sequenceserver 2.0.0.rc7 → 2.0.0.rc8

data/spec/dotdir/diamond_0.9.24/blastx/job.yaml

@@ -1,8 +0,0 @@
---- !ruby/object:SequenceServer::BLAST::Job
-id: 'diamond_0.9.24/blastx'
-submitted_at: 2019-06-18 15:49:12.135304300 +01:00
-imported_xml_file: DIAMOND_BLASTX_0.9.24.xml
-advanced_params: {}
-databases: []
-completed_at: 2019-06-18 15:49:12.144588000 +01:00
-exitstatus: 0

data/spec/dotdir/diamond_0.9.24/blastx_nohits/DIAMOND_BLASTX_NOHITS_0.9.24.xml

@@ -1,41 +0,0 @@
-<?xml version="1.0"?>
-<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
-<BlastOutput>
-  <BlastOutput_program>blastx</BlastOutput_program>
-  <BlastOutput_version>diamond 0.9.24</BlastOutput_version>
-  <BlastOutput_reference>Benjamin Buchfink, Xie Chao, and Daniel Huson (2015), &quot;Fast and sensitive protein alignment using DIAMOND&quot;, Nature Methods 12:59-60.</BlastOutput_reference>
-  <BlastOutput_db>nr.dmnd</BlastOutput_db>
-  <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>
-  <BlastOutput_query-def>SI2.2.0_13722 Si_gnF.scaffold06207[1925625..1928536].pep_1</BlastOutput_query-def>
-  <BlastOutput_query-len>704</BlastOutput_query-len>
-  <BlastOutput_param>
-    <Parameters>
-      <Parameters_matrix>blosum62</Parameters_matrix>
-      <Parameters_expect>0.001</Parameters_expect>
-      <Parameters_gap-open>11</Parameters_gap-open>
-      <Parameters_gap-extend>1</Parameters_gap-extend>
-      <Parameters_filter>F</Parameters_filter>
-    </Parameters>
-  </BlastOutput_param>
-<BlastOutput_iterations>
-<Iteration>
-  <Iteration_iter-num>1</Iteration_iter-num>
-  <Iteration_query-ID>Query_1</Iteration_query-ID>
-  <Iteration_query-def>SI2.2.0_13722 Si_gnF.scaffold06207[1925625..1928536].pep_1</Iteration_query-def>
-  <Iteration_query-len>704</Iteration_query-len>
-<Iteration_hits>
-</Iteration_hits>
-  <Iteration_stat>
-    <Statistics>
-      <Statistics_db-num>459708</Statistics_db-num>
-      <Statistics_db-len>170771147</Statistics_db-len>
-      <Statistics_hsp-len>0</Statistics_hsp-len>
-      <Statistics_eff-space>0</Statistics_eff-space>
-      <Statistics_kappa>0.041000</Statistics_kappa>
-      <Statistics_lambda>0.267000</Statistics_lambda>
-      <Statistics_entropy>0</Statistics_entropy>
-    </Statistics>
-  </Iteration_stat>
-</Iteration>
-</BlastOutput_iterations>
-</BlastOutput>

data/spec/dotdir/diamond_0.9.24/blastx_nohits/job.yaml

@@ -1,8 +0,0 @@
---- !ruby/object:SequenceServer::BLAST::Job
-id: 'diamond_0.9.24/blastx_nohits'
-submitted_at: 2019-07-01 14:20:40.624064600 +01:00
-imported_xml_file: DIAMOND_BLASTX_NOHITS_0.9.24.xml
-advanced_params: {}
-databases: []
-completed_at: 2019-07-01 14:20:40.627058200 +01:00
-exitstatus: 0

