sequenceserver 1.0.0.pre.5 → 1.0.0

data/spec/sample_reports/no_hits_sample.asn

@@ -0,0 +1,130 @@
+Blast4-archive ::= {
+  request {
+    ident "2.2.30+",
+    body queue-search {
+      program "blastn",
+      service "plain",
+      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 32,
+              seq-data ncbi2na '39C9155555555555'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 4482944
+        }
+      },
+      program-options {
+        {
+          name "LCaseMask",
+          value query-mask {
+            locations {
+              packed-int {
+                {
+                  from 9,
+                  to 31,
+                  id local str "Query_1"
+                },
+                {
+                  from 9,
+                  to 31,
+                  id local str "Query_1"
+                }
+              }
+            },
+            frame plus1
+          }
+        }
+      }
+    }
+  },
+  results {
+    alignments {
+    },
+    masks {
+      {
+        locations {
+          packed-int {
+            {
+              from 9,
+              to 31,
+              id local str "Query_1"
+            }
+          }
+        },
+        frame plus1
+      }
+    },
+    ka-blocks {
+      {
+        lambda { 633731443099174, 10, -15 },
+        k { 408145662544724, 10, -15 },
+        h { 91243839227971, 10, -14 },
+        gapped FALSE
+      },
+      {
+        lambda { 625, 10, -3 },
+        k { 41, 10, -2 },
+        h { 78, 10, -2 },
+        gapped TRUE
+      }
+    },
+    search-stats {
+      "Effective search space: 4482944",
+      "Effective search space used: 4482944",
+      "Length adjustment: 16"
+    }
+  }
+}

data/spec/sample_reports/tblastn_sample.asn

@@ -0,0 +1,1107 @@
+Blast4-archive ::= {
+  request {
+    ident "2.2.30+",
+    body queue-search {
+      program "tblastn",
+      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/transcripts/Solenopsis_invicta/Si
+nvicta2-2-3.cdna.subset.fasta",
+      algorithm-options {
+        {
+          name "EvalueThreshold",
+          value cutoff e-value { 1, 10, 1 }
+        },
+        {
+          name "DbGeneticCode",
+          value integer 1
+        },
+        {
+          name "UngappedMode",
+          value boolean FALSE
+        },
+        {
+          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 "HitlistSize",
+          value integer 500
+        },
+        {
+          name "CompositionBasedStats",
+          value integer 2
+        },
+        {
+          name "SmithWatermanMode",
+          value boolean FALSE
+        },
+        {
+          name "EffectiveSearchSpace",
+          value big-integer 9254832
+        }
+      }
+    }
+  },
+  results {
+    alignments {
+      {
+        type partial,
+        dim 2,
+        score {
+          {
+            id str "score",
+            value int 1046
+          },
+          {
+            id str "e_value",
+            value real { 991472001167032, 10, -162 }
+          },
+          {
+            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 std {
+          {
+            dim 2,
+            ids {
+              local str "Query_1",
+              local str "SI2.2.0_06267"
+            },
+            loc {
+              int {
+                from 0,
+                to 198,
+                strand unknown,
+                id local str "Query_1"
+              },
+              int {
+                from 0,
+                to 596,
+                strand plus,
+                id local str "SI2.2.0_06267"
+              }
+            }
+          }
+        }
+      },
+      {
+        type partial,
+        dim 2,
+        score {
+          {
+            id str "score",
+            value int 46
+          },
+          {
+            id str "e_value",
+            value real { 158151944731805, 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 std {
+          {
+            dim 2,
+            ids {
+              local str "Query_1",
+              local str "SI2.2.0_06904"
+            },
+            loc {
+              int {
+                from 31,
+                to 56,
+                strand unknown,
+                id local str "Query_1"
+              },
+              int {
+                from 117,
+                to 194,
+                strand plus,
+                id local str "SI2.2.0_06904"
+              }
+            }
+          }
+        }
+      },
+      {
+        type partial,
+        dim 2,
+        score {
+          {
+            id str "score",
+            value int 44
+          },
+          {
+            id str "e_value",
+            value real { 264755365382425, 10, -14 }
+          },
+          {
+            id str "bit_score",
+            value real { 215570136204075, 10, -13 }
+          },
+          {
+            id str "num_ident",
+            value int 8
+          },
+          {
+            id str "comp_adjustment_method",
