Documentation ¶
Index ¶
- type BlastConfig
- type BlastFormatter
- type BlastN
- type BlastP
- type BlastX
- type DeltaBlast
- func (d *DeltaBlast) NKeys() int
- func (b *DeltaBlast) SetFormat(f field.Format)
- func (b *DeltaBlast) SetOut(out string)
- func (b *DeltaBlast) SetQuery(q string)
- func (d *DeltaBlast) ToCLI() *exec.Cmd
- func (d *DeltaBlast) Tool() Tool
- func (d *DeltaBlast) UnmarshalJSONObject(dec *gojay.Decoder, key string) error
- type PSIBlast
- type RPSBlast
- type RPSTBlastN
- func (r *RPSTBlastN) NKeys() int
- func (b *RPSTBlastN) SetFormat(f field.Format)
- func (b *RPSTBlastN) SetOut(out string)
- func (b *RPSTBlastN) SetQuery(q string)
- func (r *RPSTBlastN) ToCLI() *exec.Cmd
- func (*RPSTBlastN) Tool() Tool
- func (r *RPSTBlastN) UnmarshalJSONObject(dec *gojay.Decoder, key string) error
- type TBlastN
- type TBlastX
- type Tool
Constants ¶
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Variables ¶
This section is empty.
Functions ¶
This section is empty.
Types ¶
type BlastConfig ¶
type BlastConfig interface { cli.CommandSerializable Tool() Tool SetQuery(query string) SetFormat(fmt field.Format) SetOut(out string) }
func DecodeConfig ¶
func DecodeConfig(tool Tool, b []byte) (BlastConfig, error)
type BlastFormatter ¶
type BlastFormatter struct { ShortHelp field.ShortHelp LongHelp field.LongHelp Version field.Version RequestID field.RequestID ArchiveFile field.ArchiveFile Format field.Format ShowGIs field.ShowGIs NumDescriptions field.NumDescriptions NumAlignments field.NumAlignments LineLength field.LineLength HTML field.HTML HitSorting field.HitSorting HSPSorting field.HSPSorting MaxTargetSequences field.MaxTargetSequences OutFile field.OutFile ParseDefLines field.ParseDefLines }
func (*BlastFormatter) NKeys ¶
func (b *BlastFormatter) NKeys() int
func (*BlastFormatter) ToCLI ¶
func (b *BlastFormatter) ToCLI() *exec.Cmd
func (*BlastFormatter) UnmarshalJSONObject ¶
func (b *BlastFormatter) UnmarshalJSONObject(dec *gojay.Decoder, key string) error
type BlastN ¶
type BlastN struct { Strand field.Strand Task field.BlastNTask WordSize field.WordSize GapOpen field.GapOpen GapExtend field.GapExtend Penalty field.Penalty Reward field.Reward UseIndex field.UseIndex IndexName field.IndexName SubjectFile field.SubjectFile SubjectLocation field.SubjectLocation Dust field.Dust FilteringDB field.FilteringDB WindowMaskerTaxID field.WindowMaskerTaxID WindowMaskerDB field.WindowMaskerDB DBSoftMask field.DBSoftMask DBHardMask field.DBHardMask PercentIdentity field.PercentIdentity CullingLimit field.CullingLimit TemplateType field.TemplateType TemplateLength field.TemplateLength SumStats field.SumStats ExtensionDropoffPrelimGapped field.ExtensionDropoffPrelimGapped ExtensionDropoffFinalGapped field.ExtensionDropoffFinalGapped NonGreedy field.NonGreedy MinRawGappedScore field.MinRawGappedScore UngappedAlignmentsOnly field.UngappedAlignmentsOnly OffDiagonalRange field.OffDiagonalRange NumThreads field.ThreadCount // contains filtered or unexported fields }
type BlastP ¶