data/spec/download_helper.rb

@@ -1,35 +0,0 @@
-# Based on https://stackoverflow.com/a/29544674
-module DownloadHelpers
-  def downloads_dir
-    File.join(__dir__, 'downloads')
-  end
-
-  def wait_for_download
-    Timeout.timeout(Capybara.default_max_wait_time) do
-      loop do
-        sleep 1
-        break if downloaded?
-      end
-    end
-  end
-
-  def downloaded_file
-    downloads.first
-  end
-
-  def clear_downloads
-    FileUtils.rm(downloads)
-  end
-
-  def downloaded?
-    !downloading? && downloads.any?
-  end
-
-  def downloading?
-    downloads.grep(/\.part$/).any?
-  end
-
-  def downloads
-    Dir[File.join(downloads_dir, '*')]
-  end
-end

data/spec/makeblastdb_spec.rb

@@ -1,121 +0,0 @@
-require 'spec_helper'
-require 'sequenceserver/database'
-
-# Test Database class.
-module SequenceServer
-  describe 'Database' do
-    let 'root' do
-      __dir__
-    end
-
-    let 'makeblastdb' do
-      SequenceServer.makeblastdb
-    end
-
-    let 'database_dir' do
-      File.join(root, 'database')
-    end
-
-    let 'database_dir_sample' do
-      File.join(database_dir, 'sample')
-    end
-
-    let 'database_dir_v4' do
-      File.join(database_dir, 'v4')
-    end
-
-    let 'database_dir_unformatted' do
-      File.join(database_dir, 'unformatted')
-    end
-
-    let 'database_dir_without_parse_seqids' do
-      File.join(database_dir, 'without_parse_seqids')
-    end
-
-    let 'fasta_file_prot_seqs' do
-      File.join(database_dir_sample, 'proteins', 'Solenopsis_invicta',
-                'Sinvicta2-2-3.prot.subset.fasta')
-    end
-
-    let 'fasta_file_nucl_seqs' do
-      File.join(database_dir_sample, 'transcripts', 'Solenopsis_invicta',
-                'Sinvicta2-2-3.cdna.subset.fasta')
-    end
-
-    let 'text_file' do
-      File.join(database_dir_sample, 'links.rb')
-    end
-
-    let 'binary_file' do
-      File.join(database_dir_sample, 'proteins', 'Solenopsis_invicta',
-                'Sinvicta2-2-3.prot.subset.fasta.phr')
-    end
-
-    let 'data_for_makeblastdb' do
-      [
-        File.join(database_dir_unformatted, 'Cardiocondyla_obscurior',
-                  'Cobs1.4.proteins.fa'),
-        :protein,
-        'Cobs 1.4 proteins',
-        true
-      ]
-    end
-
-    let 'makeblastdb_result_pattern' do
-      File.join(database_dir_unformatted, 'Cardiocondyla_obscurior',
-                'Cobs1.4.proteins.fa.*')
-    end
-
-    before do
-      SequenceServer.init
-    end
-
-    it 'can tell FASTA file' do
-      makeblastdb.send(:probably_fasta?, text_file).should be_falsey
-      makeblastdb.send(:probably_fasta?, binary_file).should be_falsey
-      makeblastdb.send(:probably_fasta?, fasta_file_prot_seqs).should be_truthy
-      makeblastdb.send(:probably_fasta?, fasta_file_nucl_seqs).should be_truthy
-    end
-
-    it 'can tell type of sequences in FASTA file' do
-      makeblastdb.send(:guess_sequence_type_in_fasta, fasta_file_prot_seqs).should eq :protein
-      makeblastdb.send(:guess_sequence_type_in_fasta, fasta_file_nucl_seqs).should eq :nucleotide
-    end
-
-    it 'can tell FASTA files that are yet to be made into a BLAST+ database' do
-      makeblastdb.instance_variable_set(:@database_dir, database_dir_unformatted)
-      makeblastdb.scan.should be_truthy
-    end
-
-    it 'can tell databases that require reformatting' do
-      # Control: shouldn't report sample v5 databases created using -parse_seqids
-      # as requiring reformatting.
-      makeblastdb.instance_variable_set(:@database_dir, database_dir_sample)
-      makeblastdb.scan.should be_falsey
-
-      # v4 databases require reformatting.
-      makeblastdb.instance_variable_set(:@database_dir, database_dir_v4)
-      makeblastdb.scan.should be_truthy
-
-      # non -parse_seqids databases require reformatting.
-      makeblastdb.instance_variable_set(:@database_dir, database_dir_without_parse_seqids)
-      makeblastdb.scan.should be_truthy
-    end
-
-    # it 'can make BLAST+ database from a FASTA file' do
-    #   Database._make_blast_database(*data_for_makeblastdb).should be_truthy
-    #   system "rm #{makeblastdb_result_pattern}"
-    # end
-
-    it 'can make intelligent database name suggestions' do
-      db_name_pairs = [['Si_gnf.fasta', 'Si gnf'],
-                       ['Aech.3.8.cds.fasta', 'Aech 3.8 cds'],
-                       ['Cobs1.4.proteins.fasta', 'Cobs 1.4 proteins'],
-                       ['S_inv.x.small.2.5.nucl.fa', 'S inv x small 2.5 nucl'],
-                       ['Sinvicta2-2-3.prot.fasta', 'Sinvicta 2-2-3 prot']]
-      db_name_pairs.each do |db|
-        makeblastdb.send(:make_db_title, db[0]).should eql(db[1])
-      end
-    end
-  end
-end