+            value int 2
+          },
+          {
+            id str "num_positives",
+            value int 13
+          },
+          {
+            id str "hsp_percent_coverage",
+            value real { 803768844221105, 10, -14 }
+          }
+        },
+        segs std {
+          {
+            dim 2,
+            ids {
+              local str "Query_1",
+              local str "SI2.2.0_03432"
+            },
+            loc {
+              int {
+                from 50,
+                to 64,
+                strand unknown,
+                id local str "Query_1"
+              },
+              int {
+                from 37,
+                to 81,
+                strand plus,
+                id local str "SI2.2.0_03432"
+              }
+            }
+          }
+        }
+      },
+      {
+        type partial,
+        dim 2,
+        score {
+          {
+            id str "score",
+            value int 42
+          },
+          {
+            id str "e_value",
+            value real { 738402284079177, 10, -14 }
+          },
+          {
+            id str "bit_score",
+            value real { 207866144685728, 10, -13 }
+          },
+          {
+            id str "num_ident",
+            value int 8
+          },
+          {
+            id str "comp_adjustment_method",
+            value int 2
+          },
+          {
+            id str "num_positives",
+            value int 11
+          },
+          {
+            id str "hsp_percent_coverage",
+            value real { 100477386934673, 10, -13 }
+          }
+        },
+        segs std {
+          {
+            dim 2,
+            ids {
+              local str "Query_1",
+              local str "SI2.2.0_05280"
+            },
+            loc {
+              int {
+                from 69,
+                to 87,
+                strand unknown,
+                id local str "Query_1"
+              },
+              int {
+                from 52,
+                to 108,
+                strand minus,
+                id local str "SI2.2.0_05280"
+              }
+            }
+          }
+        }
+      },
+      {
+        type partial,
+        dim 2,
+        score {
+          {
+            id str "score",
+            value int 917
+          },
+          {
+            id str "e_value",
+            value real { 163109526812422, 10, -142 }
+          },
+          {
+            id str "bit_score",
+            value real { 357836243396257, 10, -12 }
+          },
+          {
+            id str "num_ident",
+            value int 170
+          },
+          {
+            id str "comp_adjustment_method",
+            value int 2
+          },
+          {
+            id str "num_positives",
+            value int 170
+          },
+          {
+            id str "hsp_percent_coverage",
+            value real { 1, 10, 2 }
+          }
+        },
+        segs std {
+          {
+            dim 2,
+            ids {
+              local str "Query_2",
+              local str "SI2.2.0_13722"
+            },
+            loc {
+              int {
+                from 0,
+                to 185,
+                strand unknown,
+                id local str "Query_2"
+              },
+              int {
+                from 0,
+                to 557,
+                strand plus,
+                id local str "SI2.2.0_13722"
+              }
+            }
+          }
+        }
+      },
+      {
+        type partial,
+        dim 2,
+        score {
+          {
+            id str "score",
+            value int 70
+          },
+          {
+            id str "e_value",
+            value real { 973505195823272, 10, -18 }
+          },
+          {
+            id str "bit_score",
+            value real { 315722025942587, 10, -13 }
+          },
+          {
+            id str "num_ident",
+            value int 20
+          },
+          {
+            id str "comp_adjustment_method",
+            value int 2
+          },
+          {
+            id str "num_positives",
+            value int 27
+          },
+          {
+            id str "hsp_percent_coverage",
+            value real { 241559139784946, 10, -13 }
+          }
+        },
+        segs std {
+          {
+            dim 2,
+            ids {
+              local str "Query_2",
+              local str "SI2.2.0_13149"
+            },
+            loc {
+              int {
+                from 32,
+                to 42,
+                strand unknown,
+                id local str "Query_2"
+              },
+              int {
+                from 87,
+                to 119,
+                strand plus,
+                id local str "SI2.2.0_13149"
+              }
+            }
+          },
+          {
+            dim 2,
+            ids {
+              local str "Query_2",
+              local str "SI2.2.0_13149"
+            },
+            loc {
+              int {
+                from 43,
