sequenceserver 1.1.0.beta12 → 2.0.0.beta1

data/spec/sample_reports/tblastx_sample/job.yaml

@@ -1,10 +0,0 @@
---- !ruby/object:SequenceServer::BLAST::Job
-id: tblastx_sample
-method: tblastx
-advanced_params: {}
-exitstatus: 0
-
-databases:
-- !ruby/struct:SequenceServer::Database
-  name: "../database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta"
-  type: nucleotide

data/spec/sample_reports/tblastx_sample/stdout

@@ -1,2422 +0,0 @@
-Blast4-archive ::= {
-  request {
-    ident "2.2.30+",
-    body queue-search {
-      program "tblastx",
-      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
- Si_gnF.scaffold02592[1282609..1284114].pep_2"
-                  }
-                }
-              },
-              title "SI2.2.0_06267 Si_gnF.scaffold02592[1282609..1284114].pep_2"
-            },
-            inst {
-              repr raw,
-              mol na,
-              length 540,
-              seq-data ncbi2na '38315DE9DDFCEA3CD5AC27D5F01F4EBBF8460A38DE4249
-B3E888D7C493177A4BCDF628554163344987CCCE03CA1835F4C47F9651650503ECF79D634BED80
-83007AD1E8E8613FCD8C005AE0DFB56F043C7E4F7A7DFA779038C1A334408C03E803DE1B843168
-CF01D30EFD70225B316787A39E97D22FBCF59FC4EB7E9DDD90FCD1F37DE35C32FA62'H
-            }
-          }
-        }
-      },
-      subject database "../database/sample/transcripts/Solenopsis_invicta/Si
-nvicta2-2-3.cdna.subset.fasta",
-      algorithm-options {
-        {
-          name "EvalueThreshold",
-          value cutoff e-value { 1, 10, 1 }
-        },
-        {
-          name "LongestIntronLength",
-          value integer 0
-        },
-        {
-          name "MaskAtHash",
-          value boolean FALSE
-        },
-        {
-          name "SegFilteringWindow",
-          value integer 12
-        },
-        {
-          name "SegFilteringLocut",
-          value real { 22, 10, -1 }
-        },
-        {
-          name "SegFilteringHicut",
-          value real { 25, 10, -1 }
-        },
-        {
-          name "WordThreshold",
-          value integer 13
-        },
-        {
-          name "WindowSize",
-          value integer 40
-        },
-        {
-          name "QueryGeneticCode",
-          value integer 1
-        },
-        {
-          name "DbGeneticCode",
-          value integer 1
-        },
-        {
-          name "HitlistSize",
-          value integer 500
-        },
-        {
-          name "EffectiveSearchSpace",
-          value big-integer 11955588
-        }
-      }
-    }
-  },
-  results {
-    alignments {
-      {
-        type diags,
-        segs std {
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_06267"
-            },
-            loc {
-              int {
-                from 0,
-                to 539,
-                strand plus,
-                id local str "Query_1"
-              },
-              int {
-                from 0,
-                to 539,
-                strand plus,
-                id local str "SI2.2.0_06267"
-              }
-            },
-            scores {
-              {
-                id str "score",
-                value int 961
-              },
-              {
-                id str "e_value",
-                value real { 886238171826621, 10, -141 }
-              },
-              {
-                id str "bit_score",
-                value real { 44323857431301, 10, -11 }
-              },
-              {
-                id str "num_ident",
-                value int 180
-              },
-              {
-                id str "num_positives",
-                value int 180
-              },
-              {
-                id str "hsp_percent_coverage",
-                value real { 338333333333333, 10, -13 }
-              }
-            }
-          },
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_06267"
-            },
-            loc {
-              int {
-                from 0,
-                to 539,
-                strand minus,
-                id local str "Query_1"
-              },
-              int {
-                from 0,
-                to 539,
-                strand minus,
-                id local str "SI2.2.0_06267"
-              }
-            },
-            scores {
-              {
-                id str "score",
-                value int 938
-              },
-              {
-                id str "e_value",
-                value real { 132735983926242, 10, -137 }
-              },
-              {
-                id str "bit_score",
-                value real { 43269977789214, 10, -11 }
-              },
-              {
-                id str "num_ident",
-                value int 180
-              },
-              {
-                id str "num_positives",
-                value int 180
-              },
-              {
-                id str "hsp_percent_coverage",
-                value real { 338333333333333, 10, -13 }
-              }
-            }
-          },
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_06267"
-            },
-            loc {
-              int {
-                from 1,
-                to 537,
-                strand plus,
-                id local str "Query_1"
-              },
-              int {
-                from 1,
-                to 537,
-                strand plus,
-                id local str "SI2.2.0_06267"
-              }
-            },
-            scores {
-              {
-                id str "score",
-                value int 921
-              },
-              {
-                id str "e_value",
-                value real { 291696383535039, 10, -135 }
-              },
-              {
-                id str "bit_score",
-                value real { 424910232711496, 10, -12 }
-              },
-              {
-                id str "num_ident",
-                value int 179
-              },
-              {
-                id str "num_positives",
-                value int 179
-              },
-              {
-                id str "hsp_percent_coverage",
-                value real { 336481481481481, 10, -13 }
-              }
-            }
-          },
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_06267"
-            },
-            loc {
-              int {
-                from 2,
-                to 538,
-                strand plus,
-                id local str "Query_1"
