sequenceserver 1.1.0.beta12 → 2.0.0.beta1

data/spec/sample_reports/blastx_sample/job.yaml

@@ -1,10 +0,0 @@
---- !ruby/object:SequenceServer::BLAST::Job
-id: blastx_sample
-method: blastx
-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/blastx_sample/stdout

@@ -1,1191 +0,0 @@
-Blast4-archive ::= {
-  request {
-    ident "2.2.30+",
-    body queue-search {
-      program "blastx",
-      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/proteins/Solenopsis_invicta/Sinvi
-cta2-2-3.prot.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 12
-        },
-        {
-          name "WindowSize",
-          value integer 40
-        },
-        {
-          name "UngappedMode",
-          value boolean FALSE
-        },
-        {
-          name "QueryGeneticCode",
-          value integer 1
-        },
-        {
-          name "HitlistSize",
-          value integer 500
-        },
-        {
-          name "CompositionBasedStats",
-          value integer 2
-        },
-        {
-          name "SmithWatermanMode",
-          value boolean FALSE
-        },
-        {
-          name "EffectiveSearchSpace",
-          value big-integer 22643392
-        }
-      }
-    }
-  },
-  results {
-    alignments {
-      {
-        type partial,
-        dim 2,
-        score {
-          {
-            id str "score",
-            value int 945
-          },
-          {
-            id str "e_value",
-            value real { 328061049691817, 10, -146 }
-          },
-          {
-            id str "bit_score",
-            value real { 368621831521943, 10, -12 }
-          },
-          {
-            id str "num_ident",
-            value int 180
-          },
-          {
-            id str "comp_adjustment_method",
-            value int 2
-          },
-          {
-            id str "num_positives",
-            value int 180
-          },
-          {
-            id str "hsp_percent_coverage",
-            value real { 338333333333333, 10, -13 }
-          }
-        },
-        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 179,
-                strand unknown,
-                id local str "SI2.2.0_06267"
-              }
-            }
-          }
-        }
-      },
-      {
-        type partial,
-        dim 2,
-        score {
-          {
-            id str "score",
-            value int 52
-          },
-          {
-            id str "e_value",
-            value real { 48276466190711, 10, -14 }
-          },
-          {
-            id str "bit_score",
-            value real { 246386102277464, 10, -13 }
-          },
-          {
-            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 { 103148148148148, 10, -13 }
-          }
-        },
-        segs std {
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_10694"
-            },
-            loc {
-              int {
-                from 159,
-                to 239,
-                strand plus,
-                id local str "Query_1"
-              },
-              int {
-                from 4,
-                to 30,
-                strand unknown,
-                id local str "SI2.2.0_10694"
-              }
-            }
-          },
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_10694"
-            },
-            loc {
-              int {
-                from 240,
-                to 263,
-                strand plus,
-                id local str "Query_1"
-              },
-              empty local str "SI2.2.0_10694"
-            }
-          },
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_10694"
-            },
-            loc {
-              int {
-                from 264,
-                to 317,
-                strand plus,
-                id local str "Query_1"
-              },
-              int {
-                from 31,
-                to 48,
-                strand unknown,
-                id local str "SI2.2.0_10694"
-              }
-            }
-          }
-        }
-      },
-      {
-        type partial,
-        dim 2,
-        score {
-          {
-            id str "score",
-            value int 54
-          },
-          {
-            id str "e_value",
-            value real { 514023496716278, 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 { 494444444444444, 10, -14 }
-          }
-        },
-        segs std {
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_11870"
-            },
-            loc {
-              int {
-                from 78,
-                to 149,
-                strand plus,
-                id local str "Query_1"
-              },
-              int {
-                from 61,
-                to 84,
-                strand unknown,
-                id local str "SI2.2.0_11870"
-              }
-            }
-          }
-        }
-      },
-      {
-        type partial,
-        dim 2,
-        score {
-          {
-            id str "score",
-            value int 53
-          },
-          {
-            id str "e_value",
-            value real { 763322899384652, 10, -15 }
-          },
-          {
-            id str "bit_score",
-            value real { 250238098036637, 10, -13 }
-          },
-          {
-            id str "num_ident",
-            value int 15
-          },
-          {
-            id str "comp_adjustment_method",
-            value int 2
-          },
-          {
-            id str "num_positives",
-            value int 21
-          },
-          {
-            id str "hsp_percent_coverage",
-            value real { 772222222222222, 10, -14 }
-          }
-        },
-        segs std {
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_12250"
-            },