+                to 43,
+                strand unknown,
+                id local str "Query_2"
+              },
+              empty local str "SI2.2.0_13149"
+            }
+          },
+          {
+            dim 2,
+            ids {
+              local str "Query_2",
+              local str "SI2.2.0_13149"
+            },
+            loc {
+              int {
+                from 44,
+                to 59,
+                strand unknown,
+                id local str "Query_2"
+              },
+              int {
+                from 120,
+                to 167,
+                strand plus,
+                id local str "SI2.2.0_13149"
+              }
+            }
+          },
+          {
+            dim 2,
+            ids {
+              local str "Query_2",
+              local str "SI2.2.0_13149"
+            },
+            loc {
+              empty local str "Query_2",
+              int {
+                from 168,
+                to 170,
+                strand plus,
+                id local str "SI2.2.0_13149"
+              }
+            }
+          },
+          {
+            dim 2,
+            ids {
+              local str "Query_2",
+              local str "SI2.2.0_13149"
+            },
+            loc {
+              int {
+                from 60,
+                to 75,
+                strand unknown,
+                id local str "Query_2"
+              },
+              int {
+                from 171,
+                to 218,
+                strand plus,
+                id local str "SI2.2.0_13149"
+              }
+            }
+          }
+        }
+      },
+      {
+        type partial,
+        dim 2,
+        score {
+          {
+            id str "score",
+            value int 64
+          },
+          {
+            id str "e_value",
+            value real { 591430689703162, 10, -17 }
+          },
+          {
+            id str "bit_score",
+            value real { 292610051387546, 10, -13 }
+          },
+          {
+            id str "num_ident",
+            value int 10
+          },
+          {
+            id str "comp_adjustment_method",
+            value int 2
+          },
+          {
+            id str "num_positives",
+            value int 15
+          },
+          {
+            id str "hsp_percent_coverage",
+            value real { 123279569892473, 10, -13 }
+          }
+        },
+        segs std {
+          {
+            dim 2,
+            ids {
+              local str "Query_2",
+              local str "SI2.2.0_13149"
+            },
+            loc {
+              int {
+                from 164,
+                to 185,
+                strand unknown,
+                id local str "Query_2"
+              },
+              int {
+                from 237,
+                to 302,
+                strand plus,
+                id local str "SI2.2.0_13149"
+              }
+            }
+          }
+        }
+      },
+      {
+        type partial,
+        dim 2,
+        score {
+          {
+            id str "score",
+            value int 48
+          },
+          {
+            id str "e_value",
+            value real { 489490109366324, 10, -15 }
+          },
+          {
+            id str "bit_score",
+            value real { 23097811924077, 10, -12 }
+          },
+          {
+            id str "num_ident",
+            value int 13
+          },
+          {
+            id str "comp_adjustment_method",
+            value int 2
+          },
+          {
+            id str "num_positives",
+            value int 17
+          },
+          {
+            id str "hsp_percent_coverage",
+            value real { 160913978494624, 10, -13 }
+          }
+        },
+        segs std {
+          {
+            dim 2,
+            ids {
+              local str "Query_2",
+              local str "SI2.2.0_09379"
+            },
+            loc {
+              int {
+                from 58,
+                to 72,
+                strand unknown,
+                id local str "Query_2"
+              },
+              int {
+                from 103,
+                to 147,
+                strand minus,
+                id local str "SI2.2.0_09379"
+              }
+            }
+          },
+          {
+            dim 2,
+            ids {
+              local str "Query_2",
+              local str "SI2.2.0_09379"
+            },
+            loc {
+              int {
+                from 73,
+                to 73,
+                strand unknown,
+                id local str "Query_2"
+              },
+              empty local str "SI2.2.0_09379"
+            }
+          },
+          {
+            dim 2,
+            ids {
+              local str "Query_2",
+              local str "SI2.2.0_09379"
+            },
+            loc {
+              int {
+                from 74,
+                to 86,
+                strand unknown,
+                id local str "Query_2"
