sequenceserver 1.0.0.pre.5 → 1.0.0

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 +1,129 @@
+require 'spec_helper'
+require 'sequenceserver/database'
+
+# Test Database class.
+module SequenceServer
+  describe 'Database' do
+    let 'root' do
+      SequenceServer.root
+    end
+
+    let 'database_dir' do
+      File.join(root, 'spec', 'database')
+    end
+
+    let 'database_dir_sample' do
+      File.join(database_dir, 'sample')
+    end
+
+    let 'database_dir_unformatted' do
+      File.join(database_dir, 'unformatted')
+    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 :each do
+      # Empty Database collection so we can use different directories as
+      # needed.
+      Database.clear
+    end
+
+    it 'can tell FASTA file' do
+      Database.probably_fasta?(text_file).should be_falsey
+      Database.probably_fasta?(binary_file).should be_falsey
+      Database.probably_fasta?(fasta_file_prot_seqs).should be_truthy
+      Database.probably_fasta?(fasta_file_nucl_seqs).should be_truthy
+    end
+
+    it 'can tell type of sequences in FASTA file' do
+      Database.guess_sequence_type_in_fasta(fasta_file_prot_seqs)
+        .should eq :protein
+      Database.guess_sequence_type_in_fasta(fasta_file_nucl_seqs)
+        .should eq :nucleotide
+    end
+
+    it 'can tell BLAST+ databases in a directory' do
+      SequenceServer.config[:database_dir] = database_dir_sample
+      Database.scan_databases_dir
+      Database.all.length.should eq 2
+    end
+
+    it 'can tell NCBI multipart database name' do
+      sample_name1 = '/home/ben/pd.ben/sequenceserver/db/nr'
+      sample_name2 = '/home/ben/pd.ben/sequenceserver/db/nr.00'
+      sample_name3 = '/home/ben/pd.ben/sequenceserver/db/img3.5.finished.faa.01'
+      Database.multipart_database_name?(sample_name1).should be_falsey
+      Database.multipart_database_name?(sample_name2).should be_truthy
+      Database.multipart_database_name?(sample_name3).should be_truthy
+    end
+
+    it 'can tell FASTA files that are yet to be made into a BLAST+ database' do
+      SequenceServer.config[:database_dir] = database_dir_unformatted
+      # rubocop:disable Style/RescueModifier
+      Database.scan_databases_dir rescue NO_BLAST_DATABASE_FOUND
+      # rubocop:enable Style/RescueModifier
+      Database.unformatted_fastas.should_not be_empty
+    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|
+        Database.make_db_title(db[0]).should eql(db[1])
+      end
+    end
+
+    let 'solenopsis_protein_database' do
+      path = 'spec/database/sample/proteins/Solenopsis_invicta/'\
+             'Sinvicta2-2-3.prot.subset.fasta'
+      id = Digest::MD5.hexdigest File.expand_path path
+      Database[id].first
+    end
+
+    it 'knows if a given accession is in the database or not' do
+      SequenceServer.config[:database_dir] = database_dir_sample
+      Database.scan_databases_dir
+      solenopsis_protein_database.include?('SI2.2.0_06267').should be_truthy
+    end
+  end
+end

data/spec/routes_spec.rb

@@ -0,0 +1,103 @@
+require 'spec_helper'
+
+# Basic unit tests for HTTP / Rack interface.
+module SequenceServer
+  describe 'Routes' do
+    ENV['RACK_ENV'] = 'test'
+    include Rack::Test::Methods
+
+    let 'root' do
+      SequenceServer.root
+    end
+
+    let 'empty_config' do
+      File.join(root, 'spec', 'empty_config.yml')
+    end
+
+    let 'database_dir' do
+      File.join(root, 'spec', 'database')
+    end
+
+    before :each do
+      SequenceServer.init(:config_file  => empty_config,
+                          :database_dir => database_dir)
+
+      algorithm = Database.first.type == 'protein' ? 'blastp' : 'blastn'
+      sequence  = 'AGCTAGCTAGCT'
+      databases = [Database.first.id]
+
+      @params   = {
+        'method'    => algorithm,
+        'sequence'  => sequence,
+        'databases' => databases
+      }
+    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 'returns OK (200) when correct method, sequence, and database ids are'\
+       'provided but no advanced params' do
+      post '/', @params
+      last_response.status.should eq 200
+
+      @params['advanced'] = '  '
+      post '/', @params
+      last_response.status.should == 200
+    end
+
+    it 'returns OK (200) when correct method, sequence, and database ids and'\
+       'advanced params are provided' do
+      @params['advanced'] = '-evalue 1'
+      post '/', @params
+      last_response.status.should == 200
+    end
+  end
+end

