sequenceserver 1.1.0.beta12 → 2.0.0.beta1
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- checksums.yaml +4 -4
- data/.rspec +1 -0
- data/.travis.yml +5 -5
- data/README.md +86 -43
- data/bin/sequenceserver +29 -32
- data/lib/sequenceserver.rb +86 -123
- data/lib/sequenceserver/api_errors.rb +3 -1
- data/lib/sequenceserver/blast/hit.rb +48 -28
- data/lib/sequenceserver/blast/job.rb +28 -8
- data/lib/sequenceserver/blast/report.rb +52 -15
- data/lib/sequenceserver/database.rb +71 -0
- data/lib/sequenceserver/exceptions.rb +5 -10
- data/lib/sequenceserver/job.rb +8 -1
- data/lib/sequenceserver/links.rb +49 -17
- data/lib/sequenceserver/logger.rb +2 -2
- data/lib/sequenceserver/routes.rb +20 -14
- data/lib/sequenceserver/sys.rb +86 -0
- data/lib/sequenceserver/version.rb +1 -1
- data/public/css/sequenceserver.min.css +3 -3
- data/public/js/alignment_exporter.js +1 -1
- data/public/js/hsp.js +1 -1
- data/public/js/report.js +76 -63
- data/public/js/search.js +29 -6
- data/public/sequenceserver-report.min.js +4 -4
- data/public/sequenceserver-search.min.js +2 -2
- data/sequenceserver.gemspec +3 -2
- data/spec/blast_versions/blast_2.2.30/blast_2.2.30_spec.rb +228 -0
- data/spec/blast_versions/blast_2.2.30/import_spec_capybara_local_2.2.30.rb +53 -0
- data/spec/blast_versions/blast_2.2.31/blast_2.2.31_spec.rb +228 -0
- data/spec/blast_versions/blast_2.2.31/import_spec_capybara_local_2.2.31.rb +53 -0
- data/spec/{blast_spec.rb → blast_versions/blast_2.3.0/blast_2.3.0_spec.rb} +8 -37
- data/spec/blast_versions/blast_2.3.0/import_spec_capybara_local_2.3.0.rb +52 -0
- data/spec/blast_versions/blast_2.4.0/blast_2.4.0_spec.rb +228 -0
- data/spec/blast_versions/blast_2.4.0/import_spec_capybara_local_2.4.0.rb +52 -0
- data/spec/blast_versions/blast_2.5.0/blast_2.5.0_spec.rb +228 -0
- data/spec/blast_versions/blast_2.5.0/import_spec_capybara_local_2.5.0.rb +53 -0
- data/spec/blast_versions/blast_2.6.0/blast_2.6.0_spec.rb +228 -0
- data/spec/blast_versions/blast_2.6.0/import_spec_capybara_local_2.6.0.rb +52 -0
- data/spec/blast_versions/blast_2.7.1/blast_2.7.1_spec.rb +228 -0
- data/spec/blast_versions/blast_2.7.1/import_spec_capybara_local_2.7.1.rb +56 -0
- data/spec/blast_versions/blast_2.8.1/blast_2.8.1_spec.rb +228 -0
- data/spec/blast_versions/blast_2.8.1/import_spec_capybara_local_2.8.1.rb +55 -0
- data/spec/blast_versions/blast_2.9.0/blast_2.9.0_spec.rb +228 -0
- data/spec/blast_versions/blast_2.9.0/import_spec_capybara_local_2.9.0.rb +53 -0
- data/spec/blast_versions/diamond_0.9.24/diamond_0.9.24_spec.rb +176 -0
- data/spec/blast_versions/diamond_0.9.24/import_spec_capybara_local_0.9.24.rb +39 -0
- data/spec/capybara_spec.local.rb +190 -0
- data/spec/capybara_spec.rb +15 -13
- data/spec/config_spec.rb +1 -1
- data/spec/database/funky_ids/funky_ids.fa +2 -0
- data/spec/database/funky_ids/funky_ids.fa.nhd +8 -0
- data/spec/database/funky_ids/funky_ids.fa.nhi +0 -0
- data/spec/database/funky_ids/funky_ids.fa.nhr +0 -0
- data/spec/database/funky_ids/funky_ids.fa.nin +0 -0
- data/spec/database/funky_ids/funky_ids.fa.nog +0 -0
- data/spec/database/funky_ids/funky_ids.fa.nsd +15 -13
- data/spec/database/funky_ids/funky_ids.fa.nsi +0 -0
- data/spec/database/funky_ids/funky_ids.fa.nsq +0 -0
- data/spec/database_spec.rb +2 -2
- data/spec/dotdir/blast_2.2.30/blastn/BLASTN_XML_2.2.30.xml +1201 -0
- data/spec/dotdir/blast_2.2.30/blastn/job.yaml +8 -0
- data/spec/dotdir/blast_2.2.30/blastn_nohits/BLASTN_NO_HITS_XML_2.2.30.xml +866 -0
- data/spec/dotdir/blast_2.2.30/blastn_nohits/job.yaml +8 -0
- data/spec/dotdir/blast_2.2.30/blastp/BLASTP_XML_2.2.30.xml +1181 -0
- data/spec/dotdir/blast_2.2.30/blastp/job.yaml +8 -0
- data/spec/dotdir/blast_2.2.30/blastx/BLASTX_XML_2.2.30.xml +1181 -0
- data/spec/dotdir/blast_2.2.30/blastx/job.yaml +8 -0
- data/spec/dotdir/blast_2.2.30/tblastn/TBLASTN_XML_2.2.30.xml +1181 -0
- data/spec/dotdir/blast_2.2.30/tblastn/job.yaml +8 -0
- data/spec/dotdir/blast_2.2.30/tblastx/TBLASTX_XML_2.2.30.xml +8857 -0
- data/spec/dotdir/blast_2.2.30/tblastx/job.yaml +8 -0
- data/spec/dotdir/blast_2.2.31/blastn/BLASTN_XML_2.2.31.xml +1201 -0
- data/spec/dotdir/blast_2.2.31/blastn/job.yaml +8 -0
- data/spec/dotdir/blast_2.2.31/blastn_nohits/BLASTN_NO_HITS_XML_2.2.31.xml +866 -0
- data/spec/dotdir/blast_2.2.31/blastn_nohits/job.yaml +8 -0
- data/spec/dotdir/blast_2.2.31/blastp/BLASTP_XML_2.2.31.xml +1181 -0
- data/spec/dotdir/blast_2.2.31/blastp/job.yaml +8 -0
- data/spec/dotdir/blast_2.2.31/blastx/BLASTX_XML_2.2.31.xml +1181 -0
- data/spec/dotdir/blast_2.2.31/blastx/job.yaml +8 -0
- data/spec/dotdir/blast_2.2.31/tblastn/TBLASTN_XML_2.2.31.xml +1181 -0
- data/spec/dotdir/blast_2.2.31/tblastn/job.yaml +8 -0
- data/spec/dotdir/blast_2.2.31/tblastx/TBLASTX_XML_2.2.31.xml +8857 -0
- data/spec/dotdir/blast_2.2.31/tblastx/job.yaml +8 -0
