MakeBlastDbParams (BioFSharp) | BioFSharp

MakeBlastDbParams Type

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

DSL for command line arguments for the NCBI makeblastdb tool

Union cases

Union case	Description
`DbType DbType` Full Usage: `DbType DbType` Parameters: Item : `DbType`	Molecule type of input, values can be nucl or prot Item : `DbType`
`HashIndex` Full Usage: `HashIndex`	Create index of sequence hash values
`Input string` Full Usage: `Input string` Parameters: Item : `string`	Input file/database name Item : `string`
`InputType MakeBlastDBInputType` Full Usage: `InputType MakeBlastDBInputType` Parameters: Item : `MakeBlastDBInputType`	Input file type for makeblastdb Item : `MakeBlastDBInputType`
`Logfile string` Full Usage: `Logfile string` Parameters: Item : `string`	Program log file (default is stderr). Item : `string`
`MaskData string list` Full Usage: `MaskData string list` Parameters: Item : `string list`	Comma-separated list of input files containing masking data as produced by NCBI masking applications (e.g. dustmasker, segmasker, windowmasker Item : `string list`
`MaxFileSize string` Full Usage: `MaxFileSize string` Parameters: Item : `string`	Maximum file size to use for BLAST database. 4GB is the maximum supported by the database structure Item : `string`
`Output string` Full Usage: `Output string` Parameters: Item : `string`	Name of BLAST database to be created. Input file name is used if none provided. This field is required if input consists of multiple files Item : `string`
`ParseSeqIds` Full Usage: `ParseSeqIds`	Parse bar delimited sequence identifiers (e.g., gi\|129295) in FASTA input
`TaxId int` Full Usage: `TaxId int` Parameters: Item : `int`	Taxonomy ID to assign to all sequences. Item : `int`
`TaxIdMapFile string` Full Usage: `TaxIdMapFile string` Parameters: Item : `string`	File with two columns mapping sequence ID to the taxonomy ID. The first column is the sequence ID represented as one of: 1 fasta with accessions (e.g., emb\|X17276.1\|) 2 fasta with GI (e.g., gi\|4) 3 GI as a bare number (e.g., 4) 4 A local ID. The local ID must be prefixed with "lcl" (e.g., lcl\|4). The second column should be the NCBI taxonomy ID (e.g., 9606 for human). Item : `string`
`Title string` Full Usage: `Title string` Parameters: Item : `string`	Title for BLAST database. If not set, the input file name will be used Item : `string`

Static members

Static member	Description
`MakeBlastDbParams.makeCmd` Full Usage: `MakeBlastDbParams.makeCmd` Returns: `MakeBlastDbParams -> string list`	returns the string form of command line argument DSL for makeblastdb Returns: `MakeBlastDbParams -> string list`
`MakeBlastDbParams.makeCmdWith m` Full Usage: `MakeBlastDbParams.makeCmdWith m` Parameters: m : `MountInfo` Returns: `MakeBlastDbParams -> string list`	returns the string form of command line argument DSL for makeblastdb with paths adjusted for container localization m : `MountInfo` Returns: `MakeBlastDbParams -> string list`