-            loc {
-              int {
-                from 97,
-                to 126,
-                strand plus,
-                id local str "Query_1"
-              },
-              int {
-                from 314,
-                to 323,
-                strand unknown,
-                id local str "SI2.2.0_12250"
-              }
-            }
-          },
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_12250"
-            },
-            loc {
-              int {
-                from 127,
-                to 135,
-                strand plus,
-                id local str "Query_1"
-              },
-              empty local str "SI2.2.0_12250"
-            }
-          },
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_12250"
-            },
-            loc {
-              int {
-                from 136,
-                to 165,
-                strand plus,
-                id local str "Query_1"
-              },
-              int {
-                from 324,
-                to 333,
-                strand unknown,
-                id local str "SI2.2.0_12250"
-              }
-            }
-          },
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_12250"
-            },
-            loc {
-              int {
-                from 166,
-                to 177,
-                strand plus,
-                id local str "Query_1"
-              },
-              empty local str "SI2.2.0_12250"
-            }
-          },
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_12250"
-            },
-            loc {
-              int {
-                from 178,
-                to 213,
-                strand plus,
-                id local str "Query_1"
-              },
-              int {
-                from 334,
-                to 345,
-                strand unknown,
-                id local str "SI2.2.0_12250"
-              }
-            }
-          }
-        }
-      },
-      {
-        type partial,
-        dim 2,
-        score {
-          {
-            id str "score",
-            value int 53
-          },
-          {
-            id str "e_value",
-            value real { 959504494511501, 10, -15 }
-          },
-          {
-            id str "bit_score",
-            value real { 250238098036637, 10, -13 }
-          },
-          {
-            id str "num_ident",
-            value int 26
-          },
-          {
-            id str "comp_adjustment_method",
-            value int 2
-          },
-          {
-            id str "num_positives",
-            value int 53
-          },
-          {
-            id str "hsp_percent_coverage",
-            value real { 192037037037037, 10, -13 }
-          }
-        },
-        segs std {
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_00013"
-            },
-            loc {
-              int {
-                from 12,
-                to 20,
-                strand plus,
-                id local str "Query_1"
-              },
-              int {
-                from 247,
-                to 249,
-                strand unknown,
-                id local str "SI2.2.0_00013"
-              }
-            }
-          },
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_00013"
-            },
-            loc {
-              empty local str "Query_1",
-              int {
-                from 250,
-                to 250,
-                strand unknown,
-                id local str "SI2.2.0_00013"
-              }
-            }
-          },
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_00013"
-            },
-            loc {
-              int {
-                from 21,
-                to 59,
-                strand plus,
-                id local str "Query_1"
-              },
-              int {
-                from 251,
-                to 263,
-                strand unknown,
-                id local str "SI2.2.0_00013"
-              }
-            }
-          },
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_00013"
-            },
-            loc {
-              empty local str "Query_1",
-              int {
-                from 264,
-                to 267,
-                strand unknown,
-                id local str "SI2.2.0_00013"
-              }
-            }
-          },
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_00013"
-            },
-            loc {
-              int {
-                from 60,
-                to 143,
-                strand plus,
-                id local str "Query_1"
-              },
-              int {
-                from 268,
-                to 295,
-                strand unknown,
-                id local str "SI2.2.0_00013"
-              }
-            }
-          },
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_00013"
-            },
-            loc {
-              int {
-                from 144,
-                to 149,
-                strand plus,
-                id local str "Query_1"
-              },
-              empty local str "SI2.2.0_00013"
-            }
-          },
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_00013"
-            },
-            loc {
-              int {
-                from 150,
-                to 203,
-                strand plus,
-                id local str "Query_1"
-              },
-              int {
-                from 296,
-                to 313,
-                strand unknown,
-                id local str "SI2.2.0_00013"
-              }
-            }
-          },
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_00013"
-            },
-            loc {
-              int {
