sequenceserver 1.1.0.beta12 → 2.0.0.beta1

data/spec/protein_query.fa

@@ -1,21 +0,0 @@
-ATGAATACCCTCTGGCTCTCTTTATGGGATTATCCCGGTAAGCTTCCCTTAAACTTCATG
-GTGTTTGACACGAAGGATGATCTGCAAGCAGCGTATTGGAGAGATCCTTACAGCATACCT
-CTGGCAGTTATCTTCGAGGACCCCCAACCGATATCACAGCGACTTATATATGAAATTAGG
-ACGAATCCTTCATACACTTTGCCGCCACCGCCAACCAAATTGTATTCTGCTCCGATCAGT
-TGTCGAAAGAATAAAACTGGTCACTGGATGGACGACATTTTATCGATAAAAACCGGTGAA
-TCTTGTCCCGTTAACAATTACTTGCATTCTGGCTTCTTGGCTCTGCAAATGATAACGGAT
-ATCACAAAGATAAAATTGGAAAATTCTGACGTGACAATACCGGATATTAAACTCATAATG
-TTTCCTAAAGAGCCGTATACCGCTGACTGGATGCTGGCCTTCAGAGTTGTTATTCCGCTT
-TACATGGTCTTGGCTCTCTCGCAATTTATCACTTATCTTCTGATCCTAATAGTTGGCGAG
-AAGGAAAATAAGATTAAAGAGGGAATGAAGATGATGGGCTTAAATGATTCTGTGTTT
->SI2.2.0_13722 Si_gnF.scaffold06207[1925625..1928536].pep_1
-ATGTCCGCGAATCGATTGAACGTGCTGGTGACCCTGATGCTCGCCGTCGCGCTTCTTGTG
-ACGGAATCAGGAAATGCACAGGTGGATGGCTATCTCCAATTCAACCCAAAGCGATCCGCC
-GTGAGCTCGCCGCAGAAGTATTGCGGCAAAAAGCTTTCTAATGCTCTACAGATAATCTGT
-GATGGCGTGTACAATTCCATGTTTAAGAAGAGTGGTCAAGATTTTCCCCCGCAAAATAAG
-AGACACATAGCACACAGAATAAATGGGAATGAGGAAGAGAGCTTTACTACGTTAAAGTCG
-AATTTTTTAAACTGGTGTGTTGAAGTTTATCATCGTCACTACAGATTCGTTTTTGTTTCA
-GAGATGGAAATGGCCGATTACCCGCTCGCCTATGATATTTCCCCGTATCTTCCGCCGTTC
-CTGTCGCGAGCGAGGGCACGGGGAATGTTAGACGGTCGCTTCGCCGGCAGACGCTACCGA
-AGGGAGTCGCGGGGCATTCACGAGGAGTGTTGCATCAACGGATGTACGATAAACGAATTG
-ACCAGCTACTGCGGCCCC

data/spec/sample_reports/blastn_sample/job.yaml

@@ -1,10 +0,0 @@
---- !ruby/object:SequenceServer::BLAST::Job
-id: blastn_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/blastn_sample/stdout

@@ -1,144 +0,0 @@
-Blast4-archive ::= {
-  request {
-    ident "2.2.30+",
-    body queue-search {
-      program "blastn",
-      service "megablast",
-      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 544,
-              seq-data ncbi2na 'C6298086D9826EB37C0E98A3C6080E8218765A03368213
-A79AC4AAD060E0B6108A80C5808E76AF0888D09A23F480E7630350B60D6863D2403C822D821E65
-100F7CF66E1BF766D83ED802FF0619B50BD021F6898204D3F40340EBF7508D4A052624CB679B50
-88860D019A0C62019BA08A23D2682363D8F0A08CF61884F82649060C2213628410E503'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 146351625
-        }
-      }
-    }
-  },
-  results {
-    alignments {
-      {
-        type partial,
-        dim 2,
-        score {
-          {
-            id str "score",
-            value int 544
-          },
-          {
-            id str "e_value",
-            value real { 0, 10, 0 }
-          },
-          {
-            id str "bit_score",
-            value real { 100569770510552, 10, -11 }
-          },
-          {
-            id str "num_ident",
-            value int 544
-          },
-          {
-            id str "hsp_percent_coverage",
-            value real { 1, 10, 2 }
-          }
-        },
-        segs denseg {
-          dim 2,
-          numseg 1,
-          ids {
-            local str "Query_1",
-            local str "SI2.2.0_08256"
-          },
-          starts {
-            0,
-            480
-          },
-          lens {
-            544
-          },
-          strands {
-            plus,
-            plus
-          }
-        }
-      }
-    },
-    masks {
-    },
-    ka-blocks {
-      {
-        lambda { 133270576282382, 10, -14 },
-        k { 620991117264207, 10, -15 },
-        h { 112409184650115, 10, -14 },
-        gapped FALSE
-      },
-      {
-        lambda { 128, 10, -2 },
-        k { 46, 10, -2 },
-        h { 85, 10, -2 },
-        gapped TRUE
-      }
-    },
-    search-stats {
-      "Effective search space: 146351625",
-      "Effective search space used: 146351625",
-      "Length adjustment: 19"
-    }
-  }
-}

data/spec/sample_reports/blastp_sample/job.yaml

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

@@ -1,1187 +0,0 @@
-Blast4-archive ::= {
-  request {
-    ident "2.2.30+",
-    body queue-search {
-      program "blastp",
-      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 "../database/sample/proteins/Solenopsis_invicta/Sinvi
-cta2-2-3.prot.subset.fasta",
-      algorithm-options {
-        {
-          name "EvalueThreshold",
-          value cutoff e-value { 1, 10, 1 }
-        },
-        {
-          name "MaskAtHash",
-          value boolean FALSE
-        },
-        {
-          name "SegFiltering",
-          value boolean FALSE
-        },
-        {
-          name "WordThreshold",
-          value integer 11
-        },
-        {
-          name "WindowSize",
-          value integer 40
-        },
-        {
-          name "HitlistSize",
-          value integer 500
-        },
-        {
-          name "UngappedMode",
-          value boolean FALSE
-        },
-        {
-          name "CompositionBasedStats",
-          value integer 2
-        },
-        {
-          name "SmithWatermanMode",
-          value boolean FALSE
-        },
-        {
-          name "EffectiveSearchSpace",
-          value big-integer 26094545
-        }
-      }
-    }
-  },
-  results {
-    alignments {
-      {
-        type partial,
-        dim 2,
-        score {
-          {
-            id str "score",
-            value int 1046
-          },
-          {
-            id str "e_value",
-            value real { 260530337228793, 10, -161 }
-          },
-          {
-            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 denseg {
-          dim 2,
-          numseg 1,
-          ids {
-            local str "Query_1",
-            local str "SI2.2.0_06267"
-          },
-          starts {
-            0,
-            0
-          },
-          lens {
-            199
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