data/spec/routes_spec.rb

@@ -1,93 +0,0 @@
-require 'spec_helper'
-
-require 'rack/test'
-
-# Basic unit tests for HTTP / Rack interface.
-module SequenceServer
-  describe 'Routes' do
-    ENV['RACK_ENV'] = 'test'
-    include Rack::Test::Methods
-
-    before do
-      SequenceServer.init
-    end
-
-    before :each do
-      @params = {
-        'sequence'  => 'AGCTAGCTAGCT',
-        'databases' => [Database.first.id],
-        'method'    => (Database.first.type == 'protein' ? 'blastp' : 'blastn')
-      }
-    end
-
-    let 'app' do
-      SequenceServer
-    end
-
-    it 'returns Bad Request (400) if no blast method is provided' do
-      @params.delete('method')
-      post '/', @params
-      last_response.status.should == 400
-    end
-
-    it 'returns Bad Request (400) if no input sequence is provided' do
-      @params.delete('sequence')
-      post '/', @params
-      last_response.status.should == 400
-    end
-
-    it 'returns Bad Request (400) if no database id is provided' do
-      @params.delete('databases')
-      post '/', @params
-      last_response.status.should == 400
-    end
-
-    it 'returns Bad Request (400) if an empty database list is provided' do
-      @params['databases'].pop
-
-      # ensure the list of databases is empty
-      @params['databases'].should be_empty
-
-      post '/', @params
-      last_response.status.should == 400
-    end
-
-    it 'returns Bad Request (400) if incorrect database id is provided' do
-      @params['databases'] = ['123']
-      post '/', @params
-      last_response.status.should == 400
-    end
-
-    it 'returns Bad Request (400) if an incorrect blast method is supplied' do
-      @params['method'] = 'foo'
-      post '/', @params
-      last_response.status.should == 400
-    end
-
-    it 'returns Bad Request (400) if incorrect advanced params are supplied' do
-      @params['advanced'] = '-word_size 5; rm -rf /'
-      post '/', @params
-      last_response.status.should == 400
-    end
-
-    it 'redirects to /:jobid (302) when correct method, sequence, and database ids are'\
-       'provided but no advanced params' do
-      post '/', @params
-      last_response.should be_redirect
-      last_response.status.should eq 302
-
-      @params['advanced'] = '  '
-      post '/', @params
-      last_response.should be_redirect
-      last_response.status.should == 302
-    end
-
-    it 'redirects to /jobid (302) when correct method, sequence, and database ids and'\
-       'advanced params are provided' do
-      @params['advanced'] = '-evalue 1'
-      post '/', @params
-      last_response.should be_redirect
-      last_response.status.should == 302
-    end
-  end
-end

data/spec/sample.conf

@@ -1,2 +0,0 @@
-num_threads: 10
-:database: 'database_dir'