-                from 204,
-                to 212,
-                strand plus,
-                id local str "Query_1"
-              },
-              empty local str "SI2.2.0_00013"
-            }
-          },
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_00013"
-            },
-            loc {
-              int {
-                from 213,
-                to 296,
-                strand plus,
-                id local str "Query_1"
-              },
-              int {
-                from 314,
-                to 341,
-                strand unknown,
-                id local str "SI2.2.0_00013"
-              }
-            }
-          },
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_00013"
-            },
-            loc {
-              int {
-                from 297,
-                to 305,
-                strand plus,
-                id local str "Query_1"
-              },
-              empty local str "SI2.2.0_00013"
-            }
-          },
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_00013"
-            },
-            loc {
-              int {
-                from 306,
-                to 314,
-                strand plus,
-                id local str "Query_1"
-              },
-              int {
-                from 342,
-                to 344,
-                strand unknown,
-                id local str "SI2.2.0_00013"
-              }
-            }
-          }
-        }
-      },
-      {
-        type partial,
-        dim 2,
-        score {
-          {
-            id str "score",
-            value int 51
-          },
-          {
-            id str "e_value",
-            value real { 998127990626386, 10, -15 }
-          },
-          {
-            id str "bit_score",
-            value real { 24253410651829, 10, -12 }
-          },
-          {
-            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 { 642592592592593, 10, -14 }
-          }
-        },
-        segs std {
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_04285"
-            },
-            loc {
-              int {
-                from 285,
-                to 296,
-                strand plus,
-                id local str "Query_1"
-              },
-              int {
-                from 82,
-                to 85,
-                strand unknown,
-                id local str "SI2.2.0_04285"
-              }
-            }
-          },
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_04285"
-            },
-            loc {
-              int {
-                from 297,
-                to 302,
-                strand plus,
-                id local str "Query_1"
-              },
-              empty local str "SI2.2.0_04285"
-            }
-          },
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_04285"
-            },
-            loc {
-              int {
-                from 303,
-                to 380,
-                strand plus,
-                id local str "Query_1"
-              },
-              int {
-                from 86,
-                to 111,
-                strand unknown,
-                id local str "SI2.2.0_04285"
-              }
-            }
-          }
-        }
-      },
-      {
-        type partial,
-        dim 2,
-        score {
-          {
-            id str "score",
-            value int 48
-          },
-          {
-            id str "e_value",
-            value real { 296470399107044, 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 { 661111111111111, 10, -14 }
-          }
-        },
-        segs std {
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_00562"
-            },
-            loc {
-              int {
-                from 102,
-                to 200,
-                strand plus,
-                id local str "Query_1"
-              },
-              int {
-                from 26,
-                to 58,
-                strand unknown,
-                id local str "SI2.2.0_00562"
-              }
-            }
-          }
-        }
-      },
-      {
-        type partial,
-        dim 2,
-        score {
-          {
-            id str "score",
-            value int 46
-          },
-          {
-            id str "e_value",
-            value real { 406293844119382, 10, -14 }
-          },
-          {
-            id str "bit_score",
-            value real { 223274127722423, 10, -13 }
-          },
-          {
-            id str "num_ident",
-            value int 10
-          },
-          {
-            id str "comp_adjustment_method",
-            value int 2
-          },
-          {
-            id str "num_positives",
-            value int 11
-          },
-          {
-            id str "hsp_percent_coverage",
-            value real { 42037037037037, 10, -13 }
-          }
-        },
-        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 40,
-                to 59,
-                strand unknown,
-                id local str "SI2.2.0_08520"
-              }
-            }
-          }
-        }
-      },
-      {
-        type partial,
-        dim 2,
-        score {
-          {
-            id str "score",
-            value int 46
-          },
-          {
-            id str "e_value",
-            value real { 412487581921973, 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 16
-          },
-          {
-            id str "hsp_percent_coverage",
-            value real { 531481481481481, 10, -14 }
-          }
-        },
-        segs std {
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_06904"
-            },
-            loc {
-              int {
-                from 93,
-                to 170,