- data/spec/dotdir/blast_2.3.0/blastn/BLASTN_XML_2.3.0.xml +1201 -0
- data/spec/dotdir/blast_2.3.0/blastn/job.yaml +8 -0
- data/spec/dotdir/blast_2.3.0/blastn_nohits/BLASTN_NO_HITS_XML_2.3.0.xml +866 -0
- data/spec/dotdir/blast_2.3.0/blastn_nohits/job.yaml +8 -0
- data/spec/dotdir/blast_2.3.0/blastp/BLASTP_XML_2.3.0.xml +1181 -0
- data/spec/dotdir/blast_2.3.0/blastp/job.yaml +8 -0
- data/spec/dotdir/blast_2.3.0/blastx/BLASTX_XML_2.3.0.xml +1181 -0
- data/spec/dotdir/blast_2.3.0/blastx/job.yaml +8 -0
- data/spec/dotdir/blast_2.3.0/tblastn/TBLASTN_XML_2.3.0.xml +1181 -0
- data/spec/dotdir/blast_2.3.0/tblastn/job.yaml +8 -0
- data/spec/dotdir/blast_2.3.0/tblastx/TBLASTX_XML_2.3.0.xml +8857 -0
- data/spec/dotdir/blast_2.3.0/tblastx/job.yaml +8 -0
- data/spec/dotdir/blast_2.4.0/blastn/BLASTN_XML_2.4.0.xml +1201 -0
- data/spec/dotdir/blast_2.4.0/blastn/TBLASTN_XML_2.4.0.xml +1181 -0
- data/spec/dotdir/blast_2.4.0/blastn/job.yaml +8 -0
- data/spec/dotdir/blast_2.4.0/blastn_nohits/BLASTN_NO_HITS_XML_2.4.0.xml +866 -0
- data/spec/dotdir/blast_2.4.0/blastn_nohits/job.yaml +8 -0
- data/spec/dotdir/blast_2.4.0/blastp/BLASTP_XML_2.4.0.xml +1181 -0
- data/spec/dotdir/blast_2.4.0/blastp/job.yaml +8 -0
- data/spec/dotdir/blast_2.4.0/blastx/BLASTX_XML_2.4.0.xml +1181 -0
- data/spec/dotdir/blast_2.4.0/blastx/job.yaml +8 -0
- data/spec/dotdir/blast_2.4.0/tblastn/TBLASTN_XML_2.4.0.xml +1181 -0
- data/spec/dotdir/blast_2.4.0/tblastn/job.yaml +8 -0
- data/spec/dotdir/blast_2.4.0/tblastx/TBLASTX_XML_2.4.0.xml +8857 -0
- data/spec/dotdir/blast_2.4.0/tblastx/job.yaml +8 -0
- data/spec/dotdir/blast_2.5.0/blastn/BLASTN_LONG_XML_2.5.0.xml +18813 -0
- data/spec/dotdir/blast_2.5.0/blastn/BLASTN_XML_2.5.0.xml +1201 -0
- data/spec/dotdir/blast_2.5.0/blastn/job.yaml +8 -0
- data/spec/dotdir/blast_2.5.0/blastn_nohits/BLASTN_NO_HITS_XML_2.5.0.xml +866 -0
- data/spec/dotdir/blast_2.5.0/blastn_nohits/job.yaml +8 -0
- data/spec/dotdir/blast_2.5.0/blastp/BLASTP +2161 -0
- data/spec/dotdir/blast_2.5.0/blastp/BLASTP_XML_2.5.0.xml +1181 -0
- data/spec/dotdir/blast_2.5.0/blastp/job.yaml +8 -0
- data/spec/dotdir/blast_2.5.0/blastx/BLASTX +28080 -0
- data/spec/dotdir/blast_2.5.0/blastx/BLASTX_XML_2.5.0.xml +1181 -0
- data/spec/dotdir/blast_2.5.0/blastx/job.yaml +8 -0
- data/spec/dotdir/blast_2.5.0/tblastn/TBLASTN +29486 -0
- data/spec/dotdir/blast_2.5.0/tblastn/TBLASTN_XML_2.5.0.xml +1181 -0
- data/spec/dotdir/blast_2.5.0/tblastn/job.yaml +8 -0
- data/spec/dotdir/blast_2.5.0/tblastx/TBLASTX +180859 -0
- data/spec/dotdir/blast_2.5.0/tblastx/TBLASTX_XML_2.5.0.xml +8857 -0
- data/spec/dotdir/blast_2.5.0/tblastx/job.yaml +8 -0
- data/spec/dotdir/blast_2.6.0/blastn/BLASTN_XML_2.6.0.xml +1201 -0
- data/spec/dotdir/blast_2.6.0/blastn/job.yaml +8 -0
- data/spec/dotdir/blast_2.6.0/blastn_nohits/BLASTN_NO_HITS_XML_2.6.0.xml +866 -0
- data/spec/dotdir/blast_2.6.0/blastn_nohits/job.yaml +8 -0
- data/spec/dotdir/blast_2.6.0/blastp/BLASTP_XML_2.6.0.xml +1181 -0
- data/spec/dotdir/blast_2.6.0/blastp/job.yaml +8 -0
- data/spec/dotdir/blast_2.6.0/blastx/BLASTX_XML_2.6.0.xml +1181 -0
- data/spec/dotdir/blast_2.6.0/blastx/job.yaml +8 -0
- data/spec/dotdir/blast_2.6.0/tblastn/TBLASTN_XML_2.6.0.xml +1181 -0
- data/spec/dotdir/blast_2.6.0/tblastn/job.yaml +8 -0
- data/spec/dotdir/blast_2.6.0/tblastx/TBLASTX_XML_2.6.0.xml +8857 -0
- data/spec/dotdir/blast_2.6.0/tblastx/job.yaml +8 -0
- data/spec/dotdir/blast_2.7.1/blastn/BLASTN_XML_2.7.1.xml +1201 -0
- data/spec/dotdir/blast_2.7.1/blastn/job.yaml +8 -0
- data/spec/dotdir/blast_2.7.1/blastn_nohits/BLASTN_NO_HITS_XML_2.7.1.xml +866 -0
- data/spec/dotdir/blast_2.7.1/blastn_nohits/job.yaml +8 -0
- data/spec/dotdir/blast_2.7.1/blastp/BLASTP_XML_2.7.1.xml +1181 -0
- data/spec/dotdir/blast_2.7.1/blastp/job.yaml +8 -0
- data/spec/dotdir/blast_2.7.1/blastx/BLASTX_XML_2.7.1.xml +1181 -0
- data/spec/dotdir/blast_2.7.1/blastx/job.yaml +8 -0
- data/spec/dotdir/blast_2.7.1/tblastn/TBLASTN_XML_2.7.1.xml +1181 -0
- data/spec/dotdir/blast_2.7.1/tblastn/job.yaml +8 -0
- data/spec/dotdir/blast_2.7.1/tblastx/TBLASTX_XML_2.7.1.xml +8857 -0
- data/spec/dotdir/blast_2.7.1/tblastx/job.yaml +8 -0
- data/spec/dotdir/blast_2.8.1/blastn/BLASTN_XML_2.8.1.xml +1201 -0
- data/spec/dotdir/blast_2.8.1/blastn/job.yaml +8 -0
- data/spec/dotdir/blast_2.8.1/blastn_nohits/BLASTN_NO_HITS_XML_2.8.1.xml +866 -0
- data/spec/dotdir/blast_2.8.1/blastn_nohits/job.yaml +8 -0
- data/spec/dotdir/blast_2.8.1/blastp/BLASTP_XML_2.8.1.xml +1181 -0
- data/spec/dotdir/blast_2.8.1/blastp/job.yaml +8 -0
- data/spec/dotdir/blast_2.8.1/blastx/BLASTX_XML_2.8.1.xml +1181 -0
- data/spec/dotdir/blast_2.8.1/blastx/job.yaml +8 -0
- data/spec/dotdir/blast_2.8.1/tblastn/TBLASTN_XML_2.8.1.xml +1181 -0
- data/spec/dotdir/blast_2.8.1/tblastn/job.yaml +8 -0
