-webfont.eot - aux/files/fonts/fontawesome-webfont.svg - aux/files/fonts/fontawesome-webfont.ttf - aux/files/fonts/fontawesome-webfont.woff - aux/files/img/gene.png - aux/files/js/bootstrap.min.js - aux/files/js/d3.v3.min.js - aux/files/js/jquery-2.1.1.min.js - aux/files/js/jquery.tablesorter.min.js - aux/files/js/plots.js - aux/files/js/script.js - aux/files/json/.gitkeep - aux/template_footer.erb - aux/template_header.erb - aux/template_query.erb - bin/genevalidator - data/README.md - data/mrna_data.fasta - data/mrna_data.fasta.blast_tabular - data/mrna_data.fasta.blast_xml - data/protein_data.fasta - data/protein_data.fasta.blast_tabular - data/protein_data.fasta.blast_xml - doc/AliasDuplicationError.html - doc/AlignmentValidation.html - doc/AlignmentValidationOutput.html - doc/Blast.html - doc/BlastRFValidationOutput.html - doc/BlastReadingFrameValidation.html - doc/BlastUtils.html - doc/ClasspathError.html - doc/Cluster.html - doc/DuplciationValidationOutput.html - doc/DuplicationValidation.html - doc/DuplicationValidationOutput.html - doc/FileNotFoundException.html - doc/GeneMergeValidation.html - doc/GeneMergeValidationOutput.html - doc/HierarchicalClusterization.html - doc/Hsp.html - doc/InconsistentTabularFormat.html - doc/LengthClusterValidation.html - doc/LengthClusterValidationOutput.html - doc/LengthRankValidation.html - doc/LengthRankValidationOutput.html - doc/NoInternetError.html - doc/NoMafftInstallationError.html - doc/NoPIdentError.html - doc/NoValidationError.html - doc/NotEnoughHitsError.html - doc/ORFValidationOutput.html - doc/OpenReadingFrameValidation.html - doc/OtherError.html - doc/Output.html - doc/Pair.html - doc/PairCluster.html - doc/Plot.html - doc/QueryError.html - doc/ReportClassError.html - doc/Sequence.html - doc/SequenceTypeError.html - doc/TabularEntry.html - doc/TabularParser.html - doc/Validation.html - doc/ValidationClassError.html - doc/ValidationOutput.html - doc/ValidationReport.html - doc/ValidationTest.html - doc/_index.html - doc/class_list.html - doc/css/common.css - doc/css/full_list.css - doc/css/style.css - doc/file.README.html - doc/file_list.html - doc/frames.html - doc/index.html - doc/js/app.js - doc/js/full_list.js - doc/js/jquery.js - doc/method_list.html - doc/top-level-namespace.html - lib/genevalidator.rb - lib/genevalidator/arg_validation.rb - lib/genevalidator/blast.rb - lib/genevalidator/clusterization.rb - lib/genevalidator/exceptions.rb - lib/genevalidator/ext/array.rb - lib/genevalidator/get_raw_sequences.rb - lib/genevalidator/hsp.rb - lib/genevalidator/output.rb - lib/genevalidator/pool.rb - lib/genevalidator/sequences.rb - lib/genevalidator/tabular_parser.rb - lib/genevalidator/validation_alignment.rb - lib/genevalidator/validation_blast_reading_frame.rb - lib/genevalidator/validation_duplication.rb - lib/genevalidator/validation_gene_merge.rb - lib/genevalidator/validation_length_cluster.rb - lib/genevalidator/validation_length_rank.rb - lib/genevalidator/validation_open_reading_frame.rb - lib/genevalidator/validation_report.rb - lib/genevalidator/validation_test.rb - lib/genevalidator/version.rb - test/Readme.md - test/test_all_validations.rb - test/test_blast.rb - test/test_clusterization.rb - test/test_clusterization_2d.rb - test/test_extended_array_methods.rb - test/test_files/all_validations_mrna/all_validations_mrna.fasta - test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab - test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab.index - test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab.raw_seq - test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab.raw_seq.idx - test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_xml - test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_xml.index - test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_xml.raw_seq - test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_xml.raw_seq.idx - test/test_files/all_validations_prot/all_validations_prot.fasta - test/test_files/all_validations_prot/all_validations_prot.fasta.blast_tab - test/test_files/all_validations_prot/all_validations_prot.fasta.blast_tab.index - test/test_files/all_validations_prot/all_validations_prot.fasta.blast_tab.raw_seq - test/test_files/all_validations_prot/all_validations_prot.fasta.blast_tab.raw_seq.idx - test/test_files/all_validations_prot/all_validations_prot.fasta.blast_xml - test/test_files/all_validations_prot/all_validations_prot.fasta.blast_xml.index - test/test_files/all_validations_prot/all_validations_prot.fasta.blast_xml.raw_seq - test/test_files/all_validations_prot/all_validations_prot.fasta.blast_xml.raw_seq.idx - test/test_files/mixed_type.fasta - test/test_files/ncbi_mrna.tab.20 - test/test_files/ncbi_mrna.xml.20 - test/test_files/output.tab.6 - test/test_files/output.tab.6.mixed - test/test_files/output.tab.7 - test/test_files/output.xml - test/test_files/test_sequences.fasta - test/test_files/test_sequences.fasta.blast_xml - test/test_files/test_sequences.fasta.blast_xml.index - test/test_files/test_sequences.fasta.blast_xml.raw_seq - test/test_files/test_sequences.fasta.blast_xml.raw_seq.idx - test/test_files/test_validations.fasta - test/test_helper.rb - test/test_sequences.rb - test/test_validation_open_reading_frame.rb - test/test_validations.rb homepage: https://github.com/wurmlab/GeneValidator licenses: - AGPL metadata: {} post_install_message: |2+ ------------------------------------------------------------------------ Thank you for validating your gene predictions with GeneValidator! To launch GeneValidator execute 'genevalidator' from command line. $ genevalidator [options] FASTA_FILE Visit https://github.com/wurmlab/GeneValidator 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: Identifying problems with gene predictions. test_files: - test/Readme.md - test/test_all_validations.rb - test/test_blast.rb - test/test_clusterization.rb - test/test_clusterization_2d.rb - test/test_extended_array_methods.rb - test/test_files/all_validations_mrna/all_validations_mrna.fasta - test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab - test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab.index - test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab.raw_seq - test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab.raw_seq.idx - test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_xml - test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_xml.index - test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_xml.raw_seq - test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_xml.raw_seq.idx - test/test_files/all_validations_prot/all_validations_prot.fasta - test/test_files/all_validations_prot/all_validations_prot.fasta.blast_tab - test/test_files/all_validations_prot/all_validations_prot.fasta.blast_tab.index - test/test_files/all_validations_prot/all_validations_prot.fasta.blast_tab.raw_seq - test/test_files/all_validations_prot/all_validations_prot.fasta.blast_tab.raw_seq.idx - test/test_files/all_validations_prot/all_validations_prot.fasta.blast_xml - test/test_files/all_validations_prot/all_validations_prot.fasta.blast_xml.index - test/test_files/all_validations_prot/all_validations_prot.fasta.blast_xml.raw_seq - test/test_files/all_validations_prot/all_validations_prot.fasta.blast_xml.raw_seq.idx - test/test_files/mixed_type.fasta - test/test_files/ncbi_mrna.tab.20 - test/test_files/ncbi_mrna.xml.20 - test/test_files/output.tab.6 - test/test_files/output.tab.6.mixed - test/test_files/output.tab.7 - test/test_files/output.xml - test/test_files/test_sequences.fasta - test/test_files/test_sequences.fasta.blast_xml - test/test_files/test_sequences.fasta.blast_xml.index - test/test_files/test_sequences.fasta.blast_xml.raw_seq - test/test_files/test_sequences.fasta.blast_xml.raw_seq.idx - test/test_files/test_validations.fasta - test/test_helper.rb - test/test_sequences.rb - test/test_validation_open_reading_frame.rb - test/test_validations.rb