-
Notifications
You must be signed in to change notification settings - Fork 32
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Add thin (incomplete) LastAlign BioContainer API
- Loading branch information
Showing
3 changed files
with
339 additions
and
3 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,294 @@ | ||
| namespace BioFSharp.BioTools | ||
|
|
||
| ///!! Currently many parameters are not implemented! | ||
| /// | ||
| ///From the Last docs at http://last.cbrc.jp: | ||
| /// | ||
| ///LAST finds similar regions between sequences. | ||
| /// | ||
| ///LAST can: | ||
| /// | ||
| ///Handle big sequence data, e.g: | ||
| /// | ||
| /// - Compare two vertebrate genomes | ||
| /// | ||
| /// - Align billions of DNA reads to a genome | ||
| /// | ||
| ///Indicate the reliability of each aligned column. | ||
| /// | ||
| ///Use sequence quality data properly. | ||
| /// | ||
| ///Compare DNA to proteins, with frameshifts. | ||
| /// | ||
| ///Compare PSSMs to sequences | ||
| /// | ||
| ///Calculate the likelihood of chance similarities between random sequences. | ||
| /// | ||
| ///Do split and spliced alignment. | ||
| /// | ||
| ///Train alignment parameters for unusual kinds of sequence (e.g. nanopore). | ||
| //TO-DO: Full Parameter support | ||
|
|
||
| module LastAlign = | ||
|
|
||
| open BioContainer | ||
|
|
||
| //Usage: lastdb [options] output-name fasta-sequence-file(s) | ||
| //Prepare sequences for subsequent alignment with lastal. | ||
|
|
||
| //Main Options: | ||
| //-h, --help: show all options and their default settings, and exit | ||
| //-p: interpret the sequences as proteins | ||
| //-R: repeat-marking options (default=10) | ||
| //-c: soft-mask lowercase letters (in reference *and* query sequences) | ||
| //-u: seeding scheme (default: YASS for DNA, else exact-match seeds) | ||
|
|
||
| //Advanced Options (default settings): | ||
| //-w: use initial matches starting at every w-th position in each sequence (1) | ||
| //-W: use "minimum" positions in sliding windows of W consecutive positions (1) | ||
| //-S: strand: 0=reverse, 1=forward, 2=both (1) | ||
| //-s: volume size (unlimited) | ||
| //-Q: input format: 0=fasta or fastq-ignore, | ||
| // 1=fastq-sanger, 2=fastq-solexa, 3=fastq-illumina (fasta) | ||
| //-P: number of parallel threads (1) | ||
| //-m: seed pattern | ||
| //-a: user-defined alphabet | ||
| //-i: minimum limit on initial matches per query position (0) | ||
| //-b: bucket depth | ||
| //-C: child table type: 0=none, 1=byte-size, 2=short-size, 3=full (0) | ||
| //-x: just count sequences and letters | ||
| //-v: be verbose: write messages about what lastdb is doing | ||
| //-V, --version: show version information, and exit | ||
|
|
||
| type SeedingSchemeOptions = | ||
| | YASS | ||
| | ExactMatch | ||
|
|
||
| static member make = | ||
| function | ||
| | YASS -> ["-u";"YASS"] | ||
| | ExactMatch -> ["-u";"exact-match"] | ||
|
|
||
| type InputOptions = | ||
| |Single of string | ||
| |Multiple of string list | ||
|
|
||
| static member make = | ||
| function | ||
| |Single f -> [f] | ||
| |Multiple fl -> fl | ||
|
|
||
| static member makeWith (m:MountInfo) = | ||
| let cPath p = (MountInfo.containerPathOf m p) | ||
| function | ||
| |Single f -> [cPath f] | ||
| |Multiple fl -> fl |> List.map cPath | ||
|
|
||
| type LastDBParams = | ||
| |Input of InputOptions | ||
| |OutputName of string | ||
| ///-p: interpret the sequences as proteins | ||
| |InputAsProteins | ||
| ///-R: repeat-marking options (default=10) | ||
| |RepeatMarking of int | ||
| ///-c: soft-mask lowercase letters (in reference *and* query sequence | ||
| |LowercaseSoftMasking | ||
| ///-u: seeding scheme (default: YASS for DNA, else exact-match seeds) | ||
| |SeedingScheme of SeedingSchemeOptions | ||
|
|
||
| static member make = | ||
| function | ||
| |Input i -> InputOptions.make i | ||
| |OutputName f -> [f] | ||
| |InputAsProteins -> ["-p"] | ||
| |RepeatMarking rm -> ["-R";string rm] | ||
| |LowercaseSoftMasking -> ["-c"] | ||