- data/spec/dotdir/blast_2.8.1/tblastx/TBLASTX_XML_2.8.1.xml +8857 -0
- data/spec/dotdir/blast_2.8.1/tblastx/job.yaml +8 -0
- data/spec/dotdir/blast_2.9.0/blastn/BLASTN_XML_2.9.0.xml +1201 -0
- data/spec/dotdir/blast_2.9.0/blastn/job.yaml +8 -0
- data/spec/dotdir/blast_2.9.0/blastn_nohits/BLASTN_NO_HITS_XML_2.9.0.xml +866 -0
- data/spec/dotdir/blast_2.9.0/blastn_nohits/job.yaml +8 -0
- data/spec/dotdir/blast_2.9.0/blastp/BLASTP_XML_2.9.0.xml +1181 -0
- data/spec/dotdir/blast_2.9.0/blastp/job.yaml +8 -0
- data/spec/dotdir/blast_2.9.0/blastx/BLASTX_XML_2.9.0.xml +1181 -0
- data/spec/dotdir/blast_2.9.0/blastx/job.yaml +8 -0
- data/spec/dotdir/blast_2.9.0/tblastn/TBLASTN_XML_2.9.0.xml +1181 -0
- data/spec/dotdir/blast_2.9.0/tblastn/job.yaml +8 -0
- data/spec/dotdir/blast_2.9.0/tblastx/TBLASTX_XML_2.9.0.xml +8857 -0
- data/spec/dotdir/blast_2.9.0/tblastx/job.yaml +8 -0
- data/spec/dotdir/diamond_0.9.24/blastp/DIAMOND_BLASTP_0.9.24.xml +1040 -0
- data/spec/dotdir/diamond_0.9.24/blastp/job.yaml +8 -0
- data/spec/dotdir/diamond_0.9.24/blastx/DIAMOND_BLASTX_0.9.24.xml +1040 -0
- data/spec/dotdir/diamond_0.9.24/blastx/job.yaml +8 -0
- data/spec/dotdir/diamond_0.9.24/blastx_nohits/DIAMOND_BLASTX_NOHITS_0.9.24.xml +41 -0
- data/spec/dotdir/diamond_0.9.24/blastx_nohits/job.yaml +8 -0
- data/spec/download_helper.rb +32 -0
- data/spec/import_spec_capybara_local.rb +61 -0
- data/spec/sequence_spec.rb +1 -2
- data/spec/sequences/Nucleotide_TP53_COX41.fasta +15 -0
- data/spec/sequences/Protein_TP53_COX41.fasta +12 -0
- data/spec/sequences/Query_1_SI2_2_0_06267.txt +6 -0
- data/spec/{nucleotide_query.fa → sequences/nucleotide_query.fa} +0 -0
- data/spec/sequences/problematic_query.fa +5 -0
- data/spec/sequences/protein_query.fa +9 -0
- data/spec/sequences/sample_query_fire_ant_obps.fa +44 -0
- data/spec/sequences/sequenceserver-SI2.2.0_06267.fa +5 -0
- data/spec/sequenceserver_spec.rb +3 -3
- data/spec/spec_helper.rb +59 -0
- metadata +185 -28
- data/spec/protein_query.fa +0 -21
- data/spec/sample_reports/blastn_sample/job.yaml +0 -10
- data/spec/sample_reports/blastn_sample/stdout +0 -144
- data/spec/sample_reports/blastp_sample/job.yaml +0 -10
- data/spec/sample_reports/blastp_sample/stdout +0 -1187
- data/spec/sample_reports/blastx_sample/job.yaml +0 -10
- data/spec/sample_reports/blastx_sample/stdout +0 -1191
- data/spec/sample_reports/no_hits_sample/job.yaml +0 -10
- data/spec/sample_reports/no_hits_sample/stdout +0 -130
- data/spec/sample_reports/tblastn_sample/job.yaml +0 -10
- data/spec/sample_reports/tblastn_sample/stdout +0 -1107
- data/spec/sample_reports/tblastx_sample/job.yaml +0 -10
- data/spec/sample_reports/tblastx_sample/stdout +0 -2422
- data/spec/sample_reports/with_hits_sample/job.yaml +0 -10
- data/spec/sample_reports/with_hits_sample/stdout +0 -1489
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require 'spec_helper'
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require 'sauce_whisk'
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require 'capybara/rspec'
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require 'selenium-webdriver'
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RSpec.configure do |config|
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config.include Capybara::DSL
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end
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describe 'report generated from imported XML', :js => true do
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before do |scenario|
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Capybara.app = SequenceServer.init
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Capybara.server = :webrick
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Capybara.javascript_driver = :selenium
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Capybara.default_max_wait_time = 10
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Capybara.register_driver :selenium do |app|
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options = ::Selenium::WebDriver::Firefox::Options.new
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options.args << '--headless'
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Capybara::Selenium::Driver.new(app, browser: :firefox, options: options)
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end
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end
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# Fasta files used for testing consist of TP53 and COX41 protein/nucleotide sequences for reproducibility.
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it 'loads BLASTP xml output' do
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access_by_uuid('blast_2.6.0/blastp')
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end
