sequenceserver 1.1.0.beta12 → 2.0.0.beta1

data/spec/sample_reports/with_hits_sample/job.yaml

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

@@ -1,1489 +0,0 @@
-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 ">Query 1"
-                  }
-                }
-              },
-              title "Query 1"
-            },
-            inst {
-              repr raw,
-              mol na,
-              length 642,
-              seq-data ncbi2na '33F7403C6C883318B037B103FF9C4E401C03D2FFCC0318
-C0470E1CB0735C4BB4C8180C3CC12F3FF20F41983CC42334E1DC8CCF714516DFF5F3CFE2FB3FFF
-F503CC432FBF40A0CCCFB32FFEC3E190FC08FD333FFE00331C4CE1F83C8F130FF30FFFFFFF08FC
-00CF1C3EAFFFEB30BFFD3E0493F0E5BFF17BFF802B0FF7F233312FEC33CACFF3012EECCFDF10CC
-02110F901C938FB010F9C068D0CC0F00FB0CF0B340'H
-            }
-          },
-          seq {
-            id {
-              local str "Query_2"
-            },
-            descr {
-              user {
-                type str "CFastaReader",
-                data {
-                  {
-                    label str "DefLine",
-                    data str ">Query_2"
-                  }
-                }
-              },
-              title "Query_2"
-            },
-            inst {
-              repr raw,
-              mol na,
-              length 600,
-              seq-data ncbi2na '058C3FF3F3EF4FBFBDFCFFBCFEC0C380C7807CE48C0C7A
-02D08193DCE043F0C9FC04430D20C521D1124DF1FCFC40D13F378FD808FCCFDCE0F70808FB1BFF
-032230901BDF1C3031823000F313332F7CB1031030F74E7DC30A808C44EE2B058FD3E0FFC1F31C
-CC5DD1F3D32CC0707EF5CC64B2F0E22B87BC60FFD319ECECF4BD709789013ED892106F2B04F18E
-F813B866114BD037E7FF'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 "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 172525599
-        }
-      },
-      program-options {
-        {
-          name "LCaseMask",
-          value query-mask {
-            locations {
-              packed-int {
-                {
-                  from 241,
-                  to 249,
-                  id local str "Query_1"
-                },
-                {
-                  from 241,
-                  to 249,
-                  id local str "Query_1"
-                },
-                {
-                  from 382,
-                  to 479,
-                  id local str "Query_1"
-                },
-                {
-                  from 382,
-                  to 479,
-                  id local str "Query_1"
-                }
-              }
-            },
-            frame plus1
-          }
-        },
-        {
-          name "LCaseMask",
-          value query-mask {
-            locations {
-              packed-int {
-                {
-                  from 8,
-                  to 52,
-                  id local str "Query_2"
-                },
-                {
-                  from 8,
-                  to 52,
-                  id local str "Query_2"
-                }
-              }
-            },
-            frame plus1
-          }
-        }
-      }
-    }
-  },
-  results {
-    alignments {
-      {
-        type partial,
-        dim 2,
-        score {
-          {
-            id str "score",
-            value int 34
-          },
-          {
-            id str "e_value",
-            value real { 417714604974915, 10, -16 }
-          },
-          {
-            id str "bit_score",
-            value real { 319435738040471, 10, -13 }
-          },
-          {
-            id str "num_ident",
-            value int 23
-          },
-          {
-            id str "hsp_percent_coverage",
-            value real { 470560747663551, 10, -14 }
-          }
-        },
-        segs denseg {
-          dim 2,
-          numseg 1,
-          ids {
-            local str "Query_1",
-            local str "SI2.2.0_00883"
-          },
-          starts {
-            321,
-            145
-          },
-          lens {
-            27
-          },
-          strands {
-            plus,
-            plus
-          }
-        }
-      },
-      {
-        type partial,
-        dim 2,
-        score {
-          {
-            id str "score",
-            value int 32
-          },
-          {
-            id str "e_value",
-            value real { 145796722970315, 10, -15 }
-          },
-          {
-            id str "bit_score",
-            value real { 301402050029359, 10, -13 }
-          },
-          {
-            id str "num_ident",
-            value int 19
-          },
-          {
-            id str "hsp_percent_coverage",
-            value real { 377102803738318, 10, -14 }
-          }
-        },
-        segs denseg {
-          dim 2,
-          numseg 1,
-          ids {
-            local str "Query_1",
-            local str "SI2.2.0_04990"
-          },
-          starts {
-            362,
-            401
-          },
-          lens {
-            21
-          },
-          strands {
-            plus,
-            plus
-          }
-        }
-      },
-      {
-        type partial,
-        dim 2,
-        score {
-          {
-            id str "score",
-            value int 32
-          },
-          {
-            id str "e_value",
-            value real { 145796722970315, 10, -15 }
-          },
-          {
-            id str "bit_score",
-            value real { 301402050029359, 10, -13 }
-          },
-          {
-            id str "num_ident",
-            value int 19
-          },
-          {
-            id str "hsp_percent_coverage",
-            value real { 377102803738318, 10, -14 }
-          }
-        },
-        segs denseg {
-          dim 2,
-          numseg 1,
-          ids {
-            local str "Query_1",
-            local str "SI2.2.0_05000"
-          },
-          starts {
-            38,
-            562
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-          lens {
-            21
-          },
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-      },
-      {
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-        dim 2,
-        score {
-          {
-            id str "score",
-            value int 28
-          },
-          {
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-            value real { 177616769707622, 10, -14 }
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-            value int 17
-          },
-          {
-            id str "hsp_percent_coverage",
-            value real { 34595015576324, 10, -13 }
-          }
-        },
-        segs denseg {
-          dim 2,
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-          ids {
-            local str "Query_1",
-            local str "SI2.2.0_07659"
-          },
-          starts {
-            316,
-            571
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-          lens {
-            19
-          },
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-      {
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-            value int 14
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-          {
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-            value real { 268068535825545, 10, -14 }
-          }
-        },
-        segs denseg {
-          dim 2,
-          numseg 1,
-          ids {
-            local str "Query_1",
-            local str "SI2.2.0_00941"
-          },
-          starts {
-            371,
-            620
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-            value real { 314797507788162, 10, -14 }
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