data/spec/sequence_spec.rb

@@ -1,99 +0,0 @@
-require 'spec_helper'
-require 'sequenceserver/sequence'
-require 'digest/md5'
-
-# Test Sequence class.
-module SequenceServer
-  describe 'Sequence type detection' do
-    it 'should be able to detect nucleotide sequences' do
-      sequences = [
-        'AAAAAAAAAAAAAAAAAAAAAT',
-        '           CAGATGCRRCAAAGCAAACGGCAA 34523453 652352',
-        'ACCNNNNNNXXXXCAUUUUUU',
-        "ACGT\n\t\t\nACCACGGACCACGAAAGCG"
-      ]
-      sequences.each do |sequence|
-        Sequence.guess_type(sequence).should == :nucleotide
-      end
-    end
-
-    it 'should be able to detect protein sequences' do
-      sequences = [
-        'ADSACGHKSJLFCVMGTL',
-        '  345   KSSYPHYSPPPPHS      345 23453 652352',
-        'GEYSNLNNNNNNXXXXSSSSSSSSSSSSSSSSSSSSSSS',
-        "EE\n\t\t\n         \t\t\EEQRRQQSARTSRRQR"
-      ]
-      sequences.each do |sequence|
-        Sequence.guess_type(sequence).should == :protein
-      end
-    end
-
-    it 'should be able to say sequence type detection impossible' do
-      Sequence.guess_type('ACSFGT').should be_nil
-    end
-
-    it 'should be able to tell composition of a sequence string' do
-      Sequence.composition('asdfasdfffffAsdf').should == { 'a' => 2, 'd' => 3,
-                                                           'f' => 7, 's' => 3,
-                                                           'A' => 1 }
-    end
-  end
-
-  describe 'Sequence retrieval' do
-    database_dir = File.join(__dir__, 'database')
-
-    let 'a_normal_database_id' do
-      Digest::MD5.hexdigest File.join(database_dir, 'sample', 'proteins',
-                                      'Solenopsis_invicta',
-                                      'Sinvicta2-2-3.prot.subset.fasta')
-    end
-
-    let 'funky_ids_database_id' do
-      Digest::MD5.hexdigest File.join(database_dir, 'funky_ids', 'v5',
-                                      'funky_ids.fa')
-    end
-
-    before :all do
-      SequenceServer.init(database_dir: database_dir)
-    end
-
-    it 'should be able to retrieve sequences from database' do
-      sequences = Sequence::Retriever.new('SI2.2.0_06267',
-                                          a_normal_database_id).sequences
-
-      sequences.length.should eq 1
-      sequences.first.gi.should be_nil
-      sequences.first.seqid.should eq 'SI2.2.0_06267'
-      sequences.first.accession.should eq 'SI2.2.0_06267'
-      sequences.first.id.should eq 'SI2.2.0_06267'
-      sequences.first.title.should eq 'locus=Si_gnF.scaffold02592'\
-                                      '[1282609..1284114].pep_2 quality=100.00'
-      sequences.first.value.should == "\
-MNTLWLSLWDYPGKLPLNFMVFDTKDDLQAAYWRDPYSIPLAVIFEDPQPISQRLIYEIRTNPSYTLPPPPTKLYSAPI\
-SCRKNKTGHWMDDILSIKTGESCPVNNYLHSGFLALQMITDITKIKLENSDVTIPDIKLIMFPKEPYTADWMLAFRVVI\
-PLYMVLALSQFITYLLILIVGEKENKIKEGMKMMGLNDSVF"
-    end
-
-    it 'should be able to retrieve more than one sequence from a database' do
-      sequences = Sequence::Retriever.new(['SI2.2.0_06267', 'SI2.2.0_13722'],
-                                          a_normal_database_id).sequences
-      sequences.length.should == 2
-    end
-
-    # it 'should be able to retrieve sequences from database even if accession'\
-    #    'contains only numbers' do
-    #   Database.scan_databases_dir
-    #   sequences = Sequence.from_blastdb(123456, funky_ids_database_id)
-    #   sequences.length.should == 1
-    # end
-
-    it 'should be able to retrieve sequences from database for all kinds of'\
-       'funky accessions' do
-      funky_accessions = ['abcdef#', 'abc#def', '123#456'] # , '123456#']
-      sequences = Sequence::Retriever.new(funky_accessions,
-                                          funky_ids_database_id).sequences
-      sequences.length.should == 3
-    end
-  end
-end