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it 'loads BLASTX xml output' do
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access_by_uuid('blast_2.6.0/blastx')
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end
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it 'loads BLASTN xml output' do
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access_by_uuid('blast_2.6.0/blastn')
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end
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it 'loads TBLASTN xml output' do
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access_by_uuid('blast_2.6.0/tblastn')
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end
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it 'loads TBLASTX xml output' do
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access_by_uuid('blast_2.6.0/tblastx')
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end
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## Helpers ##
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def access_by_uuid(id)
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url = url_encode(id)
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visit "/#{url}"
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page.should have_content('Query')
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end
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end
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require 'spec_helper'
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# Test BLAST module.
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module SequenceServer
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with_hits = Job.fetch('blast_2.7.1/blastn')
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no_hits = Job.fetch('blast_2.7.1/blastn_nohits')
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init
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describe 'Report' do
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hits_report = BLAST::Report.new(with_hits)
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no_hits_report = BLAST::Report.new(no_hits)
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it 'will return an Array of queries' do
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hits_report.queries.should be_a Array
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no_hits_report.queries.should be_a Array
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end
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it 'will return a Hash of stats' do
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hits_report.stats.should be_a Hash
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no_hits_report.stats.should be_a Hash
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end
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it 'contains all the necessary stats' do
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hits_report.stats.length.should eql(7)
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no_hits_report.stats.length.should eql(7)
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end
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end
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describe 'Query' do
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hits_report = BLAST::Report.new(with_hits)
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no_hits_report = BLAST::Report.new(no_hits)
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it 'will return queries with valid length' do
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|
+
hits_report.queries.first.length.should be_a Fixnum
|
36
|
+
hits_report.queries.first.length.should satisfy { |n| n > 0 }
|
37
|
+
no_hits_report.queries.first.length.should be_a Fixnum
|
38
|
+
no_hits_report.queries.first.length.should satisfy { |n| n > 0 }
|
39
|
+
end
|
40
|
+
|
41
|
+
it 'will return an Array of hits' do
|
42
|
+
hits_report.queries.first.hits.should be_a Array
|
43
|
+
no_hits_report.queries.first.hits.should be_a Array
|
44
|
+
end
|
45
|
+
end
|
46
|
+
|
47
|
+
describe 'Hits' do
|
48
|
+
hits_report = BLAST::Report.new(with_hits)
|
49
|
+
no_hits_report = BLAST::Report.new(no_hits)
|
50
|
+
|
51
|
+
it 'will have non zero length' do
|
52
|
+
hits_report.queries.last.hits.first.length.should satisfy { |n| n > 0 }
|
53
|
+
end
|
54
|
+
|
55
|
+
it 'will return an Array of HSPs' do
|
56
|
+
hits_report.queries.first.hits.first.hsps.should be_a Array
|
57
|
+
end
|
58
|
+
|
59
|
+
it 'will return an Array with atleast one HSP' do
|
60
|
+
hits_report.queries.first.hits.first.hsps.length.should be >= 1
|
61
|
+
end
|
62
|
+
|
63
|
+
it 'will contain no element if no hits were obtained' do
|
64
|
+
no_hits_report.queries.first.hits.length.should eql(0)