type BlastP struct { Task field.BlastPTask WordSize field.WordSize GapOpen field.GapOpen GapExtend field.GapExtend Matrix field.Matrix Threshold field.Threshold CompBasedStats field.FullCompBasedStats SubjectFile field.SubjectFile SubjectLocation field.SubjectLocation Seg field.Seg DBSoftMask field.DBSoftMask DBHardMask field.DBHardMask CullingLimit field.CullingLimit ExtensionDropoffPrelimGapped field.ExtensionDropoffPrelimGapped ExtensionDropoffFinalGapped field.ExtensionDropoffFinalGapped UngappedAlignmentsOnly field.UngappedAlignmentsOnly NumThreads field.ThreadCount UseSmithWatermanTraceback field.UseSmithWatermanTraceback // contains filtered or unexported fields }
type BlastX ¶
type BlastX struct { Strand field.Strand QueryGenCode field.QueryGenCode Task field.BlastXTask WordSize field.WordSize GapOpen field.GapOpen GapExtend field.GapExtend MaxIntronLength field.MaxIntronLength Matrix field.Matrix Threshold field.Threshold CompBasedStats field.FullCompBasedStats SubjectFile field.SubjectFile SubjectLocation field.SubjectLocation Seg field.Seg DBSoftMask field.DBSoftMask DBHardMask field.DBHardMask CullingLimit field.CullingLimit SumStats field.SumStats ExtensionDropoffPrelimGapped field.ExtensionDropoffPrelimGapped ExtensionDropoffFinalGapped field.ExtensionDropoffFinalGapped UngappedAlignmentsOnly field.UngappedAlignmentsOnly NumThreads field.ThreadCount UseSmithWatermanTraceback field.UseSmithWatermanTraceback // contains filtered or unexported fields }
type DeltaBlast ¶
type DeltaBlast struct { WordSize field.WordSize GapOpen field.GapOpen GapExtend field.GapExtend Matrix field.Matrix Threshold field.Threshold CompBasedStats field.ShortCompBasedStats SubjectFile field.SubjectFile SubjectLocation field.SubjectLocation Seg field.Seg CullingLimit field.CullingLimit SumStats field.SumStats ExtensionDropoffPrelimGapped field.ExtensionDropoffPrelimGapped ExtensionDropoffFinalGapped field.ExtensionDropoffFinalGapped GapTrigger field.GapTrigger NumThreads field.ThreadCount UseSmithWatermanTraceback field.UseSmithWatermanTraceback NumIterations field.NumIterations OutPSSMFile field.OutPSSMFile OutASCIIPSSMFile field.OutASCIIPSSMFile SavePSSMAfterLastRound field.SavePSSMAfterLastRound SaveEachPSSM field.SaveEachPSSM Pseudocount field.Pseudocount DomainInclusionEThreshold field.DomainInclusionEThreshold InclusionEThreshold field.InclusionEThreshold RPSDBFile field.RPSDBFile ShowDomainHits field.ShowDomainHits // contains filtered or unexported fields }
func (*DeltaBlast) NKeys ¶
func (d *DeltaBlast) NKeys() int
func (*DeltaBlast) ToCLI ¶
func (d *DeltaBlast) ToCLI() *exec.Cmd
func (*DeltaBlast) Tool ¶
func (d *DeltaBlast) Tool() Tool
func (*DeltaBlast) UnmarshalJSONObject ¶
func (d *DeltaBlast) UnmarshalJSONObject(dec *gojay.Decoder, key string) error
type PSIBlast ¶
type PSIBlast struct { WordSize field.WordSize GapOpen field.GapOpen GapExtend field.GapExtend Matrix field.Matrix Threshold field.Threshold CompBasedStats field.FullCompBasedStats SubjectFile field.SubjectFile SubjectLocation field.SubjectLocation Seg field.Seg CullingLimit field.CullingLimit SumStats field.SumStats ExtensionDropoffPrelimGapped field.ExtensionDropoffPrelimGapped ExtensionDropoffFinalGapped field.ExtensionDropoffFinalGapped GapTrigger field.GapTrigger NumThreads field.ThreadCount UseSmithWatermanTraceback field.UseSmithWatermanTraceback NumIterations field.NumIterations OutPSSMFile field.OutPSSMFile OutASCIIPSSMFile field.OutASCIIPSSMFile SavePSSMAfterLastRound field.SavePSSMAfterLastRound SaveEachPSSM field.SaveEachPSSM InMSAFile field.InMSAFile MSAMasterIDX field.MSAMasterIDX IgnoreMSAMaster field.IgnoreMSAMaster InPSSMFile field.InPSSMFile Pseudocount field.Pseudocount InclusionEThreshold field.InclusionEThreshold PhiPatternFile field.PhiPatternFile // contains filtered or unexported fields }