+              },
+              int {
+                from 64,
+                to 102,
+                strand minus,
+                id local str "SI2.2.0_09379"
+              }
+            }
+          }
+        }
+      },
+      {
+        type partial,
+        dim 2,
+        score {
+          {
+            id str "score",
+            value int 45
+          },
+          {
+            id str "e_value",
+            value real { 724328385986037, 10, -15 }
+          },
+          {
+            id str "bit_score",
+            value real { 219422131963249, 10, -13 }
+          },
+          {
+            id str "num_ident",
+            value int 7
+          },
+          {
+            id str "comp_adjustment_method",
+            value int 1
+          },
+          {
+            id str "num_positives",
+            value int 14
+          },
+          {
+            id str "hsp_percent_coverage",
+            value real { 117903225806452, 10, -13 }
+          }
+        },
+        segs std {
+          {
+            dim 2,
+            ids {
+              local str "Query_2",
+              local str "SI2.2.0_02019"
+            },
+            loc {
+              int {
+                from 119,
+                to 139,
+                strand unknown,
+                id local str "Query_2"
+              },
+              int {
+                from 46,
+                to 108,
+                strand minus,
+                id local str "SI2.2.0_02019"
+              }
+            }
+          }
+        }
+      },
+      {
+        type partial,
+        dim 2,
+        score {
+          {
+            id str "score",
+            value int 48
+          },
+          {
+            id str "e_value",
+            value real { 137339689136456, 10, -14 }
+          },
+          {
+            id str "bit_score",
+            value real { 23097811924077, 10, -12 }
+          },
+          {
+            id str "num_ident",
+            value int 14
+          },
+          {
+            id str "comp_adjustment_method",
+            value int 2
+          },
+          {
+            id str "num_positives",
+            value int 25
+          },
+          {
+            id str "hsp_percent_coverage",
+            value real { 252311827956989, 10, -13 }
+          }
+        },
+        segs std {
+          {
+            dim 2,
+            ids {
+              local str "Query_2",
+              local str "SI2.2.0_03352"
+            },
+            loc {
+              int {
+                from 41,
+                to 52,
+                strand unknown,
+                id local str "Query_2"
+              },
+              int {
+                from 495,
+                to 530,
+                strand plus,
+                id local str "SI2.2.0_03352"
+              }
+            }
+          },
+          {
+            dim 2,
+            ids {
+              local str "Query_2",
+              local str "SI2.2.0_03352"
+            },
+            loc {
+              empty local str "Query_2",
+              int {
+                from 531,
+                to 551,
+                strand plus,
+                id local str "SI2.2.0_03352"
+              }
+            }
+          },
+          {
+            dim 2,
+            ids {
+              local str "Query_2",
+              local str "SI2.2.0_03352"
+            },
+            loc {
+              int {
+                from 53,
+                to 86,
+                strand unknown,
+                id local str "Query_2"
+              },
+              int {
+                from 552,
+                to 653,
+                strand plus,
+                id local str "SI2.2.0_03352"
+              }
+            }
+          }
+        }
+      },
+      {
+        type partial,
+        dim 2,
+        score {
+          {
+            id str "score",
+            value int 44
+          },
+          {
+            id str "e_value",
+            value real { 3025295033467, 10, -12 }
+          },
+          {
+            id str "bit_score",
+            value real { 215570136204075, 10, -13 }
+          },
+          {
+            id str "num_ident",
+            value int 22
+          },
+          {
+            id str "comp_adjustment_method",
+            value int 2
+          },
+          {
+            id str "num_positives",
+            value int 32
+          },
+          {
+            id str "hsp_percent_coverage",
+            value real { 354462365591398, 10, -13 }
+          }
+        },
+        segs std {
+          {
+            dim 2,
+            ids {
+              local str "Query_2",
+              local str "SI2.2.0_05451"
+            },
+            loc {
+              int {
+                from 97,
+                to 115,
+                strand unknown,
+                id local str "Query_2"
+              },
+              int {
+                from 26,