data/spec/sample.conf

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

data/spec/sample_reports/blastn_sample.asn

@@ -0,0 +1,144 @@
+Blast4-archive ::= {
+  request {
+    ident "2.2.30+",
+    body queue-search {
+      program "blastn",
+      service "megablast",
+      queries bioseq-set {
+        seq-set {
+          seq {
+            id {
+              local str "Query_1"
+            },
+            descr {
+              user {
+                type str "CFastaReader",
+                data {
+                  {
+                    label str "DefLine",
+                    data str ">"
+                  }
+                }
+              }
+            },
+            inst {
+              repr raw,
+              mol na,
+              length 544,
+              seq-data ncbi2na 'C6298086D9826EB37C0E98A3C6080E8218765A03368213
+A79AC4AAD060E0B6108A80C5808E76AF0888D09A23F480E7630350B60D6863D2403C822D821E65
+100F7CF66E1BF766D83ED802FF0619B50BD021F6898204D3F40340EBF7508D4A052624CB679B50
+88860D019A0C62019BA08A23D2682363D8F0A08CF61884F82649060C2213628410E503'H
+            }
+          }
+        }
+      },
+      subject database "spec/database/sample/transcripts/Solenopsis_invicta/Si
+nvicta2-2-3.cdna.subset.fasta",
+      algorithm-options {
+        {
+          name "EvalueThreshold",
+          value cutoff e-value { 1, 10, 1 }
+        },
+        {
+          name "MaskAtHash",
+          value boolean TRUE
+        },
+        {
+          name "DustFilteringLevel",
+          value integer 20
+        },
+        {
+          name "DustFilteringWindow",
+          value integer 64
+        },
+        {
+          name "DustFilteringLinker",
+          value integer 1
+        },
+        {
+          name "UngappedMode",
+          value boolean FALSE
+        },
+        {
+          name "HitlistSize",
+          value integer 500
+        },
+        {
+          name "EffectiveSearchSpace",
+          value big-integer 146351625
+        }
+      }
+    }
+  },
+  results {
+    alignments {
+      {
+        type partial,
+        dim 2,
+        score {
+          {
+            id str "score",
+            value int 544
+          },
+          {
+            id str "e_value",
+            value real { 0, 10, 0 }
+          },
+          {
+            id str "bit_score",
+            value real { 100569770510552, 10, -11 }
+          },
+          {
+            id str "num_ident",
+            value int 544
+          },
+          {
+            id str "hsp_percent_coverage",
+            value real { 1, 10, 2 }
+          }
+        },
+        segs denseg {
+          dim 2,
+          numseg 1,
+          ids {
+            local str "Query_1",
+            local str "SI2.2.0_08256"
+          },
+          starts {
+            0,
+            480
+          },
+          lens {
+            544
+          },
+          strands {
+            plus,
+            plus
+          }
+        }
+      }
+    },
+    masks {
+    },
+    ka-blocks {
+      {
+        lambda { 133270576282382, 10, -14 },
+        k { 620991117264207, 10, -15 },
+        h { 112409184650115, 10, -14 },
+        gapped FALSE
+      },
+      {
+        lambda { 128, 10, -2 },
+        k { 46, 10, -2 },
+        h { 85, 10, -2 },
+        gapped TRUE
+      }
+    },
+    search-stats {
+      "Effective search space: 146351625",
+      "Effective search space used: 146351625",
+      "Length adjustment: 19"
+    }
+  }
+}

