sequenceserver 1.0.0.pre.5 → 1.0.0

data/spec/sample_reports/blastx_sample.asn

@@ -0,0 +1,1191 @@
+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 "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 "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"
+    }
+  }
+}