-              },
-              int {
-                from 2,
-                to 538,
-                strand plus,
-                id local str "SI2.2.0_06267"
-              }
-            },
-            scores {
-              {
-                id str "score",
-                value int 895
-              },
-              {
-                id str "e_value",
-                value real { 112519664897538, 10, -131 }
-              },
-              {
-                id str "bit_score",
-                value real { 412996810670512, 10, -12 }
-              },
-              {
-                id str "num_ident",
-                value int 179
-              },
-              {
-                id str "num_positives",
-                value int 179
-              },
-              {
-                id str "hsp_percent_coverage",
-                value real { 336481481481481, 10, -13 }
-              }
-            }
-          },
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_06267"
-            },
-            loc {
-              int {
-                from 1,
-                to 537,
-                strand minus,
-                id local str "Query_1"
-              },
-              int {
-                from 1,
-                to 537,
-                strand minus,
-                id local str "SI2.2.0_06267"
-              }
-            },
-            scores {
-              {
-                id str "score",
-                value int 881
-              },
-              {
-                id str "e_value",
-                value real { 966620537509094, 10, -130 }
-              },
-              {
-                id str "bit_score",
-                value real { 406581891109982, 10, -12 }
-              },
-              {
-                id str "num_ident",
-                value int 179
-              },
-              {
-                id str "num_positives",
-                value int 179
-              },
-              {
-                id str "hsp_percent_coverage",
-                value real { 336481481481481, 10, -13 }
-              }
-            }
-          },
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_06267"
-            },
-            loc {
-              int {
-                from 2,
-                to 538,
-                strand minus,
-                id local str "Query_1"
-              },
-              int {
-                from 2,
-                to 538,
-                strand minus,
-                id local str "SI2.2.0_06267"
-              }
-            },
-            scores {
-              {
-                id str "score",
-                value int 812
-              },
-              {
-                id str "e_value",
-                value real { 318227378269189, 10, -120 }
-              },
-              {
-                id str "bit_score",
-                value real { 374965501847369, 10, -12 }
-              },
-              {
-                id str "num_ident",
-                value int 179
-              },
-              {
-                id str "num_positives",
-                value int 179
-              },
-              {
-                id str "hsp_percent_coverage",
-                value real { 336481481481481, 10, -13 }
-              }
-            }
-          },
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_06267"
-            },
-            loc {
-              int {
-                from 329,
-                to 370,
-                strand plus,
-                id local str "Query_1"
-              },
-              int {
-                from 121,
-                to 162,
-                strand plus,
-                id local str "SI2.2.0_06267"
-              }
-            },
-            scores {
-              {
-                id str "score",
-                value int 40
-              },
-              {
-                id str "e_value",
-                value real { 966581774245886, 10, -14 }
-              },
-              {
-                id str "bit_score",
-                value real { 212285089381423, 10, -13 }
-              },
-              {
-                id str "num_ident",
-                value int 7
-              },
-              {
-                id str "num_positives",
-                value int 7
-              },
-              {
-                id str "hsp_percent_coverage",
-                value real { 309259259259259, 10, -14 }
-              }
-            }
-          },
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_06267"
-            },
-            loc {
-              int {
-                from 121,
-                to 162,
-                strand plus,
-                id local str "Query_1"
-              },
-              int {
-                from 329,
-                to 370,
-                strand plus,
-                id local str "SI2.2.0_06267"
-              }
-            },
-            scores {
-              {
-                id str "score",
-                value int 40
-              },
-              {
-                id str "e_value",
-                value real { 966581774245886, 10, -14 }
-              },
-              {
-                id str "bit_score",
-                value real { 212285089381423, 10, -13 }
-              },
-              {
-                id str "num_ident",
-                value int 7
-              },
-              {
-                id str "num_positives",
-                value int 7
-              },
-              {
-                id str "hsp_percent_coverage",
-                value real { 309259259259259, 10, -14 }
-              }
-            }
-          }
-        }
-      },
-      {
-        type diags,
-        segs std {
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_03649"
-            },
-            loc {
-              int {
-                from 168,
-                to 212,
-                strand plus,
-                id local str "Query_1"
-              },
-              int {
-                from 733,
-                to 777,
-                strand minus,
-                id local str "SI2.2.0_03649"
-              }
-            },
-            scores {
-              {
-                id str "score",
-                value int 42
-              },
-              {
-                id str "sum_n",