| |SeedingScheme sm -> SeedingSchemeOptions.make sm | ||
|
|
||
| static member makeCmdWith (m:MountInfo) = | ||
| let cPath p = (MountInfo.containerPathOf m p) | ||
| function | ||
| |Input i -> InputOptions.makeWith m i | ||
| |OutputName f -> [cPath f] | ||
| |InputAsProteins -> ["-p"] | ||
| |RepeatMarking rm -> ["-R";string rm] | ||
| |LowercaseSoftMasking -> ["-c"] | ||
| |SeedingScheme sm -> SeedingSchemeOptions.make sm | ||
|
|
||
| let runLastDBAsync (bcContext:BioContainer.BcContext) (opt:LastDBParams list) = | ||
| //Usage: lastdb [options] output-name fasta-sequence-file(s) | ||
| let input = | ||
| opt | ||
| |> List.filter (fun p -> match p with |Input _ -> true |_ -> false) | ||
| |> fun x -> if List.isEmpty x then | ||
| failwith "no input sequence given" | ||
| else | ||
| LastDBParams.makeCmdWith bcContext.Mount x.[0] | ||
|
|
||
| let output = | ||
| opt | ||
| |> List.filter (fun p -> match p with |OutputName _ -> true |_ -> false) | ||
| |> fun x -> if List.isEmpty x then | ||
| failwith "no output sequence given" | ||
| else | ||
| LastDBParams.makeCmdWith bcContext.Mount x.[0] | ||
|
|
||
| let options = opt |> List.filter (fun p -> match p with |Input _ |OutputName _ -> false |_ -> true) | ||
| let cmds = (options |> List.map (LastDBParams.makeCmdWith bcContext.Mount)) | ||
| let tp = ("lastdb"::(cmds |> List.concat)@output@input) | ||
|
|
||
| printfn "Starting process lastdb\r\nparameters:" | ||
| cmds |> List.iter (fun op -> printfn "\t%s" (String.concat " " op)) | ||
|
|
||
| async { | ||
| let! res = BioContainer.execAsync bcContext tp | ||
| return res | ||
|
|
||
| } | ||
|
|
||
|
|
||
| //Usage: lastal [options] lastdb-name fasta-sequence-file(s) | ||
|
|
||
| //Find and align similar sequences. | ||
| //Cosmetic options: | ||
| //-h, --help: show all options and their default settings, and exit | ||
| //-V, --version: show version information, and exit | ||
| //-v: be verbose: write messages about what lastal is doing | ||
| //-f: output format: TAB, MAF, BlastTab, BlastTab+ (default=MAF) | ||
|
|
||
| //E-value options (default settings): | ||
| //-D: query letters per random alignment (1e+06) | ||
| //-E: maximum expected alignments per square giga (1e+18/D/refSize/numOfStrands) | ||
| //-r: match score (2 if -M, else 6 if 0<Q<5, else 1 if DNA) | ||
| //-q: mismatch cost (3 if -M, else 18 if 0<Q<5, else 1 if DNA) | ||
| //-p: match/mismatch score matrix (protein-protein: BL62, DNA-protein: BL80) | ||
| //-a: gap existence cost (DNA: 7, protein: 11, 0<Q<5: 21) | ||
| //-b: gap extension cost (DNA: 1, protein: 2, 0<Q<5: 9) | ||
| //-A: insertion existence cost (a) | ||
| //-B: insertion extension cost (b) | ||
| //-c: unaligned residue pair cost (off) | ||
| //-F: frameshift cost (off) | ||
| //-x: maximum score drop for preliminary gapped alignments (z) | ||
| //-y: maximum score drop for gapless alignments (min[t*10, x]) | ||
| //-z: maximum score drop for final gapped alignments (e-1) | ||
| //-d: minimum score for gapless alignments (min[e, t*ln(1000*refSize/n)]) | ||
| //-e: minimum score for gapped alignments | ||
|
|
||
| //Initial-match options (default settings): | ||
| //-m: maximum initial matches per query position (10) | ||
| //-l: minimum length for initial matches (1) | ||
| //-L: maximum length for initial matches (infinity) | ||
| //-k: use initial matches starting at every k-th position in each query (1) | ||
| //-W: use "minimum" positions in sliding windows of W consecutive positions | ||
|
|
||
| //Miscellaneous options (default settings): | ||
| //-s: strand: 0=reverse, 1=forward, 2=both (2 for DNA, 1 for protein) | ||
| //-S: score matrix applies to forward strand of: 0=reference, 1=query (0) | ||
| //-K: omit alignments whose query range lies in >= K others with > scor12e (off) | ||
| //-C: omit gapless alignments in >= C others with > score-per-length (off) | ||
| //-P: number of parallel threads (1) | ||
| //-i: query batch size (8 KiB, unless there is > 1 thread or lastdb volume) | ||
