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Add DSL for fasterq-dump in SRATools BioContainer API
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| Original file line number | Diff line number | Diff line change |
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| @@ -1 +1,212 @@ | ||
| namespace BioFSharp.BioContainers | ||
| namespace BioFSharp.BioContainers | ||
| open BioContainer | ||
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| module SRATools = | ||
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| //type PrefetchParams = | ||
| // |Placeholder | ||
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| // static member makeCmd = function | ||
| // |Placeholder -> [""] | ||
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| // static member makeCmdWith (m:MountInfo) = function | ||
| // |Placeholder -> [""] | ||
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| //let runPrefetchAsync (bcContext:BioContainer.BcContext) (opt:PrefetchParams list) = | ||
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| // let cmds = (opt |> List.map (PrefetchParams.makeCmdWith bcContext.Mount)) | ||
| // let tp = "prefetch"::(cmds |> List.concat) | ||
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| // printfn "Starting process prefetch\r\nparameters:" | ||
| // cmds |> List.iter (fun op -> printfn "\t%s" (String.concat " " op)) | ||
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| // async { | ||
| // let! res = BioContainer.execAsync bcContext tp | ||
| // return res | ||
| // } | ||
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| type SplitOptions = | ||
| ///Split spots into reads | ||
| |SplitSpot | ||
| ///Write reads into different files | ||
| |SplitFiles | ||
| ///Writes single reads into special file | ||
| |Split3 | ||
| ///Writes whole spots into one file | ||
| |ConcatenateReads | ||
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| static member make = function | ||
| |SplitSpot -> "--split-spot" | ||
| |SplitFiles -> "--split-files" | ||
| |Split3 -> "--split-3" | ||
| |ConcatenateReads -> "--concatenate-read" | ||
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| //type FastQDumpParams = | ||
| // |Placeholder | ||
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| // static member makeCmd = function | ||
| // |Placeholder -> [""] | ||
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| // static member makeCmdWith (m:MountInfo) = function | ||
| // |Placeholder -> [""] | ||
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| //let runFastQDumpAsync (bcContext:BioContainer.BcContext) (opt:FastQDumpParams list) = | ||
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| // let cmds = (opt |> List.map (FastQDumpParams.makeCmdWith bcContext.Mount)) | ||
| // let tp = "fastq-dump"::(cmds |> List.concat) | ||
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| // printfn "Starting process fastq-dump\r\nparameters:" | ||
| // cmds |> List.iter (fun op -> printfn "\t%s" (String.concat " " op)) | ||
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| // async { | ||
| // let! res = BioContainer.execAsync bcContext tp | ||
| // return res | ||
| // } | ||
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| ///DSL for command line arguments for the fasterq-dump tool contained in the SRA Toolkit | ||
| type FasterQDumpParams = | ||
| ///full path of outputfile (overrides usage of current directory and given accession) | ||
| |OutFile of string | ||
| ///path for outputfile (overrides usage of current directory, but uses given accession) | ||
| |OutDirectory of string | ||
| ///path to directory for temp. files (dflt=current dir.) | ||
| |TempDirectory of string | ||
| //size of file-buffer (dflt=1MB) | ||
| |BufferSize of string | ||
| ///Determine how to handle paired reads | ||
| |Split of SplitOptions | ||
| ///size of cursor-cache (dflt=10MB, takes number or number and unit) | ||
| |CursorCacheSize of string | ||
| ///memory limit for sorting (dflt=100MB, takes number or number and unit) | ||
| |SortingMemoryLimit of string | ||
| ///how many threads to use (dflt=6) | ||
| |Threads of int | ||
| ///show progress (not possible if stdout used) | ||
| |ShowProgress | ||
| ///print details of all options selected | ||
| |PrintDetails | ||
| ///print output to stdout | ||
| |StdOut | ||
| //force overwrite of existing file(s) | ||
| |Force | ||
| ///use rowid as name (avoids using the name column) | ||
| |RowIdAsName | ||
| ///skip technical reads | ||
| |SkipTechnical | ||
| ///explicitly include technical reads | ||