-                value int 2
-              },
-              {
-                id str "e_value",
-                value real { 223266389357325, 10, -15 }
-              },
-              {
-                id str "bit_score",
-                value real { 22144926018218, 10, -12 }
-              },
-              {
-                id str "num_ident",
-                value int 8
-              },
-              {
-                id str "num_positives",
-                value int 10
-              },
-              {
-                id str "hsp_percent_coverage",
-                value real { 327777777777778, 10, -14 }
-              }
-            }
-          },
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_03649"
-            },
-            loc {
-              int {
-                from 201,
-                to 254,
-                strand plus,
-                id local str "Query_1"
-              },
-              int {
-                from 688,
-                to 741,
-                strand minus,
-                id local str "SI2.2.0_03649"
-              }
-            },
-            scores {
-              {
-                id str "score",
-                value int 40
-              },
-              {
-                id str "sum_n",
-                value int 2
-              },
-              {
-                id str "e_value",
-                value real { 223266389357325, 10, -15 }
-              },
-              {
-                id str "bit_score",
-                value real { 212285089381423, 10, -13 }
-              },
-              {
-                id str "num_ident",
-                value int 7
-              },
-              {
-                id str "num_positives",
-                value int 10
-              },
-              {
-                id str "hsp_percent_coverage",
-                value real { 383333333333333, 10, -14 }
-              }
-            }
-          }
-        }
-      },
-      {
-        type diags,
-        segs std {
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_00906"
-            },
-            loc {
-              int {
-                from 166,
-                to 234,
-                strand plus,
-                id local str "Query_1"
-              },
-              int {
-                from 4,
-                to 72,
-                strand plus,
-                id local str "SI2.2.0_00906"
-              }
-            },
-            scores {
-              {
-                id str "score",
-                value int 50
-              },
-              {
-                id str "e_value",
-                value real { 403546377981801, 10, -15 }
-              },
-              {
-                id str "bit_score",
-                value real { 258105943385209, 10, -13 }
-              },
-              {
-                id str "num_ident",
-                value int 9
-              },
-              {
-                id str "num_positives",
-                value int 14
-              },
-              {
-                id str "hsp_percent_coverage",
-                value real { 475925925925926, 10, -14 }
-              }
-            }
-          }
-        }
-      },
-      {
-        type diags,
-        segs std {
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_10643"
-            },
-            loc {
-              int {
-                from 316,
-                to 396,
-                strand minus,
-                id local str "Query_1"
-              },
-              int {
-                from 165,
-                to 245,
-                strand minus,
-                id local str "SI2.2.0_10643"
-              }
-            },
-            scores {
-              {
-                id str "score",
-                value int 46
-              },
-              {
-                id str "e_value",
-                value real { 143757831456381, 10, -14 }
-              },
-              {
-                id str "bit_score",
-                value real { 239777601783694, 10, -13 }
-              },
-              {
-                id str "num_ident",
-                value int 14
-              },
-              {
-                id str "num_positives",
-                value int 15
-              },
-              {
-                id str "hsp_percent_coverage",
-                value real { 55, 10, -1 }
-              }
-            }
-          }
-        }
-      },
-      {
-        type diags,
-        segs std {
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_08520"
-            },
-            loc {
-              int {
-                from 58,
-                to 117,
-                strand plus,
-                id local str "Query_1"
-              },
-              int {
-                from 120,
-                to 179,
-                strand plus,
-                id local str "SI2.2.0_08520"
-              }
-            },
-            scores {
-              {
-                id str "score",
-                value int 46
-              },
-              {
-                id str "e_value",
-                value real { 143757831456381, 10, -14 }
-              },
-              {
-                id str "bit_score",
-                value real { 239777601783694, 10, -13 }
-              },
-              {
-                id str "num_ident",
-                value int 10
-              },
-              {
-                id str "num_positives",
-                value int 11
-              },
-              {
-                id str "hsp_percent_coverage",
-                value real { 42037037037037, 10, -13 }
-              }
-            }
-          }
-        }
-      },
-      {
-        type diags,
-        segs std {
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_08362"
-            },
-            loc {
-              int {
-                from 186,
-                to 236,
-                strand plus,
-                id local str "Query_1"
-              },
-              int {
-                from 265,
-                to 315,
-                strand minus,
-                id local str "SI2.2.0_08362"
-              }
-            },
-            scores {
-              {
-                id str "score",
-                value int 46
-              },
-              {
-                id str "e_value",