data/spec/sample_reports/blastp_sample.asn

@@ -0,0 +1,1187 @@
+Blast4-archive ::= {
+  request {
+    ident "2.2.30+",
+    body queue-search {
+      program "blastp",
+      service "plain",
+      queries bioseq-set {
+        seq-set {
+          seq {
+            id {
+              local str "Query_1"
+            },
+            descr {
+              user {
+                type str "CFastaReader",
+                data {
+                  {
+                    label str "DefLine",
+                    data str ">SI2.2.0_06267
+ locus=Si_gnF.scaffold02592[1282609..1284114].pep_2 quality=100.00"
+                  }
+                }
+              },
+              title "SI2.2.0_06267
+ locus=Si_gnF.scaffold02592[1282609..1284114].pep_2 quality=100.00"
+            },
+            inst {
+              repr raw,
+              mol aa,
+              length 199,
+              seq-data ncbieaa "MNTLWLSLWDYPGKLPLNFMVFDTKDDLQAAYWRDPYSIPLAVIFE
+DPQPISQRLIYEIRTNPSYTLPPPPTKLYSAPISCRKNKTGHWMDDILSIKTGESCPVNNYLHSGFLALQMITDITKI
+KLENSDVTIPDIKLIMFPKEPYTADWMLAFRVVIPLYMVLALSQFITYLLILIVGEKENKIKEGMKMMGLNDSVF"
+            }
+          },
+          seq {
+            id {
+              local str "Query_2"
+            },
+            descr {
+              user {
+                type str "CFastaReader",
+                data {
+                  {
+                    label str "DefLine",
+                    data str ">SI2.2.0_13722
+ locus=Si_gnF.scaffold06207[1925625..1928536].pep_1 quality=100.00"
+                  }
+                }
+              },
+              title "SI2.2.0_13722
+ locus=Si_gnF.scaffold06207[1925625..1928536].pep_1 quality=100.00"
+            },
+            inst {
+              repr raw,
+              mol aa,
+              length 186,
+              seq-data ncbieaa "MSANRLNVLVTLMLAVALLVTESGNAQVDGYLQFNPKRSAVSSPQK
+YCGKKLSNALQIICDGVYNSMFKKSGQDFPPQNKRHIAHRINGNEEESFTTLKSNFLNWCVEVYHRHYRFVFVSEMEM
+ADYPLAYDISPYLPPFLSRARARGMLDGRFAGRRYRRESRGIHEECCINGCTINELTSYCGP"
+            }
+          }
+        }
+      },
+      subject database "spec/database/sample/proteins/Solenopsis_invicta/Sinvi
+cta2-2-3.prot.subset.fasta",
+      algorithm-options {
+        {
+          name "EvalueThreshold",
+          value cutoff e-value { 1, 10, 1 }
+        },
+        {
+          name "MaskAtHash",
+          value boolean FALSE
+        },
+        {
+          name "SegFiltering",
+          value boolean FALSE
+        },
+        {
+          name "WordThreshold",
+          value integer 11
+        },
+        {
+          name "WindowSize",
+          value integer 40
+        },
+        {
+          name "HitlistSize",
+          value integer 500
+        },
+        {
+          name "UngappedMode",
+          value boolean FALSE
+        },
+        {
+          name "CompositionBasedStats",
+          value integer 2
+        },
+        {
+          name "SmithWatermanMode",
+          value boolean FALSE
+        },
+        {
+          name "EffectiveSearchSpace",
+          value big-integer 26094545
+        }
+      }
+    }
+  },
+  results {
+    alignments {
+      {
+        type partial,
+        dim 2,
+        score {
+          {
+            id str "score",
+            value int 1046
+          },
+          {
+            id str "e_value",
+            value real { 260530337228793, 10, -161 }
+          },
+          {
+            id str "bit_score",
+            value real { 407526988689595, 10, -12 }
+          },
+          {
+            id str "num_ident",
+            value int 199
+          },
+          {
+            id str "comp_adjustment_method",
+            value int 2
+          },
+          {
+            id str "num_positives",
+            value int 199
+          },
+          {
+            id str "hsp_percent_coverage",
+            value real { 1, 10, 2 }
+          }
+        },
+        segs denseg {
+          dim 2,
+          numseg 1,
+          ids {
+            local str "Query_1",
+            local str "SI2.2.0_06267"
+          },
+          starts {
+            0,
+            0
+          },
+          lens {
+            199
+          },
+          strands {
+            unknown,
+            unknown
+          }
+        }
+      },
+      {
+        type partial,
+        dim 2,
+        score {
+          {
+            id str "score",
+            value int 54
+          },
+          {
+            id str "e_value",
+            value real { 482179947621224, 10, -15 }
+          },
+          {
+            id str "bit_score",
+            value real { 254090093795811, 10, -13 }
+          },
+          {
+            id str "num_ident",
+            value int 8
+          },
+          {
+            id str "comp_adjustment_method",
+            value int 2
+          },
+          {
+            id str "num_positives",
+            value int 17
+          },
+          {
+            id str "hsp_percent_coverage",
+            value real { 125603015075377, 10, -13 }
+          }
+        },
+        segs denseg {
+          dim 2,
+          numseg 1,
+          ids {
+            local str "Query_1",
+            local str "SI2.2.0_11870"
+          },
+          starts {
+            26,
+            61
+          },
+          lens {
+            24
+          },
+          strands {
+            unknown,
+            unknown
+          }
+        }
+      },
+      {
+        type partial,
+        dim 2,
+        score {
+          {
+            id str "score",
+            value int 51
+          },
+          {
+            id str "e_value",
+            value real { 680938982241635, 10, -15 }
+          },
+          {
+            id str "bit_score",
+            value real { 24253410651829, 10, -12 }
+          },
+          {
+            id str "num_ident",
+            value int 13
+          },
+          {