|
65
|
+
end
|
66
|
+
end
|
67
|
+
|
68
|
+
# Test general features of HSPs. Algorithm specific customizations are
|
69
|
+
# tested separetly.
|
70
|
+
describe 'HSPs' do
|
71
|
+
hits_report = BLAST::Report.new(with_hits)
|
72
|
+
|
73
|
+
# Currently using all 17 HSP parameters in BLAST Report + 1 to refer to the
|
74
|
+
# hit object it belongs to.
|
75
|
+
it 'have all the necessary values' do
|
76
|
+
hits_report.queries.last.hits.first.hsps.last.count.should eql(19)
|
77
|
+
end
|
78
|
+
|
79
|
+
# Test Random HSPs to ensure that all the values from HSP struct are valid.
|
80
|
+
it 'have correct alignment values' do
|
81
|
+
hits_report.queries.last.hits.first.hsps.last.bit_score.should be_a Float
|
82
|
+
hits_report.queries.last.hits.first.hsps.last.score.should be_a Fixnum
|
83
|
+
|
84
|
+
hits_report.queries.first.hits.first.hsps.first.evalue.should be_a Float
|
85
|
+
hits_report.queries.first.hits.first.hsps.first.evalue
|
86
|
+
.should_not satisfy { |n| n < 0 }
|
87
|
+
|
88
|
+
hits_report.queries.first.hits.last.hsps.first.qstart.should be_a Fixnum
|
89
|
+
hits_report.queries.first.hits.last.hsps.first.qstart
|
90
|
+
.should_not satisfy { |n| n < 0 }
|
91
|
+
|
92
|
+
hits_report.queries.first.hits.last.hsps.first.qend.should be_a Fixnum
|
93
|
+
hits_report.queries.first.hits.last.hsps.first.qend
|
94
|
+
.should_not satisfy { |n| n < 0 }
|
95
|
+
|
96
|
+
hits_report.queries.last.hits.last.hsps.last.sstart.should be_a Fixnum
|
97
|
+
hits_report.queries.last.hits.last.hsps.last.sstart
|
98
|
+
.should_not satisfy { |n| n < 0 }
|
99
|
+
|
100
|
+
hits_report.queries.first.hits.first.hsps.last.send.should be_a Fixnum
|
101
|
+
hits_report.queries.first.hits.first.hsps.last.send
|
102
|
+
.should_not satisfy { |n| n < 0 }
|
103
|
+
|
104
|
+
hits_report.queries.first.hits.first.hsps.last.qframe.should be_a Fixnum
|
105
|
+
hits_report.queries.first.hits.first.hsps.last.sframe.should be_a Fixnum
|
106
|
+
|
107
|
+
hits_report.queries.first.hits.first.hsps.last.identity.should be_a Fixnum
|
108
|
+
hits_report.queries.first.hits.first.hsps.last.identity
|
109
|
+
.should_not satisfy { |n| n < 0 }
|
110
|
+
|
111
|
+
hits_report.queries.first.hits.first.hsps.last.gaps.should be_a Fixnum
|
112
|
+
hits_report.queries.first.hits.first.hsps.last.gaps
|
113
|
+
.should_not satisfy { |n| n < 0 }
|
114
|
+
|
115
|
+
hits_report.queries.first.hits.first.hsps.last.positives
|
116
|
+
.should be_a Fixnum
|
117
|
+
hits_report.queries.first.hits.first.hsps.last.positives
|
118
|
+
.should_not satisfy { |n| n < 0 }
|
119
|
+
|
120
|
+
hits_report.queries.first.hits.first.hsps.last.length.should be_a Fixnum
|
121
|
+
hits_report.queries.first.hits.first.hsps.last.length
|
122
|
+
.should satisfy { |n| n > 0 }
|
123
|
+
|
124
|
+
hits_report.queries.last.hits.last.hsps.first.qseq.should be_a String
|
125
|
+
hits_report.queries.last.hits.last.hsps.first.sseq.should be_a String
|
126
|
+
hits_report.queries.last.hits.last.hsps.first.midline.should be_a String
|
127
|
+
end
|
128
|
+
|
129
|
+
it 'have correctly matched query, hit and midline alignments' do
|
130
|
+
hsp = hits_report.queries.last.hits.last.hsps.first
|
131
|
+
hsp.qseq.length.should eql(hsp.sseq.length)
|
132
|
+
hsp.sseq.length.should eql(hsp.midline.length)
|
133
|
+
hsp.midline.length.should eql(hsp.qseq.length)
|
134
|
+
end
|
135
|
+
end
|
136
|
+
|
137
|
+
# Individually test different BLAST+ algorithms
|
138
|
+
#
|
139
|
+
describe 'BLASTN' do
|
140
|
+
let 'hsp' do
|
141
|
+
report = BLAST::Report.new(Job.fetch('blast_2.7.1/blastn'))
|
142
|
+
report.queries.first.hits.last.hsps.first
|
143
|
+
end
|
144
|
+
|
145
|
+
it 'have correct query and subject frame' do
|
146
|
+
[1, -1].should include(hsp.qframe)
|
147
|
+
[1, -1].should include(hsp.sframe)
|
148
|
+
end
|
149
|
+
|
150
|
+
it 'have correct qstart, qend, sstart, send' do
|
151
|
+
if hsp.sframe > 0
|
152
|
+
hsp.sstart.should be <= hsp.send
|
153
|
+
else
|
154
|
+
hsp.sstart.should be >= hsp.send
|
155
|
+
end
|
156
|
+
end
|
157
|
+
end
|
158
|
+
|
159
|
+
describe 'BLASTP' do
|