data/spec/sequences/MH011443_1_gi_1486783306_gb_MH011443_1.txt

@@ -1,6 +0,0 @@
->MH011443.1:1-123
-TGGGTTGATTCCACACCCCCGCCCGGCACCCGCGTCCGCGCCGTGGCCATCTACAAGCAGTCACAGCACATGACGGAGGTTGTGAGGCGCTGCCCCCACCATGAGCGCTGCTCAGATAGCGAT
->MH011443.1:1-123_alignment_gi|1486783306|gb|MH011443.1|:1-123
-|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
->gi|1486783306|gb|MH011443.1|:1-123
-TGGGTTGATTCCACACCCCCGCCCGGCACCCGCGTCCGCGCCGTGGCCATCTACAAGCAGTCACAGCACATGACGGAGGTTGTGAGGCGCTGCCCCCACCATGAGCGCTGCTCAGATAGCGAT

data/spec/sequences/MH011443_1_gi_1486783307_gb_AYF55702_1.txt

@@ -1,6 +0,0 @@
->MH011443.1:1-123
-WVDSTPPPGTRVRAVAIYKQSQHMTEVVRRCPHHERCSDSD
->MH011443.1:1-123_alignment_gi|1486783307|gb|AYF55702.1|:1-41
-WVDSTPPPGTRVRAVAIYKQSQHMTEVVRRCPHHERCSDSD
->gi|1486783307|gb|AYF55702.1|:1-41
-WVDSTPPPGTRVRAVAIYKQSQHMTEVVRRCPHHERCSDSD

data/spec/sequences/MH011443_1_gi_1528997474_gb_MH447967_1.txt

@@ -1,30 +0,0 @@
->MH011443.1:1-123
-WVDSTPPPGTRVRAVAIYKQSQHMTEVVRRCPHHERCSDSD
->MH011443.1:1-123_alignment_gi|1528997474|gb|MH447967.1|:34-156
-WVDSTPPPGTRVRA+AIYKQSQHMTEVVRRCPHHERCSDSD
->gi|1528997474|gb|MH447967.1|:34-156
-WVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSD
->MH011443.1:2-121
-RYLSSAHGGGSASQPPSCAVTACRWPRRGRGCRAGVWNQP
->MH011443.1:2-121_alignment_gi|1528997474|gb|MH447967.1|:35-154
-RYLSSAHGGGSASQPPSCAVTACRWP RGRGCRAGVWNQP
->gi|1528997474|gb|MH447967.1|:35-154
-RYLSSAHGGGSASQPPSCAVTACRWPWRGRGCRAGVWNQP
->MH011443.1:3-122
-SLSEQRSWWGQRLTTSVMCCDCL*MATARTRVPGGGVEST
->MH011443.1:3-122_alignment_gi|1528997474|gb|MH447967.1|:36-155
-SLSEQRSWWGQRLTTSVMCCDCL*MA ARTRVPGGGVEST
->gi|1528997474|gb|MH447967.1|:36-155
-SLSEQRSWWGQRLTTSVMCCDCL*MAMARTRVPGGGVEST
->MH011443.1:3-86
-G*FHTPARHPRPRRGHLQAVTAHDGGCE
->MH011443.1:3-86_alignment_gi|1528997474|gb|MH447967.1|:36-119
-G*FHTPARHPRPR GHLQAVTAHDGGCE
->gi|1528997474|gb|MH447967.1|:36-119
-G*FHTPARHPRPRHGHLQAVTAHDGGCE
->MH011443.1:80-121
-L*GAAPTMSAAQIA
->MH011443.1:80-121_alignment_gi|1528997474|gb|MH447967.1|:113-154
-L*GAAPTMSAAQIA
->gi|1528997474|gb|MH447967.1|:113-154
-L*GAAPTMSAAQIA