+            id str "comp_adjustment_method",
+            value int 2
+          },
+          {
+            id str "num_positives",
+            value int 25
+          },
+          {
+            id str "hsp_percent_coverage",
+            value real { 271331658291457, 10, -13 }
+          }
+        },
+        segs denseg {
+          dim 2,
+          numseg 3,
+          ids {
+            local str "Query_1",
+            local str "SI2.2.0_10694"
+          },
+          starts {
+            53,
+            4,
+            80,
+            -1,
+            88,
+            31
+          },
+          lens {
+            27,
+            8,
+            18
+          },
+          strands {
+            unknown,
+            unknown,
+            unknown,
+            unknown,
+            unknown,
+            unknown
+          }
+        }
+      },
+      {
+        type partial,
+        dim 2,
+        score {
+          {
+            id str "score",
+            value int 52
+          },
+          {
+            id str "e_value",
+            value real { 880164550170316, 10, -15 }
+          },
+          {
+            id str "bit_score",
+            value real { 246386102277464, 10, -13 }
+          },
+          {
+            id str "num_ident",
+            value int 11
+          },
+          {
+            id str "comp_adjustment_method",
+            value int 2
+          },
+          {
+            id str "num_positives",
+            value int 22
+          },
+          {
+            id str "hsp_percent_coverage",
+            value real { 165804020100502, 10, -13 }
+          }
+        },
+        segs denseg {
+          dim 2,
+          numseg 3,
+          ids {
+            local str "Query_1",
+            local str "SI2.2.0_04285"
+          },
+          starts {
+            95,
+            82,
+            99,
+            -1,
+            101,
+            86
+          },
+          lens {
+            4,
+            2,
+            26
+          },
+          strands {
+            unknown,
+            unknown,
+            unknown,
+            unknown,
+            unknown,
+            unknown
+          }
+        }
+      },
+      {
+        type partial,
+        dim 2,
+        score {
+          {
+            id str "score",
+            value int 48
+          },
+          {
+            id str "e_value",
+            value real { 291747949190001, 10, -14 }
+          },
+          {
+            id str "bit_score",
+            value real { 23097811924077, 10, -12 }
+          },
+          {
+            id str "num_ident",
+            value int 12
+          },
+          {
+            id str "comp_adjustment_method",
+            value int 2
+          },
+          {
+            id str "num_positives",
+            value int 19
+          },
+          {
+            id str "hsp_percent_coverage",
+            value real { 170829145728643, 10, -13 }
+          }
+        },
+        segs denseg {
+          dim 2,
+          numseg 1,
+          ids {
+            local str "Query_1",
+            local str "SI2.2.0_00562"
+          },
+          starts {
+            34,
+            26
+          },
+          lens {
+            33
+          },
+          strands {
+            unknown,
+            unknown
+          }
+        }
+      },
+      {
+        type partial,
+        dim 2,
+        score {
+          {
+            id str "score",
+            value int 46
+          },
+          {
+            id str "e_value",
+            value real { 415577842297789, 10, -14 }
+          },
+          {
+            id str "bit_score",
+            value real { 223274127722423, 10, -13 }
+          },
+          {
+            id str "num_ident",
+            value int 9
+          },
+          {
+            id str "comp_adjustment_method",
+            value int 2
+          },
+          {
+            id str "num_positives",
+            value int 15
+          },
+          {
+            id str "hsp_percent_coverage",
+            value real { 135653266331658, 10, -13 }
+          }
+        },
+        segs denseg {
+          dim 2,
+          numseg 1,
+          ids {
+            local str "Query_1",
+            local str "SI2.2.0_06904"
+          },
+          starts {
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+            id str "num_positives",
+            value int 20
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+            value int 186
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+          {
+            id str "hsp_percent_coverage",
+            value real { 1, 10, 2 }
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+        },
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+            id str "hsp_percent_coverage",
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+            id str "hsp_percent_coverage",
+            value real { 11252688172043, 10, -12 }
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+            value int 35
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+          {
+            id str "hsp_percent_coverage",
+            value real { 39747311827957, 10, -12 }
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+      {
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+            id str "hsp_percent_coverage",
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+        lambda { 322429245874507, 10, -15 },
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+        h { 436862255107731, 10, -15 },
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+      {
+        lambda { 267, 10, -3 },
+        k { 41, 10, -3 },
+        h { 14, 10, -2 },
+        gapped TRUE
+      }
+    },
+    search-stats {
+      "Effective search space: 26094545",
+      "Effective search space used: 26094545",
+      "Length adjustment: 68"
+    }
+  }
+}