160
|
+
let 'hsp' do
|
161
|
+
report = BLAST::Report.new(Job.fetch('blast_2.7.1/blastp'))
|
162
|
+
report.queries.first.hits.last.hsps.first
|
163
|
+
end
|
164
|
+
|
165
|
+
it 'have correct query and subject frame' do
|
166
|
+
hsp.qframe.should eql(0)
|
167
|
+
hsp.sframe.should eql(0)
|
168
|
+
end
|
169
|
+
|
170
|
+
it 'have correct qstart, qend, sstart, send values' do
|
171
|
+
hsp.qstart.should be <= hsp.qend
|
172
|
+
hsp.sstart.should be <= hsp.send
|
173
|
+
end
|
174
|
+
|
175
|
+
end
|
176
|
+
|
177
|
+
describe 'BLASTX' do
|
178
|
+
let 'hsp' do
|
179
|
+
report = BLAST::Report.new(Job.fetch('blast_2.7.1/blastx'))
|
180
|
+
|
181
|
+
report.queries.first.hits.last.hsps.first
|
182
|
+
end
|
183
|
+
|
184
|
+
it 'have correct query and subject frame' do
|
185
|
+
hsp.qframe.should_not eql(0)
|
186
|
+
hsp.sframe.should eql(0)
|
187
|
+
end
|
188
|
+
|
189
|
+
it 'have correct qstart, qend, sstart, send' do
|
190
|
+
hsp.qstart.should be <= hsp.qend
|
191
|
+
hsp.sstart.should be <= hsp.send
|
192
|
+
end
|
193
|
+
end
|
194
|
+
|
195
|
+
describe 'TBLASTX' do
|
196
|
+
let 'hsp' do
|
197
|
+
report = BLAST::Report.new(Job.fetch('blast_2.7.1/tblastx'))
|
198
|
+
report.queries.first.hits.last.hsps.first
|
199
|
+
end
|
200
|
+
|
201
|
+
it 'have correct query and subject frame' do
|
202
|
+
hsp.qframe.should_not eql(0)
|
203
|
+
hsp.sframe.should_not eql(0)
|
204
|
+
end
|
205
|
+
|
206
|
+
it 'have correct qstart, qend, sstart, send' do
|
207
|
+
hsp.qstart.should be <= hsp.qend
|
208
|
+
hsp.sstart.should be <= hsp.send
|
209
|
+
end
|
210
|
+
end
|
211
|
+
|
212
|
+
describe 'TBLASTN' do
|
213
|
+
let 'hsp' do
|
214
|
+
report = BLAST::Report.new(Job.fetch('blast_2.7.1/tblastn'))
|
215
|
+
report.queries.first.hits.last.hsps.first
|
216
|
+
end
|
217
|
+
|
218
|
+
it 'have correct query and subject frame' do
|
219
|
+
hsp.qframe.should eql(0)
|
220
|
+
hsp.sframe.should_not eql(0)
|
221
|
+
end
|
222
|
+
|
223
|
+
it 'have correct qstart, qend, sstart, send' do
|
224
|
+
hsp.qstart.should be <= hsp.qend
|
225
|
+
hsp.sstart.should be <= hsp.send
|
226
|
+
end
|
227
|
+
end
|
228
|
+
end
|
@@ -0,0 +1,56 @@
|
|
1
|
+
require 'spec_helper'
|
2
|
+
require 'sauce_whisk'
|
3
|
+
require 'capybara/rspec'
|
4
|
+
require 'selenium-webdriver'
|
5
|
+
|
6
|
+
RSpec.configure do |config|
|
7
|
+
config.include Capybara::DSL
|
8
|
+
end
|
9
|
+
|
10
|
+
describe 'report generated from imported XML', :js => true do
|
11
|
+
before do |scenario|
|
12
|
+
Capybara.app = SequenceServer.init
|
13
|
+
Capybara.server = :webrick
|
14
|
+
Capybara.javascript_driver = :selenium
|
15
|
+
Capybara.default_max_wait_time = 120
|
16
|
+
|
17
|
+
Capybara.register_driver :selenium do |app|
|
18
|
+
capabilities = Selenium::WebDriver::Remote::Capabilities.firefox(
|
19
|
+
takesScreenshot: true,
|
20
|
+
firefox_options: {args: ["--headless","disable-gpu" "window-size=1024,768"]})
|
21
|
+
client = Selenium::WebDriver::Remote::Http::Default.new
|
22
|
+
client.read_timeout = 120
|
23
|
+
Capybara::Selenium::Driver.new(app, browser: :firefox, desired_capabilities: capabilities, http_client: client)
|
24
|
+
end
|
25
|
+
end
|
26
|
+
|
27
|
+
|
28
|
+
# Fasta files used for testing consist of TP53 and COX41 protein/nucleotide sequences for reproducibility.
|
29
|
+
it 'loads BLASTP xml output' do
|
30
|
+
access_by_uuid('blast_2.7.1/blastp')
|
31
|
+
end
|
32
|
+
|
33
|
+
it 'loads BLASTX xml output' do
|
34
|
+
access_by_uuid('blast_2.7.1/blastx')
|
35
|
+
end
|
36
|
+
|
37
|
+
it 'loads BLASTN xml output' do
|
38
|
+
access_by_uuid('blast_2.7.1/blastn')
|
39
|
+
end
|
40
|
+
|
41
|
+
it 'loads TBLASTN xml output' do
|
42
|
+
access_by_uuid('blast_2.7.1/tblastn')
|
43
|
+
end
|
44
|
+
|
45
|
+
it 'loads TBLASTX xml output' do
|
46
|
+
access_by_uuid('blast_2.7.1/tblastx')
|
47
|
+
end
|
48
|
+
|
49
|
+
## Helpers ##
|
50
|
+
|
51
|
+
def access_by_uuid(id)
|
52
|
+
url = url_encode(id)
|
53
|
+
visit "/#{url}"
|
54
|
+
page.should have_content('Query')
|
55
|
+
end
|
56
|
+
end
|
@@ -0,0 +1,228 @@
|
|
1
|
+
require 'spec_helper'
