BlastParams (BioFSharp)

BlastParams Type

Namespace: BioFSharp.BioContainers
Assembly: BioFSharp.BioContainers.dll
Parent Module: Blast
Base Type: obj
All Interfaces: IEquatable<BlastParams> , IStructuralEquatable

DSL for command line parameters that are common to all blast applications

Union cases

Union case	Description
`BestHitOverhang float` Full Usage: `BestHitOverhang float` Parameters: Item : `float`	Best Hit algorithm overhang value (recommended value: 0.1) Item : `float`
`BestHitScoreEdge float` Full Usage: `BestHitScoreEdge float` Parameters: Item : `float`	Best Hit algorithm score edge value (recommended value: 0.1) Item : `float`
`CullingLimit int` Full Usage: `CullingLimit int` Parameters: Item : `int`	Delete a hit that is enveloped by at least this many higher-scoring hits. Item : `int`
`DBSize int` Full Usage: `DBSize int` Parameters: Item : `int`	Effective size of the database Item : `int`
`EValue float` Full Usage: `EValue float` Parameters: Item : `float`	Expect value (E) for saving hits Item : `float`
`EntrezQuery string` Full Usage: `EntrezQuery string` Parameters: Item : `string`	Restrict search with the given Entrez query. Remote searches only. Item : `string`
`ExportSearchStrategy string` Full Usage: `ExportSearchStrategy string` Parameters: Item : `string`	Record search strategy to this file. Item : `string`
`GIList string` Full Usage: `GIList string` Parameters: Item : `string`	Restrict search of database to GI’s listed in this file. Local searches only. Item : `string`
`HTML` Full Usage: `HTML`	Produce HTML output
`ImportSearchStrategy string` Full Usage: `ImportSearchStrategy string` Parameters: Item : `string`	Search strategy file to read. Item : `string`
`MaxHSPs int` Full Usage: `MaxHSPs int` Parameters: Item : `int`	Maximum number of HSPs (alignments) to keep for any single query-subject pair. The HSPs shown will be the best as judged by expect value. This number should be an int that is one or greater. If this option is not set, BLAST shows all HSPs meeting the expect value criteria. Setting it to one will show only the best HSP for every query-subject pair Item : `int`
`MaxHits int` Full Usage: `MaxHits int` Parameters: Item : `int`	Item : `int`
`NegativeGIList string` Full Usage: `NegativeGIList string` Parameters: Item : `string`	Restrict search of database to everything except the GI’s listed in this file. Local searches only. Item : `string`
`NumAlignments int` Full Usage: `NumAlignments int` Parameters: Item : `int`	Show alignments for this number of database sequences. Item : `int`
`NumThreads int` Full Usage: `NumThreads int` Parameters: Item : `int`	Item : `int`
`Num_Descriptions int` Full Usage: `Num_Descriptions int` Parameters: Item : `int`	Show one-line descriptions for this number of database sequences. Item : `int`
`Output string` Full Usage: `Output string` Parameters: Item : `string`	Item : `string`
`OutputType OutputType` Full Usage: `OutputType OutputType` Parameters: Item : `OutputType`	Item : `OutputType`
`OutputTypeCustom(OutputType, OutputCustom seq)` Full Usage: `OutputTypeCustom(OutputType, OutputCustom seq)` Parameters: Item1 : `OutputType` Item2 : `OutputCustom seq`	Item1 : `OutputType` Item2 : `OutputCustom seq`
`ParseDeflines` Full Usage: `ParseDeflines`	Parse query and subject bar delimited sequence identifiers (e.g., gi\|129295).
`Query string` Full Usage: `Query string` Parameters: Item : `string`	Item : `string`
`QueryLocation int * int` Full Usage: `QueryLocation int * int` Parameters: Item : `int * int`	Location on the query sequence (Format: start-stop) Item : `int * int`
`Remote` Full Usage: `Remote`	Execute search on NCBI servers?
`SearchDB string` Full Usage: `SearchDB string` Parameters: Item : `string`	BLAST database name. Item : `string`
`SearchSpaceLength int` Full Usage: `SearchSpaceLength int` Parameters: Item : `int`	Effective length of the search space Item : `int`
`ShowGIs` Full Usage: `ShowGIs`	Show NCBI GIs in report.
`Subject string` Full Usage: `Subject string` Parameters: Item : `string`	File with subject sequence(s) to search. Item : `string`
`SubjectLocation int * int` Full Usage: `SubjectLocation int * int` Parameters: Item : `int * int`	Location on the subject sequence (Format: start-stop). Item : `int * int`

Static members

Static member Description

Static member	Description
`BlastParams.makeCmd` Full Usage: `BlastParams.makeCmd` Returns: `BlastParams -> string list`	Returns: `BlastParams -> string list`
`BlastParams.makeCmdWith m` Full Usage: `BlastParams.makeCmdWith m` Parameters: m : `MountInfo` Returns: `BlastParams -> string list`	m : `MountInfo` Returns: `BlastParams -> string list`


                
                  
                    
                      BlastParams.makeCmd

Full Usage: BlastParams.makeCmd

Returns: BlastParams -> string list

Returns: BlastParams -> string list


                
                  
                    
                      BlastParams.makeCmdWith m

Full Usage: BlastParams.makeCmdWith m

Parameters:

m : MountInfo

Returns: BlastParams -> string list

m : MountInfo

Returns: BlastParams -> string list