+                to 82,
+                strand plus,
+                id local str "SI2.2.0_05451"
+              }
+            }
+          },
+          {
+            dim 2,
+            ids {
+              local str "Query_2",
+              local str "SI2.2.0_05451"
+            },
+            loc {
+              empty local str "Query_2",
+              int {
+                from 83,
+                to 130,
+                strand plus,
+                id local str "SI2.2.0_05451"
+              }
+            }
+          },
+          {
+            dim 2,
+            ids {
+              local str "Query_2",
+              local str "SI2.2.0_05451"
+            },
+            loc {
+              int {
+                from 116,
+                to 125,
+                strand unknown,
+                id local str "Query_2"
+              },
+              int {
+                from 131,
+                to 160,
+                strand plus,
+                id local str "SI2.2.0_05451"
+              }
+            }
+          },
+          {
+            dim 2,
+            ids {
+              local str "Query_2",
+              local str "SI2.2.0_05451"
+            },
+            loc {
+              int {
+                from 126,
+                to 138,
+                strand unknown,
+                id local str "Query_2"
+              },
+              empty local str "SI2.2.0_05451"
+            }
+          },
+          {
+            dim 2,
+            ids {
+              local str "Query_2",
+              local str "SI2.2.0_05451"
+            },
+            loc {
+              int {
+                from 139,
+                to 148,
+                strand unknown,
+                id local str "Query_2"
+              },
+              int {
+                from 161,
+                to 190,
+                strand plus,
+                id local str "SI2.2.0_05451"
+              }
+            }
+          },
+          {
+            dim 2,
+            ids {
+              local str "Query_2",
+              local str "SI2.2.0_05451"
+            },
+            loc {
+              int {
+                from 149,
+                to 154,
+                strand unknown,
+                id local str "Query_2"
+              },
+              empty local str "SI2.2.0_05451"
+            }
+          },
+          {
+            dim 2,
+            ids {
+              local str "Query_2",
+              local str "SI2.2.0_05451"
+            },
+            loc {
+              int {
+                from 155,
+                to 161,
+                strand unknown,
+                id local str "Query_2"
+              },
+              int {
+                from 191,
+                to 211,
+                strand plus,
+                id local str "SI2.2.0_05451"
+              }
+            }
+          }
+        }
+      },
+      {
+        type partial,
+        dim 2,
+        score {
+          {
+            id str "score",
+            value int 41
+          },
+          {
+            id str "e_value",
+            value real { 665464998703274, 10, -14 }
+          },
+          {
+            id str "bit_score",
+            value real { 204014148926555, 10, -13 }
+          },
+          {
+            id str "num_ident",
+            value int 8
+          },
+          {
+            id str "comp_adjustment_method",
+            value int 2
+          },
+          {
+            id str "num_positives",
+            value int 14
+          },
+          {
+            id str "hsp_percent_coverage",
+            value real { 101774193548387, 10, -13 }
+          }
+        },
+        segs std {
+          {
+            dim 2,
+            ids {
+              local str "Query_2",
+              local str "SI2.2.0_05852"
+            },
+            loc {
+              int {
+                from 141,
+                to 158,
+                strand unknown,
+                id local str "Query_2"
+              },
+              int {
+                from 192,
+                to 245,
+                strand minus,
+                id local str "SI2.2.0_05852"
+              }
+            }
+          }
+        }
+      }
+    },
+    masks {
+      {
+        locations {
+          packed-int {
+            {
+              from 5,
+              to 20,
+              id local str "Query_2"
+            }
+          }
+        },
+        frame notset
+      }
+    },
+    ka-blocks {
+      {
+        lambda { 322429245874507, 10, -15 },
+        k { 139801292049695, 10, -15 },
+        h { 436862255107731, 10, -15 },
+        gapped FALSE
+      },
+      {
+        lambda { 267, 10, -3 },
+        k { 41, 10, -3 },
+        h { 14, 10, -2 },
+        gapped TRUE
+      }
+    },
+    search-stats {
+      "Effective search space: 9254832",
+      "Effective search space used: 9254832",
+      "Length adjustment: 61"
+    }
+  }
+}