|
2
|
+
|
3
|
+
# Test BLAST module.
|
4
|
+
module SequenceServer
|
5
|
+
with_hits = Job.fetch('blast_2.8.1/blastn')
|
6
|
+
no_hits = Job.fetch('blast_2.8.1/blastn_nohits')
|
7
|
+
|
8
|
+
init
|
9
|
+
|
10
|
+
describe 'Report' do
|
11
|
+
hits_report = BLAST::Report.new(with_hits)
|
12
|
+
no_hits_report = BLAST::Report.new(no_hits)
|
13
|
+
|
14
|
+
it 'will return an Array of queries' do
|
15
|
+
hits_report.queries.should be_a Array
|
16
|
+
no_hits_report.queries.should be_a Array
|
17
|
+
end
|
18
|
+
|
19
|
+
it 'will return a Hash of stats' do
|
20
|
+
hits_report.stats.should be_a Hash
|
21
|
+
no_hits_report.stats.should be_a Hash
|
22
|
+
end
|
23
|
+
|
24
|
+
it 'contains all the necessary stats' do
|
25
|
+
hits_report.stats.length.should eql(7)
|
26
|
+
no_hits_report.stats.length.should eql(7)
|
27
|
+
end
|
28
|
+
end
|
29
|
+
|
30
|
+
describe 'Query' do
|
31
|
+
hits_report = BLAST::Report.new(with_hits)
|
32
|
+
no_hits_report = BLAST::Report.new(no_hits)
|
33
|
+
|
34
|
+
it 'will return queries with valid length' do
|
35
|
+
hits_report.queries.first.length.should be_a Fixnum
|
36
|
+
hits_report.queries.first.length.should satisfy { |n| n > 0 }
|
37
|
+
no_hits_report.queries.first.length.should be_a Fixnum
|
38
|
+
no_hits_report.queries.first.length.should satisfy { |n| n > 0 }
|
39
|
+
end
|
40
|
+
|
41
|
+
it 'will return an Array of hits' do
|
42
|
+
hits_report.queries.first.hits.should be_a Array
|
43
|
+
no_hits_report.queries.first.hits.should be_a Array
|
44
|
+
end
|
45
|
+
end
|
46
|
+
|
47
|
+
describe 'Hits' do
|
48
|
+
hits_report = BLAST::Report.new(with_hits)
|
49
|
+
no_hits_report = BLAST::Report.new(no_hits)
|
50
|
+
|
51
|
+
it 'will have non zero length' do
|
52
|
+
hits_report.queries.last.hits.first.length.should satisfy { |n| n > 0 }
|
53
|
+
end
|
54
|
+
|
55
|
+
it 'will return an Array of HSPs' do
|
56
|
+
hits_report.queries.first.hits.first.hsps.should be_a Array
|
57
|
+
end
|
58
|
+
|
59
|
+
it 'will return an Array with atleast one HSP' do
|
60
|
+
hits_report.queries.first.hits.first.hsps.length.should be >= 1
|
61
|
+
end
|
62
|
+
|
63
|
+
it 'will contain no element if no hits were obtained' do
|
64
|
+
no_hits_report.queries.first.hits.length.should eql(0)
|
65
|
+
end
|
66
|
+
end
|
67
|
+
|
68
|
+
# Test general features of HSPs. Algorithm specific customizations are
|
69
|
+
# tested separetly.
|
70
|
+
describe 'HSPs' do
|
71
|
+
hits_report = BLAST::Report.new(with_hits)
|
72
|
+
|
73
|
+
# Currently using all 17 HSP parameters in BLAST Report + 1 to refer to the
|
74
|
+
# hit object it belongs to.
|
75
|
+
it 'have all the necessary values' do
|
76
|
+
hits_report.queries.last.hits.first.hsps.last.count.should eql(19)
|
77
|
+
end
|
78
|
+
|
79
|
+
# Test Random HSPs to ensure that all the values from HSP struct are valid.
|
80
|
+
it 'have correct alignment values' do
|
81
|
+
hits_report.queries.last.hits.first.hsps.last.bit_score.should be_a Float
|
82
|
+
hits_report.queries.last.hits.first.hsps.last.score.should be_a Fixnum
|
83
|
+
|
84
|
+
hits_report.queries.first.hits.first.hsps.first.evalue.should be_a Float
|
85
|
+
hits_report.queries.first.hits.first.hsps.first.evalue
|
86
|
+
.should_not satisfy { |n| n < 0 }
|
87
|
+
|
88
|
+
hits_report.queries.first.hits.last.hsps.first.qstart.should be_a Fixnum
|
89
|
+
hits_report.queries.first.hits.last.hsps.first.qstart
|
90
|
+
.should_not satisfy { |n| n < 0 }
|
91
|
+
|
92
|
+
hits_report.queries.first.hits.last.hsps.first.qend.should be_a Fixnum
|
93
|
+
hits_report.queries.first.hits.last.hsps.first.qend
|
94
|
+
.should_not satisfy { |n| n < 0 }
|
95
|
+
|
96
|
+
hits_report.queries.last.hits.last.hsps.last.sstart.should be_a Fixnum
|
97
|
+
hits_report.queries.last.hits.last.hsps.last.sstart
|
98
|
+
.should_not satisfy { |n| n < 0 }
|
99
|
+
|
100
|
+
hits_report.queries.first.hits.first.hsps.last.send.should be_a Fixnum
|
101
|
+
hits_report.queries.first.hits.first.hsps.last.send
|
102
|
+
.should_not satisfy { |n| n < 0 }
|
103
|
+
|
104
|
+
hits_report.queries.first.hits.first.hsps.last.qframe.should be_a Fixnum
|
105
|
+
hits_report.queries.first.hits.first.hsps.last.sframe.should be_a Fixnum
|
106
|
+
|
107
|
+