-                strand plus,
-                id local str "Query_1"
-              },
-              int {
-                from 39,
-                to 64,
-                strand unknown,
-                id local str "SI2.2.0_06904"
-              }
-            }
-          }
-        }
-      },
-      {
-        type partial,
-        dim 2,
-        score {
-          {
-            id str "score",
-            value int 48
-          },
-          {
-            id str "e_value",
-            value real { 416112025497446, 10, -14 }
-          },
-          {
-            id str "bit_score",
-            value real { 23097811924077, 10, -12 }
-          },
-          {
-            id str "num_ident",
-            value int 8
-          },
-          {
-            id str "comp_adjustment_method",
-            value int 1
-          },
-          {
-            id str "num_positives",
-            value int 11
-          },
-          {
-            id str "hsp_percent_coverage",
-            value real { 346296296296296, 10, -14 }
-          }
-        },
-        segs std {
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_03512"
-            },
-            loc {
-              int {
-                from 186,
-                to 233,
-                strand plus,
-                id local str "Query_1"
-              },
-              int {
-                from 16,
-                to 31,
-                strand unknown,
-                id local str "SI2.2.0_03512"
-              }
-            }
-          }
-        }
-      },
-      {
-        type partial,
-        dim 2,
-        score {
-          {
-            id str "score",
-            value int 47
-          },
-          {
-            id str "e_value",
-            value real { 462088392354261, 10, -14 }
-          },
-          {
-            id str "bit_score",
-            value real { 227126123481596, 10, -13 }
-          },
-          {
-            id str "num_ident",
-            value int 8
-          },
-          {
-            id str "comp_adjustment_method",
-            value int 1
-          },
-          {
-            id str "num_positives",
-            value int 15
-          },
-          {
-            id str "hsp_percent_coverage",
-            value real { 457407407407407, 10, -14 }
-          }
-        },
-        segs std {
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_11705"
-            },
-            loc {
-              int {
-                from 447,
-                to 512,
-                strand minus,
-                id local str "Query_1"
-              },
-              int {
-                from 495,
-                to 516,
-                strand unknown,
-                id local str "SI2.2.0_11705"
-              }
-            }
-          }
-        }
-      },
-      {
-        type partial,
-        dim 2,
-        score {
-          {
-            id str "score",
-            value int 45
-          },
-          {
-            id str "e_value",
-            value real { 907736362058494, 10, -14 }
-          },
-          {
-            id str "bit_score",
-            value real { 219422131963249, 10, -13 }
-          },
-          {
-            id str "num_ident",
-            value int 15
-          },
-          {
-            id str "comp_adjustment_method",
-            value int 2
-          },
-          {
-            id str "num_positives",
-            value int 23
-          },
-          {
-            id str "hsp_percent_coverage",
-            value real { 772222222222222, 10, -14 }
-          }
-        },
-        segs std {
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_09298"
-            },
-            loc {
-              int {
-                from 151,
-                to 174,
-                strand plus,
-                id local str "Query_1"
-              },
-              int {
-                from 369,
-                to 376,
-                strand unknown,
-                id local str "SI2.2.0_09298"
-              }
-            }
-          },
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_09298"
-            },
-            loc {
-              empty local str "Query_1",
-              int {
-                from 377,
-                to 377,
-                strand unknown,
-                id local str "SI2.2.0_09298"
-              }
-            }
-          },
-          {
-            dim 2,
-            ids {
-              local str "Query_1",
-              local str "SI2.2.0_09298"
-            },
-            loc {
-              int {
-                from 175,
-                to 267,
-                strand plus,
-                id local str "Query_1"
-              },
-              int {
-                from 378,
-                to 408,
-                strand unknown,
-                id local str "SI2.2.0_09298"
-              }
-            }
-          }
-        }
-      }
-    },
-    masks {
-      {
-        locations {
-          packed-int {
-            {
-              from 350,
-              to 382,
-              id local str "Query_1"
-            }
-          }
-        },
-        frame minus2
-      }
-    },
-    ka-blocks {
-      {
-        lambda { 317605957635731, 10, -15 },
-        k { 133956144488482, 10, -15 },
-        h { 401214524497119, 10, -15 },
-        gapped FALSE
-      },
-      {
-        lambda { 267, 10, -3 },
-        k { 41, 10, -3 },
-        h { 14, 10, -2 },
-        gapped TRUE
-      }
-    },
-    search-stats {
-      "Effective search space: 22643392",
-      "Effective search space used: 22643392",
-      "Length adjustment: 67"
-    }
-  }
-}