blast

package
v1.0.4 Latest Latest
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 Go to latest Published: Apr 27, 2021 License: Apache-2.0 Imports: 6 Imported by: 0

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Constants

This section is empty.

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
}

func (*BlastN) NKeys 

func (b *BlastN) NKeys() int

func (*BlastN) SetFormat 

func (b *BlastN) SetFormat(f field.Format)

func (*BlastN) SetOut 

func (b *BlastN) SetOut(out string)

func (*BlastN) SetQuery 

func (b *BlastN) SetQuery(q string)

func (*BlastN) ToCLI 

func (b *BlastN) ToCLI() *exec.Cmd

func (*BlastN) Tool 

func (b *BlastN) Tool() Tool

func (*BlastN) UnmarshalJSONObject 

func (b *BlastN) UnmarshalJSONObject(dec *gojay.Decoder, key string) error

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
}

func (*BlastP) NKeys 

func (b *BlastP) NKeys() int

func (*BlastP) SetFormat 

func (b *BlastP) SetFormat(f field.Format)

func (*BlastP) SetOut 

func (b *BlastP) SetOut(out string)

func (*BlastP) SetQuery 

func (b *BlastP) SetQuery(q string)

func (*BlastP) ToCLI 

func (b *BlastP) ToCLI() *exec.Cmd

func (*BlastP) Tool 

func (b *BlastP) Tool() Tool

func (*BlastP) UnmarshalJSONObject 

func (b *BlastP) UnmarshalJSONObject(dec *gojay.Decoder, key string) error

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
}

func (*BlastX) NKeys 

func (b *BlastX) NKeys() int

func (*BlastX) SetFormat 

func (b *BlastX) SetFormat(f field.Format)

func (*BlastX) SetOut 

func (b *BlastX) SetOut(out string)

func (*BlastX) SetQuery 

func (b *BlastX) SetQuery(q string)

func (*BlastX) ToCLI 

func (b *BlastX) ToCLI() *exec.Cmd

func (*BlastX) Tool 

func (b *BlastX) Tool() Tool

func (*BlastX) UnmarshalJSONObject 

func (b *BlastX) UnmarshalJSONObject(dec *gojay.Decoder, key string) error

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) SetFormat 

func (b *DeltaBlast) SetFormat(f field.Format)

func (*DeltaBlast) SetOut 

func (b *DeltaBlast) SetOut(out string)

func (*DeltaBlast) SetQuery 

func (b *DeltaBlast) SetQuery(q string)

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
}

func (*PSIBlast) NKeys 

func (p *PSIBlast) NKeys() int

func (*PSIBlast) SetFormat 

func (b *PSIBlast) SetFormat(f field.Format)

func (*PSIBlast) SetOut 

func (b *PSIBlast) SetOut(out string)

func (*PSIBlast) SetQuery 

func (b *PSIBlast) SetQuery(q string)

func (*PSIBlast) ToCLI 

func (p *PSIBlast) ToCLI() *exec.Cmd

func (*PSIBlast) Tool 

func (*PSIBlast) Tool() Tool

func (*PSIBlast) UnmarshalJSONObject 

func (p *PSIBlast) UnmarshalJSONObject(dec *gojay.Decoder, key string) error

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
}

func (*RPSBlast) NKeys 

func (r *RPSBlast) NKeys() int

func (*RPSBlast) SetFormat 

func (b *RPSBlast) SetFormat(f field.Format)

func (*RPSBlast) SetOut 

func (b *RPSBlast) SetOut(out string)

func (*RPSBlast) SetQuery 

func (b *RPSBlast) SetQuery(q string)

func (*RPSBlast) ToCLI 

func (r *RPSBlast) ToCLI() *exec.Cmd

func (*RPSBlast) Tool 

func (*RPSBlast) Tool() Tool

func (*RPSBlast) UnmarshalJSONObject 

func (r *RPSBlast) UnmarshalJSONObject(dec *gojay.Decoder, key string) error

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) SetFormat 

func (b *RPSTBlastN) SetFormat(f field.Format)

func (*RPSTBlastN) SetOut 

func (b *RPSTBlastN) SetOut(out string)

func (*RPSTBlastN) SetQuery 

func (b *RPSTBlastN) SetQuery(q string)

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
}

func (*TBlastN) NKeys 

func (t *TBlastN) NKeys() int

func (*TBlastN) SetFormat 

func (b *TBlastN) SetFormat(f field.Format)

func (*TBlastN) SetOut 

func (b *TBlastN) SetOut(out string)

func (*TBlastN) SetQuery 

func (b *TBlastN) SetQuery(q string)

func (*TBlastN) ToCLI 

func (t *TBlastN) ToCLI() *exec.Cmd

func (*TBlastN) Tool 

func (*TBlastN) Tool() Tool

func (*TBlastN) UnmarshalJSONObject 

func (t *TBlastN) UnmarshalJSONObject(dec *gojay.Decoder, key string) error

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
}

func (*TBlastX) NKeys 

func (t *TBlastX) NKeys() int

func (*TBlastX) SetFormat 

func (b *TBlastX) SetFormat(f field.Format)

func (*TBlastX) SetOut 

func (b *TBlastX) SetOut(out string)

func (*TBlastX) SetQuery 

func (b *TBlastX) SetQuery(q string)

func (*TBlastX) ToCLI 

func (t *TBlastX) ToCLI() *exec.Cmd

func (*TBlastX) Tool 

func (*TBlastX) Tool() Tool

func (*TBlastX) UnmarshalJSONObject 

func (t *TBlastX) UnmarshalJSONObject(dec *gojay.Decoder, key string) error

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"
)

func (Tool) String 

func (t Tool) String() string

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