hits_report.queries.first.hits.first.hsps.last.identity.should be_a Fixnum
|
108
|
+
hits_report.queries.first.hits.first.hsps.last.identity
|
109
|
+
.should_not satisfy { |n| n < 0 }
|
110
|
+
|
111
|
+
hits_report.queries.first.hits.first.hsps.last.gaps.should be_a Fixnum
|
112
|
+
hits_report.queries.first.hits.first.hsps.last.gaps
|
113
|
+
.should_not satisfy { |n| n < 0 }
|
114
|
+
|
115
|
+
hits_report.queries.first.hits.first.hsps.last.positives
|
116
|
+
.should be_a Fixnum
|
117
|
+
hits_report.queries.first.hits.first.hsps.last.positives
|
118
|
+
.should_not satisfy { |n| n < 0 }
|
119
|
+
|
120
|
+
hits_report.queries.first.hits.first.hsps.last.length.should be_a Fixnum
|
121
|
+
hits_report.queries.first.hits.first.hsps.last.length
|
122
|
+
.should satisfy { |n| n > 0 }
|
123
|
+
|
124
|
+
hits_report.queries.last.hits.last.hsps.first.qseq.should be_a String
|
125
|
+
hits_report.queries.last.hits.last.hsps.first.sseq.should be_a String
|
126
|
+
hits_report.queries.last.hits.last.hsps.first.midline.should be_a String
|
127
|
+
end
|
128
|
+
|
129
|
+
it 'have correctly matched query, hit and midline alignments' do
|
130
|
+
hsp = hits_report.queries.last.hits.last.hsps.first
|
131
|
+
hsp.qseq.length.should eql(hsp.sseq.length)
|
132
|
+
hsp.sseq.length.should eql(hsp.midline.length)
|
133
|
+
hsp.midline.length.should eql(hsp.qseq.length)
|
134
|
+
end
|
135
|
+
end
|
136
|
+
|
137
|
+
# Individually test different BLAST+ algorithms
|
138
|
+
#
|
139
|
+
describe 'BLASTN' do
|
140
|
+
let 'hsp' do
|
141
|
+
report = BLAST::Report.new(Job.fetch('blast_2.8.1/blastn'))
|
142
|
+
report.queries.first.hits.last.hsps.first
|
143
|
+
end
|
144
|
+
|
145
|
+
it 'have correct query and subject frame' do
|
146
|
+
[1, -1].should include(hsp.qframe)
|
147
|
+
[1, -1].should include(hsp.sframe)
|
148
|
+
end
|
149
|
+
|
150
|
+
it 'have correct qstart, qend, sstart, send' do
|
151
|
+
if hsp.sframe > 0
|
152
|
+
hsp.sstart.should be <= hsp.send
|
153
|
+
else
|
154
|
+
hsp.sstart.should be >= hsp.send
|
155
|
+
end
|
156
|
+
end
|
157
|
+
end
|
158
|
+
|
159
|
+
describe 'BLASTP' do
|
160
|
+
let 'hsp' do
|
161
|
+
report = BLAST::Report.new(Job.fetch('blast_2.8.1/blastp'))
|
162
|
+
report.queries.first.hits.last.hsps.first
|
163
|
+
end
|
164
|
+
|
165
|
+
it 'have correct query and subject frame' do
|
166
|
+
hsp.qframe.should eql(0)
|
167
|
+
hsp.sframe.should eql(0)
|
168
|
+
end
|
169
|
+
|
170
|
+
it 'have correct qstart, qend, sstart, send values' do
|
171
|
+
hsp.qstart.should be <= hsp.qend
|
172
|
+
hsp.sstart.should be <= hsp.send
|
173
|
+
end
|
174
|
+
|
175
|
+
end
|
176
|
+
|
177
|
+
describe 'BLASTX' do
|
178
|
+
let 'hsp' do
|
179
|
+
report = BLAST::Report.new(Job.fetch('blast_2.8.1/blastx'))
|
180
|
+
|
181
|
+
report.queries.first.hits.last.hsps.first
|
182
|
+
end
|
183
|
+
|
184
|
+
it 'have correct query and subject frame' do
|
185
|
+
hsp.qframe.should_not eql(0)
|
186
|
+
hsp.sframe.should eql(0)
|
187
|
+
end
|
188
|
+
|
189
|
+
it 'have correct qstart, qend, sstart, send' do
|
190
|
+
hsp.qstart.should be <= hsp.qend
|
191
|
+
hsp.sstart.should be <= hsp.send
|
192
|
+
end
|
193
|
+
end
|
194
|
+
|
195
|
+
describe 'TBLASTX' do
|
196
|
+
let 'hsp' do
|
197
|
+
report = BLAST::Report.new(Job.fetch('blast_2.8.1/tblastx'))
|
198
|
+
report.queries.first.hits.last.hsps.first
|
199
|
+
end
|
200
|
+
|
201
|
+
it 'have correct query and subject frame' do
|
202
|
+
hsp.qframe.should_not eql(0)
|
203
|
+
hsp.sframe.should_not eql(0)
|
204
|
+
end
|
205
|
+
|
206
|
+
it 'have correct qstart, qend, sstart, send' do
|
207
|
+
hsp.qstart.should be <= hsp.qend
|
208
|
+
hsp.sstart.should be <= hsp.send
|
209
|
+
end
|
210
|
+
end
|
211
|
+
|
212
|
+
describe 'TBLASTN' do
|
213
|
+
let 'hsp' do
|
214
|
+
report = BLAST::Report.new(Job.fetch('blast_2.8.1/tblastn'))
|
215
|
+
report.queries.first.hits.last.hsps.first
|
216
|
+
end
|
217
|
+
|
218
|
+
it 'have correct query and subject frame' do
|
219
|
+
hsp.qframe.should eql(0)
|
220
|
+
hsp.sframe.should_not eql(0)
|
221
|
+
end
|
222
|
+
|
223
|
+
it 'have correct qstart, qend, sstart, send' do
|
224
|
+
hsp.qstart.should be <= hsp.qend
|
225
|
+
hsp.sstart.should be <= hsp.send
|
226
|
+
end
|
227
|
+
end
|
228
|
+
end
|