| //-M: find minimum-difference alignments (faster but cruder) | ||
| //-T: type of alignment: 0=local, 1=overlap (0) | ||
| //-n: maximum gapless alignments per query position (infinity if m=0, else m) | ||
| //-N: stop after the first N alignments per query strand | ||
| //-R: repeat-marking options (the same as was used for lastdb) | ||
| //-u: mask lowercase during extensions: 0=never, 1=gapless,2=gapless+postmask, 3=always (2 if lastdb -c and Q<5, else 0) | ||
| //-w: suppress repeats inside exact matches, offset by <= this distance (1000) | ||
| //-G: genetic code file | ||
| //-t: 'temperature' for calculating probabilities (1/lambda) | ||
| //-g: 'gamma' parameter for gamma-centroid and LAMA (1) | ||
| //-j: output type: 0=match counts, 1=gapless, 2=redundant gapped, 3=gapped,4=column ambiguity estimates, 5=gamma-centroid, 6=LAMA, 7=expected counts (3) | ||
| //-Q: input format: 0=fasta or fastq-ignore, 1=fastq-sanger, 2=fastq-solexa,3=fastq-illumina, 4=prb, 5=PSSM (fasta) | ||
|
|
||
| type OutputFormatOptions = | ||
| |TAB | ||
| |MAF | ||
| |BlastTab | ||
| |BlastTabPlus | ||
|
|
||
| static member make = | ||
| function | ||
| |TAB -> ["-f";"TAB"] | ||
| |MAF -> ["-f";"MAF"] | ||
| |BlastTab -> ["-f";"BlastTab"] | ||
| |BlastTabPlus -> ["-f";"BlastTab+"] | ||
|
|
||
| type QueryOptions = | ||
| |SingleFastaFile of string | ||
| |MultipleFilePattern of string | ||
|
|
||
| static member make = | ||
| function | ||
| |SingleFastaFile s -> [s] | ||
| |MultipleFilePattern m -> [m] | ||
|
|
||
| static member makeWith (m:MountInfo) = | ||
| let cPath p = (MountInfo.containerPathOf m p) | ||
| function | ||
| |SingleFastaFile s -> [cPath s] | ||
| |MultipleFilePattern m -> [cPath m] | ||
|
|
||
| type LastAlignParameters = | ||
| |DBName of string | ||
| |Query of QueryOptions | ||
| |OutputFileName of string | ||
| |OutputFormat of OutputFormatOptions | ||
| |Verbose | ||
|
|
||
| static member makeCmd = | ||
| function | ||
| |DBName dbn -> [dbn] | ||
| |Query q -> QueryOptions.make q | ||
| |OutputFileName on -> [">"; on] | ||
| |OutputFormat outfmt -> OutputFormatOptions.make outfmt | ||
| |Verbose -> ["-v"] | ||
|
|
||
| static member makeCmdWith (m:MountInfo) = | ||
| let cPath p = (MountInfo.containerPathOf m p) | ||
| function | ||
| |DBName dbn -> [cPath dbn] | ||
| |Query q -> QueryOptions.makeWith m q | ||
| |OutputFileName on -> [">" ;(cPath on)] | ||
| |OutputFormat outfmt -> OutputFormatOptions.make outfmt | ||
| |Verbose -> ["-v"] | ||
|
|
||
| let runLastAlignAsync (bcContext:BioContainer.BcContext) (opt:LastAlignParameters list) = | ||
| //Usage: lastal [options] lastdb-name fasta-sequence-file(s) | ||
|
|
||
| let db = | ||
| opt | ||
| |> List.filter (fun p -> match p with |DBName _ -> true |_ -> false) | ||
| |> fun x -> if List.isEmpty x then | ||
| failwith "no search DB given" | ||
| else | ||
| LastAlignParameters.makeCmdWith bcContext.Mount x.[0] | ||
| let input = | ||
| opt | ||
| |> List.filter (fun p -> match p with |Query _ -> true |_ -> false) | ||
| |> fun x -> if List.isEmpty x then | ||
| failwith "no query given" | ||
| else | ||
| LastAlignParameters.makeCmdWith bcContext.Mount x.[0] | ||
|
|
||
| let output = | ||
| opt | ||
| |> List.filter (fun p -> match p with |OutputFileName _ -> true |_ -> false) | ||
| |> fun x -> if List.isEmpty x then | ||
| failwith "no output name given" | ||
| else | ||
| LastAlignParameters.makeCmdWith bcContext.Mount x.[0] | ||
|
|
||
| let options = opt |> List.filter (fun p -> match p with |DBName _ |Query _ |OutputFileName _-> false |_ -> true) | ||
| let cmds = (options |> List.map (LastAlignParameters.makeCmdWith bcContext.Mount)) | ||
| let tp = ("lastal"::(cmds |> List.concat)@db@input@output) | ||
|
|
||
| printfn "Starting process lastal\r\nparameters:" | ||
| cmds |> List.iter (fun op -> printfn "\t%s" (String.concat " " op)) | ||
|
|
||
| async { | ||
| let! res = BioContainer.execReturnAsync bcContext tp | ||
| return res | ||
|
|
||
| } |