| |IncludeTechnical | ||
| ///include read-number in defline | ||
| |PrintReadNumber | ||
| ///filter by sequence-lenght | ||
| |MinReadLength of int | ||
| ///which seq-table to use in case of pacbio | ||
| |PacBioTableName of string | ||
| ///terminate on invalid read | ||
| |Strict | ||
| ///filter output by matching against given bases | ||
| |FilterBases of string | ||
| ///append to output-file, instead of overwriting it | ||
| |AppendOutput | ||
| ///path to ngc file | ||
| |NGCFilePath of string | ||
| ///path to permission file | ||
| |PermissionFilePath of string | ||
| ///location in cloud | ||
| |CloudLocation of string | ||
| //path to cart file | ||
| |CartPath of string | ||
| ///disable multithreading | ||
| |DisableMultiThreading | ||
| //Display the version of the program | ||
| |Version | ||
| //Logging level as number or enum string. One of (fatal|sys|int|err|warn|info|debug) or (0-6) Current/default is warn | ||
| |LogLevel of string | ||
| ///Read more options and parameters from the file. | ||
| |OptionFilePath of string | ||
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| static member makeCmd = function | ||
| |OutFile o -> ["-o"; o] | ||
| |OutDirectory o -> ["-O"; o] | ||
| |TempDirectory t -> ["-t"; t] | ||
| |NGCFilePath n -> ["--ngc"; n] | ||
| |PermissionFilePath p -> ["--perm"; p] | ||
| |CartPath c -> ["--cart"; c] | ||
| |OptionFilePath o -> ["option-file"; o] | ||
| |Split so -> [SplitOptions.make so] | ||
| |Threads t -> ["-e"; string t] | ||
| |MinReadLength l -> ["-M"; string l] | ||
| |FilterBases b -> ["-B"; b] | ||
| |BufferSize b -> ["-b"; b] | ||
| |CursorCacheSize c -> ["-c"; c] | ||
| |SortingMemoryLimit m -> ["-m"; m] | ||
| |ShowProgress -> ["-p"] | ||
| |PrintDetails -> ["-x"] | ||
| |StdOut -> ["-Z"] | ||
| |Force -> ["-f"] | ||
| |RowIdAsName -> ["-N"] | ||
| |PrintReadNumber -> ["-P"] | ||
| |AppendOutput -> ["-A"] | ||
| |Version -> ["-V"] | ||
| |LogLevel l -> ["-L"; l] | ||
| |SkipTechnical -> ["--skip-technical"] | ||
| |IncludeTechnical -> ["--include-technical"] | ||
| |PacBioTableName t -> ["--table"; t] | ||
| |Strict -> ["--strict"] | ||
| |CloudLocation c -> ["--location"; c] | ||
| |DisableMultiThreading -> ["--disable-multithreading"] | ||
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| static member makeCmdWith (m:MountInfo) = function | ||
| |OutFile o -> ["-o"; MountInfo.containerPathOf m o] | ||
| |OutDirectory o -> ["-O"; MountInfo.containerPathOf m o] | ||
| |TempDirectory t -> ["-t"; MountInfo.containerPathOf m t] | ||
| |NGCFilePath n -> ["--ngc" ; MountInfo.containerPathOf m n] | ||
| |PermissionFilePath p -> ["--perm" ; MountInfo.containerPathOf m p] | ||
| |CartPath c -> ["--cart" ; MountInfo.containerPathOf m c] | ||
| |OptionFilePath o -> ["option-file"; MountInfo.containerPathOf m o] | ||
| |Split so -> [SplitOptions.make so] | ||
| |Threads t -> ["-e"; string t] | ||
| |MinReadLength l -> ["-M"; string l] | ||
| |FilterBases b -> ["-B"; b] | ||
| |BufferSize b -> ["-b"; b] | ||
| |CursorCacheSize c -> ["-c"; c] | ||
| |SortingMemoryLimit m -> ["-m"; m] | ||
| |ShowProgress -> ["-p"] | ||
| |PrintDetails -> ["-x"] | ||
| |StdOut -> ["-Z"] | ||
| |Force -> ["-f"] | ||
| |RowIdAsName -> ["-N"] | ||
| |PrintReadNumber -> ["-P"] | ||
| |AppendOutput -> ["-A"] | ||
| |Version -> ["-V"] | ||
| |LogLevel l -> ["-L"; l] | ||
| |SkipTechnical -> ["--skip-technical"] | ||
| |IncludeTechnical -> ["--include-technical"] | ||
| |PacBioTableName t -> ["--table"; t] | ||
| |Strict -> ["--strict"] | ||
| |CloudLocation c -> ["--location"; c] | ||
| |DisableMultiThreading -> ["--disable-multithreading"] | ||
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| let runFasterQDumpAsync (bcContext:BioContainer.BcContext) (opt:FasterQDumpParams list) (accession:string) = | ||
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| let cmds = (opt |> List.map (FasterQDumpParams.makeCmdWith bcContext.Mount)) | ||
| let tp = "fasterq-dump"::(cmds |> List.concat)@[accession] | ||
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| printfn "Starting process fasterq-dump\r\nparameters:" | ||
| cmds |> List.iter (fun op -> printfn "\t%s" (String.concat " " op)) | ||
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| async { | ||
| let! res = BioContainer.execAsync bcContext tp | ||
| return res | ||
| } | ||
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| let runFasterQDump (bcContext:BioContainer.BcContext) (opt:FasterQDumpParams list) (accession:string) = | ||
| runFasterQDumpAsync bcContext opt accession | ||
| |> Async.RunSynchronously |