type RPSBlast ¶
type RPSBlast struct { CompBasedStats field.ShortCompBasedStats Seg field.Seg SumStats field.SumStats ExtensionDropoffPrelimGapped field.ExtensionDropoffPrelimGapped ExtensionDropoffFinalGapped field.ExtensionDropoffFinalGapped NumThreads field.ThreadMode MTMode field.MTMode UseSmithWatermanTraceback field.UseSmithWatermanTraceback // contains filtered or unexported fields }
type RPSTBlastN ¶
type RPSTBlastN struct { QueryGenCode field.QueryGenCode Strand field.Strand CompBasedStats field.ShortCompBasedStats Seg field.Seg SumStats field.SumStats ExtensionDropoffPrelimGapped field.ExtensionDropoffPrelimGapped ExtensionDropoffFinalGapped field.ExtensionDropoffFinalGapped UngappedAlignmentsOnly field.UngappedAlignmentsOnly NumThreads field.ThreadMode MTMode field.MTMode UseSmithWatermanTraceback field.UseSmithWatermanTraceback // contains filtered or unexported fields }
func (*RPSTBlastN) NKeys ¶
func (r *RPSTBlastN) NKeys() int
func (*RPSTBlastN) ToCLI ¶
func (r *RPSTBlastN) ToCLI() *exec.Cmd
func (*RPSTBlastN) Tool ¶
func (*RPSTBlastN) Tool() Tool
func (*RPSTBlastN) UnmarshalJSONObject ¶
func (r *RPSTBlastN) UnmarshalJSONObject(dec *gojay.Decoder, key string) error
type TBlastN ¶
type TBlastN struct { Task field.TBlastNTask WordSize field.WordSize GapOpen field.GapOpen GapExtend field.GapExtend DBGenCode field.DBGenCode MaxIntronLength field.MaxIntronLength Matrix field.Matrix Threshold field.Threshold CompBasedStats field.FullCompBasedStats SubjectFile field.SubjectFile SubjectLocation field.SubjectLocation Seg field.Seg DBSoftMask field.DBSoftMask DBHardMask field.DBHardMask CullingLimit field.CullingLimit SumStats field.SumStats ExtensionDropoffPrelimGapped field.ExtensionDropoffPrelimGapped ExtensionDropoffFinalGapped field.ExtensionDropoffFinalGapped UngappedAlignmentsOnly field.UngappedAlignmentsOnly NumThreads field.ThreadCount UseSmithWatermanTraceback field.UseSmithWatermanTraceback InPSSMFile field.InPSSMFile // contains filtered or unexported fields }
type TBlastX ¶
type TBlastX struct { Strand field.Strand QueryGenCode field.QueryGenCode WordSize field.WordSize MaxIntronLength field.MaxIntronLength Matrix field.Matrix Threshold field.Threshold DBGenCode field.DBGenCode SubjectFile field.SubjectFile SubjectLocation field.SubjectLocation Seg field.Seg DBSoftMask field.DBSoftMask DBHardMask field.DBHardMask CullingLimit field.CullingLimit SumStats field.SumStats NumThreads field.ThreadCount // contains filtered or unexported fields }
type Tool ¶
type Tool string
const ( ToolBlastN Tool = "blastn" ToolBlastP Tool = "blastp" ToolBlastX Tool = "blastx" ToolDeltaBlast Tool = "deltablast" ToolPSIBlast Tool = "psiblast" ToolRPSBlast Tool = "rpsblast" ToolRPSTBlastN Tool = "rpstblastn" ToolTBlastN Tool = "tblastn" ToolTBlastX Tool = "tblastx" ToolBlastFormatter Tool = "blast_formatter" )
Source Files ¶
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