-                value real { 144735775888057, 10, -14 }
-              },
-              {
-                id str "bit_score",
-                value real { 239777601783694, 10, -13 }
-              },
-              {
-                id str "num_ident",
-                value int 8
-              },
-              {
-                id str "num_positives",
-                value int 11
-              },
-              {
-                id str "hsp_percent_coverage",
-                value real { 364814814814815, 10, -14 }
-              }
-            }
-          }
-        }
-      },
-      {
-        type diags,
-        segs std {
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_00417"
-            },
-            loc {
-              int {
-                from 144,
-                to 257,
-                strand plus,
-                id local str "Query_1"
-              },
-              int {
-                from 91,
-                to 204,
-                strand plus,
-                id local str "SI2.2.0_00417"
-              }
-            },
-            scores {
-              {
-                id str "score",
-                value int 46
-              },
-              {
-                id str "e_value",
-                value real { 144735775888057, 10, -14 }
-              },
-              {
-                id str "bit_score",
-                value real { 239777601783694, 10, -13 }
-              },
-              {
-                id str "num_ident",
-                value int 11
-              },
-              {
-                id str "num_positives",
-                value int 19
-              },
-              {
-                id str "hsp_percent_coverage",
-                value real { 753703703703704, 10, -14 }
-              }
-            }
-          }
-        }
-      },
-      {
-        type diags,
-        segs std {
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_02651"
-            },
-            loc {
-              int {
-                from 333,
-                to 404,
-                strand minus,
-                id local str "Query_1"
-              },
-              int {
-                from 1667,
-                to 1738,
-                strand minus,
-                id local str "SI2.2.0_02651"
-              }
-            },
-            scores {
-              {
-                id str "score",
-                value int 46
-              },
-              {
-                id str "e_value",
-                value real { 144735775888057, 10, -14 }
-              },
-              {
-                id str "bit_score",
-                value real { 239777601783694, 10, -13 }
-              },
-              {
-                id str "num_ident",
-                value int 7
-              },
-              {
-                id str "num_positives",
-                value int 14
-              },
-              {
-                id str "hsp_percent_coverage",
-                value real { 494444444444444, 10, -14 }
-              }
-            }
-          },
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_02651"
-            },
-            loc {
-              int {
-                from 366,
-                to 398,
-                strand minus,
-                id local str "Query_1"
-              },
-              int {
-                from 1698,
-                to 1730,
-                strand minus,
-                id local str "SI2.2.0_02651"
-              }
-            },
-            scores {
-              {
-                id str "score",
-                value int 40
-              },
-              {
-                id str "e_value",
-                value real { 973157160465245, 10, -14 }
-              },
-              {
-                id str "bit_score",
-                value real { 212285089381423, 10, -13 }
-              },
-              {
-                id str "num_ident",
-                value int 6
-              },
-              {
-                id str "num_positives",
-                value int 8
-              },
-              {
-                id str "hsp_percent_coverage",
-                value real { 253703703703704, 10, -14 }
-              }
-            }
-          }
-        }
-      },
-      {
-        type diags,
-        segs std {
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_09826"
-            },
-            loc {
-              int {
-                from 455,
-                to 496,
-                strand plus,
-                id local str "Query_1"
-              },
-              int {
-                from 155,
-                to 196,
-                strand minus,
-                id local str "SI2.2.0_09826"
-              }
-            },
-            scores {
-              {
-                id str "score",
-                value int 44
-              },
-              {
-                id str "e_value",
-                value real { 271331704205974, 10, -14 }
-              },
-              {
-                id str "bit_score",
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-                id str "hsp_percent_coverage",
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-                value int 10
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-              {
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-                id str "score",
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-              {
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-              {
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-              {
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-              {
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-              {
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-                value real { 494444444444444, 10, -14 }
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-      }
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-    masks {
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-        k { -1, 10, 0 },
-        h { -1, 10, 0 },
-        gapped TRUE
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-      "Effective search space: 11955588",
-      "Effective search space used: 11955588",
-      "Length adjustment: 32"
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-}