Pipeline
Namespace: AppliedFSharp
Functions and values
| Function or value | Description |
blastPrimerPairs(...)
Signature: blastContext:(type) -> dbPath:string -> queryFastaPath:string -> blastResultOutputPath:string -> cleanedBlastResultOutputPath:string -> unit
|
Blast all generated primer pairs against the previously generated database. results are written to a file of choice. |
generatePrimerPairs(...)
Signature: length:int -> templateSpan:int -> item:(type) -> (type) []
|
Generates all possible primer pairs of lenght n flanking a sequence of length m from an input gene |
getResultFrame(...)
Signature: intaRNAContext:(type) -> cleanedBlastResultPath:string -> fastaHeaderConverter:(string -> string) -> queries:(type) [] -> (type)
|
Calculates hybridization energy features for the given blast results |
preparePrimerBlastSearch(...)
Signature: blastContext:(type) -> dbPath:string -> queryFastaOutputPath:string -> queries:(type) [] -> unit
|
Prepare a blast database for subsequent blast searches. For best feature calculation, use the full cDNA transcriptome of the organism |
